From d7c50255302f705e67df7ef2da0d1c288b9b1c18 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 13:58:37 +0000 Subject: [PATCH 001/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15068 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- tools/msi2lmp/frc_files/clayff.frc | 61 ++++++++++++++++-------------- 1 file changed, 33 insertions(+), 28 deletions(-) diff --git a/tools/msi2lmp/frc_files/clayff.frc b/tools/msi2lmp/frc_files/clayff.frc index bdc9c2c004..6072bea792 100644 --- a/tools/msi2lmp/frc_files/clayff.frc +++ b/tools/msi2lmp/frc_files/clayff.frc @@ -2,34 +2,36 @@ #atom_types cvff -!Ver Ref Type Mass Element Connections Comment +!Ver Ref Type Mass Element Connections Description and charge !---- --- ---- ---------- ------- ----------------------------------------- - 1.0 1 st 28.08550 Si 4 - 1.0 1 ao 26.98154 Al 6 - 1.0 1 at 26.98154 Al 4 - 1.0 1 mgo 24.30500 Mg 6 - 1.0 1 cao 40.08000 Ca 6 - 1.0 1 feo 55.84700 Fe 6 - 1.0 1 lio 6.941000 Li 6 - 1.0 1 ob 15.99940 O 2 - 1.0 1 obss 15.99940 O 3 - 1.0 1 obts 15.99940 O 2 - 1.0 1 obos 15.99940 O 2 - 1.0 1 ohs 15.99940 O 2 - 1.0 1 oh 15.99940 O 2 - 1.0 1 oh- 15.99940 O 1 - 1.0 1 o* 15.99940 O 2 - 1.0 1 ho 1.007970 H 1 - 1.0 1 h* 1.007970 H 1 - 1.0 1 Na 22.99000 Na 0 - 1.0 1 K 39.10 K 0 - 1.0 1 Cs 132.9100 Cs 0 - 1.0 1 Ca 40.07980 Ca 0 - 1.0 1 Ba 137.3300 Ba 0 - 1.0 1 Mg 24.3050 Mg 0 - 1.0 1 Sr 87.6200 Sr 0 - 1.0 1 Pb 207.2000 Pb 0 - 1.0 1 Cl 35.45300 Cl 0 + 1.0 1 st 28.08550 Si 4 tetrahedral silicon 2.1 + 1.0 1 ao 26.98154 Al 6 octahedral aluminum 1.575 + 1.0 1 at 26.98154 Al 4 tetrahedral aluminum 1.575 + 1.0 1 mgo 24.30500 Mg 6 octahedral magnesium 1.36 + 1.0 1 mgh 24.30500 Mg 6 hydroxide magnesium 1.05 + 1.0 1 cao 40.08000 Ca 6 octahedral calcium 1.36 + 1.0 1 cah 40.08000 Ca 6 hydroxide calcium 1.05 + 1.0 1 feo 55.84700 Fe 6 octahedral iron 1.575 + 1.0 1 lio 6.941000 Li 6 octahedral lithium 0.525 + 1.0 1 ob 15.99940 O 2 bridging oxygen -1.05 + 1.0 1 obss 15.99940 O 3 oxygen double sub. -1.2996 + 1.0 1 obts 15.99940 O 2 oxygen tet. sub. -1.1688 + 1.0 1 obos 15.99940 O 2 oxygen oct. sub. -1.1808 + 1.0 1 ohs 15.99940 O 2 hydroxyl O sub. -1.0808 + 1.0 1 oh 15.99940 O 2 hydroxyl O -0.95 + 1.0 1 oh- 15.99940 O 1 hydroxide O + 1.0 1 o* 15.99940 O 2 spc water O -0.82 + 1.0 1 ho 1.007970 H 1 hydroxyl H 0.425 + 1.0 1 h* 1.007970 H 1 spc water H 0.41 + 1.0 1 Na 22.99000 Na 0 sodium ion 1.0 + 1.0 1 K 39.10 K 0 potassium ion 1.0 + 1.0 1 Cs 132.9100 Cs 0 cesium ion 1.0 + 1.0 1 Ca 40.07980 Ca 0 calcium ion 2.0 + 1.0 1 Ba 137.3300 Ba 0 barium ion 2.0 + 1.0 1 Mg 24.3050 Mg 0 magnesium ion 2.0 + 1.0 1 Sr 87.6200 Sr 0 strontium ion 2.0 + 1.0 1 Pb 207.2000 Pb 0 lead ion 2.0 + 1.0 1 Cl 35.45300 Cl 0 chloride ion -1.0 #equivalence cvff @@ -74,6 +76,7 @@ !Ver Ref I J R0 K2 !---- --- ---- ---- ------- -------- + 2.1 28 o* h* 1.0000 553.9350 2.1 28 oh ho 1.0000 553.9350 2.1 28 ohs ho 1.0000 553.9350 @@ -84,7 +87,7 @@ !Ver Ref I J K Theta0 K2 !---- --- ---- ---- ---- -------- ------- - 2.3 23 cp cp c' 120.0000 34.6799 + 1.0 1 h* o* h* 109.4700 45.7530 @@ -122,7 +125,9 @@ 1.0 1 ao 196.1446 0.03230 1.0 1 at 12.3645 0.00954 1.0 1 mgo 1636.3265 0.07688 + 1.0 1 mgh 1636.3265 0.07688 1.0 1 cao 17814.73 0.5987 + 1.0 1 cah 17624.076 0.595 1.0 1 feo 702.54 0.0504 1.0 1 lio 112.01 0.0201 1.0 1 ob 629358.0000 625.50000 From 8fa54096d38f2ae3c18fa301ab6c20f11231a9f7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:48:46 +0000 Subject: [PATCH 002/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15069 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/Section_commands.txt | 2 - doc/src/change_box.txt | 12 +- doc/src/compute.txt | 13 +- doc/src/compute_property_atom.txt | 4 +- doc/src/compute_temp_deform.txt | 2 +- doc/src/fix.txt | 10 +- doc/src/fix_ave_atom.txt | 4 +- doc/src/fix_ave_chunk.txt | 4 +- doc/src/fix_ave_correlate.txt | 10 +- doc/src/fix_ave_histo.txt | 2 +- doc/src/fix_ave_spatial.txt | 418 --------------------------- doc/src/fix_ave_spatial_sphere.txt | 324 --------------------- doc/src/fix_ave_time.txt | 4 +- doc/src/fix_deform.txt | 2 +- doc/src/fix_thermal_conductivity.txt | 11 +- doc/src/fix_viscosity.txt | 6 +- doc/src/prd.txt | 6 +- doc/src/tad.txt | 6 +- doc/src/variable.txt | 2 +- 19 files changed, 47 insertions(+), 795 deletions(-) delete mode 100644 doc/src/fix_ave_spatial.txt delete mode 100644 doc/src/fix_ave_spatial_sphere.txt diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index a67f39c8e8..e02fd934cc 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -495,7 +495,6 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "ave/correlate"_fix_ave_correlate.html, "ave/histo"_fix_ave_histo.html, "ave/histo/weight"_fix_ave_histo.html, -"ave/spatial"_fix_ave_spatial.html, "ave/time"_fix_ave_time.html, "balance"_fix_balance.html, "bond/break"_fix_bond_break.html, @@ -613,7 +612,6 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, -"ave/spatial/sphere"_fix_ave_spatial_sphere.html, "colvars"_fix_colvars.html, "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index 7fc6198232..15111fec08 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -315,12 +315,12 @@ been previously used to define the lattice spacing. If you use the {ortho} or {triclinic} keywords, then at the point in the input script when this command is issued, no "dumps"_dump.html can -be active, nor can a "fix ave/spatial"_fix_ave_spatial.html or "fix -deform"_fix_deform.html be active. This is because these commands -test whether the simulation box is orthogonal when they are first -issued. Note that these commands can be used in your script before a -change_box command is issued, so long as an "undump"_undump.html or -"unfix"_unfix.html command is also used to turn them off. +be active, nor can a "fix deform"_fix_deform.html be active. This is +because these commands test whether the simulation box is orthogonal +when they are first issued. Note that these commands can be used in +your script before a change_box command is issued, so long as an +"undump"_undump.html or "unfix"_unfix.html command is also used to +turn them off. [Related commands:] diff --git a/doc/src/compute.txt b/doc/src/compute.txt index b847985bf7..3da2143411 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -99,11 +99,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. Or the values can be referenced in a "variable equal"_variable.html or "variable atom"_variable.html command. :l -Per-atom values can be output via the "dump custom"_dump.html command -or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be -time-averaged via the "fix ave/atom"_fix_ave_atom.html command or -reduced by the "compute reduce"_compute_reduce.html command. Or the -per-atom values can be referenced in an "atom-style +Per-atom values can be output via the "dump custom"_dump.html command. +Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html +command or reduced by the "compute reduce"_compute_reduce.html +command. Or the per-atom values can be referenced in an "atom-style variable"_variable.html. :l Local values can be reduced by the "compute @@ -255,7 +254,7 @@ section of "this page"_Section_commands.html#cmd_5. [Related commands:] "uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, -"fix ave/time"_fix_ave_time.html, "fix ave/histo"_fix_ave_histo.html +ave/atom"_fix_ave_atom.html, "fix ave/time"_fix_ave_time.html, "fix +ave/histo"_fix_ave_histo.html [Default:] none diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index 9b7483fd8d..6fe4c79b37 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -91,7 +91,7 @@ in the group. This is useful so that the values can be used by other "output commands"_Section_howto.html#howto_15 that take computes as inputs. See for example, the "compute reduce"_compute_reduce.html, "fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/spatial"_fix_ave_spatial.html, and "atom-style +"fix ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html commands. The list of possible attributes is the same as that used by the "dump @@ -157,7 +157,7 @@ units for q, etc. [Related commands:] "dump custom"_dump.html, "compute reduce"_compute_reduce.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, +ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, "fix property/atom"_fix_property_atom.html [Default:] none diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt index ed7da650e0..168b0b3880 100644 --- a/doc/src/compute_temp_deform.txt +++ b/doc/src/compute_temp_deform.txt @@ -88,7 +88,7 @@ matches the box deformation. If not, then the compute will subtract off an incorrect stream velocity, yielding a bogus thermal temperature. You should NOT assume that your atoms are streaming at the same rate the box is deforming. Rather, you should monitor their -velocity profile, e.g. via the "fix ave/spatial"_fix_ave_spatial.html +velocity profile, e.g. via the "fix ave/chunk"_fix_ave_chunk.html command. And you can compare the results of this compute to "compute temp/profile"_compute_temp_profile.html, which actually calculates the stream profile before subtracting it. If the two computes do not give diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 0f65677b58..577d2b1f2e 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -122,11 +122,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. Or the values can be referenced in a "variable equal"_variable.html or "variable atom"_variable.html command. :ulb,l -Per-atom values can be output via the "dump custom"_dump.html command -or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be -time-averaged via the "fix ave/atom"_fix_ave_atom.html command or -reduced by the "compute reduce"_compute_reduce.html command. Or the -per-atom values can be referenced in an "atom-style +Per-atom values can be output via the "dump custom"_dump.html command. +Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html +command or reduced by the "compute reduce"_compute_reduce.html +command. Or the per-atom values can be referenced in an "atom-style variable"_variable.html. :l Local values can be reduced by the "compute @@ -171,7 +170,6 @@ of "this page"_Section_commands.html#cmd_5. "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities "balance"_fix_balance.html - perform dynamic load-balancing "bond/break"_fix_bond_break.html - break bonds on the fly diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index af38f3a1e0..1d5053d37b 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -38,7 +38,7 @@ Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting per-atom averages can be used by other "output commands"_Section_howto.html#howto_15 such as the "fix -ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands. +ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands. The group specified with the command means only atoms within the group have their averages computed. Results are set to 0.0 for atoms not in @@ -147,7 +147,7 @@ minimization"_minimize.html. [Related commands:] "compute"_compute.html, "fix ave/histo"_fix_ave_histo.html, "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, "variable"_variable.html, [Default:] none diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index fd31369d2a..0ebbafd6ca 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -67,8 +67,8 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre [NOTE:] -If you are trying to replace an older fix ave/spatial command with the -newer, more flexible fix ave/chunk and "compute +If you are trying to replace a deprectated fix ave/spatial command +with the newer, more flexible fix ave/chunk and "compute chunk/atom"_compute_chunk_atom.html commands, you simply need to split the fix ave/spatial arguments across the two new commands. For example, this command: diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 2394185b5d..ae785b4fc5 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -83,10 +83,10 @@ Each listed value can be the result of a "compute"_compute.html or must produce a global quantity, not a per-atom or local quantity. If you wish to spatial- or time-average or histogram per-atom quantities from a compute, fix, or variable, then see the "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html, -or "fix ave/histo"_fix_ave_histo.html commands. If you wish to -convert a per-atom quantity into a single global value, see the -"compute reduce"_compute_reduce.html command. +ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, or +"fix ave/histo"_fix_ave_histo.html commands. If you wish to convert a +per-atom quantity into a single global value, see the "compute +reduce"_compute_reduce.html command. "Computes"_compute.html that produce global quantities are those which do not have the word {atom} in their style name. Only a few @@ -332,7 +332,7 @@ minimization"_minimize.html. "fix ave/correlate/long"_fix_ave_correlate_long.html, "compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, +ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, "variable"_variable.html [Default:] none diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 58b234d363..3d287d4fe4 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -331,7 +331,7 @@ minimization"_minimize.html. [Related commands:] "compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, "variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, [Default:] none diff --git a/doc/src/fix_ave_spatial.txt b/doc/src/fix_ave_spatial.txt deleted file mode 100644 index 12b452cd56..0000000000 --- a/doc/src/fix_ave_spatial.txt +++ /dev/null @@ -1,418 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix ave/spatial command :h3 - -[Syntax:] - -fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/spatial = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating averages :l -Nfreq = calculate averages every this many timesteps :l -dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins :l - dim = {x} or {y} or {z} - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) :pre -one or more input values can be listed :l -value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l - vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) - density/number, density/mass = number or mass density - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {region} or {bound} or {discard} or {norm} or {ave} or {units} or {file} or {overwrite} or {title1} or {title2} or {title3} :l - {region} arg = region-ID - {bound} args = x/y/z lo hi - x/y/z = {x} or {y} or {z} to bound bins in this dimension - lo = {lower} or coordinate value (distance units) - hi = {upper} or coordinate value (distance units) - {discard} arg = {mixed} or {no} or {yes} - mixed = discard atoms outside bins only if bin bounds are explicitly set - no = always keep out-of-bounds atoms - yes = always discard out-of-bounds atoms - {norm} arg = {all} or {sample} - region-ID = ID of region atoms must be in to contribute to spatial averaging - {ave} args = {one} or {running} or {window M} - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - {units} arg = {box} or {lattice} or {reduced} - {file} arg = filename - filename = file to write results to - {overwrite} arg = none = overwrite output file with only latest output - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {title3} arg = string - string = text to print as 3rd line of output file :pre -:ule - -[Examples:] - -fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced & - title1 "My output values" -fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile -fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running -fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running :pre - -[NOTE:] - - The fix ave/spatial command has been replaced by the more flexible -"fix ave/chunk"_fix_ave_chunk.html and "compute -chunk/atom"_compute_chunk_atom.html commands. The fix ave/spatial -command will be removed from LAMMPS sometime in the summer of 2015. - -Any fix ave/spatial command can be replaced by the two new commands. -You simply need to split the fix ave/spatial arguments across the two -new commands. For example, this command: - -fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile :pre - -could be replaced by: - -compute cc1 flow chunk/atom bin/1d y 0.0 1.0 -fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre - -[Description:] - -Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into 1d, 2d, or 3d bins based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style -custom"_thermo_style.html, and can also be written to a file. - -The group specified with the command means only atoms within the group -contribute to bin averages. If the {region} keyword is used, the atom -must be in both the specified group and the specified geometric -"region"_region.html in order to contribute to bin averages. - -Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -"compute"_compute.html or "fix"_fix.html or the evaluation of an -atom-style "variable"_variable.html. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the "fix -ave/time"_fix_ave_time.html command. - -"Computes"_compute.html that produce per-atom quantities are those -which have the word {atom} in their style name. See the doc pages for -individual "fixes"_fix.html to determine which ones produce per-atom -quantities. "Variables"_variable.html of style {atom} are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. - -The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. - -The size and dimensionality of the bins (1d = layers or slabs, 2d = -pencils, 3d = boxes) are determined by the {dim}, {origin}, and -{delta} settings and how many times they are specified (1, 2, or 3). -See details below. - -NOTE: This fix works by creating an array of size Nbins by Nvalues on -each processor. Nbins is the total number of bins; Nvalues is the -number of input values specified. Each processor loops over its -atoms, tallying its values to the appropriate bin. Then the entire -array is summed across all processors. This means that using a large -number of bins (easy to do for 2d or 3d bins) will incur an overhead -in memory and computational cost (summing across processors), so be -careful to use reasonable numbers of bins. - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of {Nfreq}. The average is over {Nrepeat} -quantities, computed in the preceding portion of the simulation every -{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and -{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - -:line - -Each per-atom property is also averaged over atoms in each bin. The -way the averaging is one across the {Nrepeat} timesteps to produce -output on the {Nfreq} timesteps, and across multiple {Nfreq} outputs, -is determined by the {norm} and {av} keyword settings, as discussed -below. - -Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends -on how many times (1, 2, or 3) the {dim}, {origin}, and {delta} -settings are specified in the fix ave/spatial command. For 2d or 3d -bins, there is no restriction on specifying dim = x before dim = y, or -dim = y before dim = z. Bins in a particular {dim} have a bin size in -that dimension given by {delta}. Every Nfreq steps, when averaging is -being performed and the per-atom property is calculated for the first -time, the number of bins and the bin sizes and boundaries are -computed. Thus if the simulation box changes size during a -simulation, the number of bins and their boundaries may also change. -In each dimension, bins are defined relative to a specified {origin}, -which may be the lower/upper edge of the simulation box in that -dimension, or its center point, or a specified coordinate value. -Starting at the origin, sufficient bins are created in both directions -to completely span the bin extent in that dimension. By default the -bin extent is the entire simulation box. - -The {bound} keyword can be used one or more times to limit the extent -of bin coverage in specified dimensions, i.e. to only bin a portion of -the box. If the {lo} setting is {lower} or the {hi} setting is -{upper}, the bin extent in that direction extends to the box boundary. -If a numeric value is used for {lo} and/or {hi}, then the bin extent -in the {lo} or {hi} direction extends only to that value, which is -assumed to be inside (or at least near) the simulation box boundaries, -though LAMMPS does not check for this. - -On each sampling timestep, each atom is mapped to the bin it currently -belongs to, based on its current position. Note that the group-ID and -region keyword can exclude specific atoms from this operation, as -discussed above. Note that between reneighboring timesteps, atoms can -move outside the current simulation box. If the box is periodic (in -that dimension) the atom is remapping into the periodic box for -purposes of binning. If the box in not periodic, the atom may have -moved outside the bounds of any bin. - -The {discard} keyword determines what is done with any atom which is -outside the bounds of any bin. If {discard} is set to {yes}, the atom -will be ignored and not contribute to any bin averages. If {discard} -is set to {no}, the atom will be counted as if it were in the first or -last bin in that dimension. If (discard} is set to {mixed}, which is -the default, it will only be counted in the first or last bin if bins -extend to the box boundary in that dimension. This is the case if the -{bound} keyword settings are {lower} and {upper}, which is the -default. If the {bound} keyword settings are numeric values, then the -atom will be ignored if it is outside the bounds of any bin. Note -that in this case, it is possible that the first or last bin extends -beyond the numeric {bounds} settings, depending on the specified -{origin}. If this is the case, the atom is only ignored if it is -outside the first or last bin, not if it is simply outside the numeric -{bounds} setting. - -For orthogonal simulation boxes, the bins are also layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bins are so that they are -parallel to the tilted faces of the simulation box. See "this -section"_Section_howto.html#howto_12 of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" -direction. Bins in y have faces normal to the "a" cross "c" -direction. And bins in z have faces normal to the "a" cross "b" -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the {units} option must be set -to {reduced} when using a triclinic simulation box, as noted below. - -:line - -The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the "compute -property/atom"_compute_property_atom.html command and then specifying -an input value from that compute. - -The {density/number} value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The {density/mass} -value means the mass density is computed in each bind, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the "units"_units.html command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -{Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -{atom} can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. - -:line - -Additional optional keywords also affect the operation of this fix. -The {region}, {bound}, and {discard} keywords were discussed above. - -The {norm} keyword affects how averaging is done for the output -produced every {Nfreq} timesteps. For an {all} setting, a bin -quantity is summed over all atoms in all {Nrepeat} samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire {Nfreq} timescale. - -For a {sample} setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the {Nrepeat} "average sample values", In -other words it is an average of an average. - -The {ave} keyword determines how the bin values produced every {Nfreq} -steps are averaged with bin values produced on previous steps that -were multiples of {Nfreq}, before they are accessed by another output -command or written to a file. - -If the {ave} setting is {one}, then the bin values produced on -timesteps that are multiples of {Nfreq} are independent of each other; -they are output as-is without further averaging. - -If the {ave} setting is {running}, then the bin values produced on -timesteps that are multiples of {Nfreq} are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the "unfix"_unfix.html command, or re-defining the fix by -re-specifying it. - -If the {ave} setting is {window}, then the bin values produced on -timesteps that are multiples of {Nfreq} are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. - -The {units} keyword determines the meaning of the distance units used -for the bin size {delta} and for {origin} and {bounds} values if they -are coordinate value. For orthogonal simulation boxes, any of the 3 -options may be used. For non-orthogonal (triclinic) simulation boxes, -only the {reduced} option may be used. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacing. A {reduced} value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an {origin} value of -0.5 means the center of the box in any dimension. A {delta} value of -0.1 means 10 bins span the box in that dimension. - -Consider a non-orthogonal box, with bins that are 1d layers or slabs -in the x dimension. No matter how the box is tilted, an {origin} of -0.0 means start layers at the lower "b" cross "c" plane of the -simulation box and an {origin} of 1.0 means to start layers at the -upper "b" cross "c" face of the box. A {delta} value of 0.1 means -there will be 10 layers from 0.0 to 1.0, regardless of the current -size or shape of the simulation box. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms -in the bin, and one or more calculated values. The number of values -in each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the {units} keyword is {box} or -{lattice}, the "coord" is printed in box units. If the value of the -{units} keyword is {reduced}, the "coord" is printed in reduced units -(0-1). - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -The {title1} and {title2} and {title3} keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the {file} keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -# Spatial-averaged data for fix ID and group name -# Timestep Number-of-bins -# Bin Coord1 Coord2 Coord3 Count value1 value2 ... :pre - -In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for -1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates -(center of the bin) in the appropriate dimensions, the next column has -the count of atoms in that bin, and the remaining columns are the -Nvalue quantities. When the array is accessed with an I that exceeds -the current number of bins, than a 0.0 is returned by the fix instead -of an error, since the number of bins can vary as a simulation runs, -depending on the simulation box size. 2d or 3d bins are ordered so -that the last dimension(s) vary fastest. The array values calculated -by this fix are "intensive", since they are already normalized by the -count of atoms in each bin. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -When the {ave} keyword is set to {running} or {window} then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the {units} keyword is set to -{reduced}. - -[Related commands:] - -"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html, -"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, -"fix ave/spatial/sphere"_fix_ave_spatial_sphere.html - -[Default:] - -The option defaults are bound = lower and upper in all dimensions, -discard = mixed, norm = all, ave = one, units = lattice, no file -output, and title 1,2,3 = strings as described above. diff --git a/doc/src/fix_ave_spatial_sphere.txt b/doc/src/fix_ave_spatial_sphere.txt deleted file mode 100644 index 8223e7fd5b..0000000000 --- a/doc/src/fix_ave_spatial_sphere.txt +++ /dev/null @@ -1,324 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix ave/spatial/sphere command :h3 - -[Syntax:] - -fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/spatial = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating averages :l -Nfreq = calculate averages every this many timesteps :l -origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) :l -r_min = radial distance at which binning begins :l -r_max = radial distance at which binning ends :l -nbins = number of spherical shells to create between r_min and r_max :l -one or more input values can be listed :l -value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l - vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) - density/number, density/mass = number or mass density - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {region} or {norm} or {units} or {ave} or {file} or {overwrite} or {title1} or {title2} or {title3} :l - {region} arg = region-ID - region-ID = ID of region atoms must be in to contribute to spatial averaging - {norm} arg = {all} or {sample} - {units} arg = {box} or {lattice} or {reduced} - {ave} args = {one} or {running} or {window M} - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - {file} arg = filename - filename = file to write results to - {overwrite} arg = none = overwrite output file with only latest output - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {title3} arg = string - string = text to print as 3rd line of output file :pre -:ule - -[Examples:] - -fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values" -fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile :pre - -[Description:] - -Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into spherical shells based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style -custom"_thermo_style.html, and can also be written to a file. - -The group specified with the command means only atoms within the group -contribute to bin averages. If the {region} keyword is used, the atom -must be in both the group and the specified geometric -"region"_region.html in order to contribute to bin averages. - -Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -"compute"_compute.html or "fix"_fix.html or the evaluation of an -atom-style "variable"_variable.html. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the "fix -ave/time"_fix_ave_time.html command. - -"Computes"_compute.html that produce per-atom quantities are those -which have the word {atom} in their style name. See the doc pages for -individual "fixes"_fix.html to determine which ones produce per-atom -quantities. "Variables"_variable.html of style {atom} are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. - -The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. - -{Nbins} specifies the number of spherical shells which will be created -between r_min and r_max centered at (origin_x, origin_y, origin_z). - -NOTE: This fix works by creating an array of size Nbins by Nvalues on -each processor. Nbins is the total number of bins; Nvalues is the -number of input values specified. Each processor loops over its -atoms, tallying its values to the appropriate bin. Then the entire -array is summed across all processors. This means that using a large -number of bins will incur an overhead in memory and computational cost -(summing across processors), so be careful to use reasonable numbers -of bins. - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of {Nfreq}. The average is over {Nrepeat} -quantities, computed in the preceding portion of the simulation every -{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and -{Nevery} must be non-zero even if {Nrepeat} is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - -:line - -The {origin_x}, {origin_y}, and {origin_z} parameters may be specified -by either a compute or a variable. This allows, for example, the -center of the spherical bins to be attached to the center of mass of a -group of atoms. If a variable origin is used and periodic boundary -conditions are in effect, then the origin will be wrapped across -periodic boundaries whenever it changes so that it is always inside -the simulation box. - -:line - -The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the "compute -property/atom"_compute_property_atom.html command and then specifying -an input value from that compute. - -The {density/number} value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The {density/mass} -value means the mass density is computed in each bin, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the "units"_units.html command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. -The bin volume will always be calculated in box units, independent -of the use of the {units} keyword in this command. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -{Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -{atom} can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. - -:line - -Additional optional keywords also affect the operation of this fix. -The {region} keyword was discussed above. - -The {norm} keyword affects how averaging is done for the output -produced every {Nfreq} timesteps. For an {all} setting, a bin -quantity is summed over all atoms in all {Nrepeat} samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire {Nfreq} timescale. - -For a {sample} setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the {Nrepeat} "average sample values", In -other words it is an average of an average. - -The {ave} keyword determines how the bin values produced every {Nfreq} -steps are averaged with bin values produced on previous steps that -were multiples of {Nfreq}, before they are accessed by another output -command or written to a file. - -If the {ave} setting is {one}, then the bin values produced on -timesteps that are multiples of {Nfreq} are independent of each other; -they are output as-is without further averaging. - -If the {ave} setting is {running}, then the bin values produced on -timesteps that are multiples of {Nfreq} are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the "unfix"_unfix.html command, or re-defining the fix by -re-specifying it. - -If the {ave} setting is {window}, then the bin values produced on -timesteps that are multiples of {Nfreq} are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. - -The {units} keyword determines the meaning of the distance units used -for the sphere origin and the two radial lengths. For orthogonal -simulation boxes, any of the 3 options may be used. For -non-orthogonal (triclinic) simulation boxes, only the {reduced} option -may be used. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacing. - -NOTE: The {lattice} style may only be used if the lattice spacing is -the same in each direction. - -A {reduced} value means normalized unitless values between 0 and 1, -which represent the lower and upper faces of the simulation box -respectively. Thus an {origin} value of 0.5 means the center of the -box in any dimension. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms in -the bin, and one or more calculated values. The number of values in -each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the {units} keyword is {box} or -{lattice}, the "coord" is printed in box units. If the value of the -{units} keyword is {reduced}, the "coord" is printed in reduced units -(0-1). - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -The {title1} and {title2} and {title3} keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the {file} keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -# Spatial-averaged data for fix ID and group name -# Timestep Number-of-bins -# Bin r Count value1 value2 ... :pre - -In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = 2+Nvalues. The first column contains the -radius at the center of the shell. For units {reduced}, this is in -reduced units, while for units {box} and {lattice} this is in box -units. The next column has the count of atoms in that bin, and the -remaining columns are the Nvalue quantities. When the array is -accessed with an I that exceeds the current number of bins, than a 0.0 -is returned by the fix instead of an error. The array values -calculated by this fix are "intensive", since they are already -normalized by the count of atoms in each bin. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -When the {ave} keyword is set to {running} or {window} then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the {units} keyword is set to -{reduced}. - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the "Making of -LAMMPS"_Section_start.html#3 section for more info. - -[Related commands:] - -"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html, -"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, -"fix ave/spatial"_fix_ave_spatial.html, - -[Default:] - -The option defaults are norm = all, ave = one, units = lattice, no -file output, and title 1,2,3 = strings as described above. diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 386bbcf6a0..7eca1abe6d 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -79,7 +79,7 @@ Each listed value can be the result of a "compute"_compute.html or must produce a global quantity, not a per-atom or local quantity. If you wish to spatial- or time-average or histogram per-atom quantities from a compute, fix, or variable, then see the "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a per-atom quantity into a single global quantity, see the "compute reduce"_compute_reduce.html command. @@ -322,7 +322,7 @@ minimization"_minimize.html. [Related commands:] "compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, "variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, [Default:] diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 1d786cc322..e2cbe14868 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -496,7 +496,7 @@ box. E.g. for a shearing system the box deformation velocity may vary from 0 at the bottom to 10 at the top of the box. But the stream velocity profile of the atoms may vary from -5 at the bottom to +5 at the top. You can monitor these effects using the "fix -ave/spatial"_fix_ave_spatial.html, "compute +ave/chunk"_fix_ave_chunk.html, "compute temp/deform"_compute_temp_deform.html, and "compute temp/profile"_compute_temp_profile.html commands. One way to induce atoms to stream consistent with the box deformation is to give them an diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 307bb9982a..05984b7e3f 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -63,8 +63,8 @@ temperature profile (assuming z = edim) to the file tmp.profile: compute ke all ke/atom variable temp atom c_ke/1.5 -fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp & - file tmp.profile units reduced :pre +compute layers all chunk/atom bin/1d z lower 0.05 units reduced +fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile :pre Note that by default, Nswap = 1, though this can be changed by the optional {swap} keyword. Setting this parameter appropriately, in @@ -145,10 +145,9 @@ bewteen solvent particles. [Related commands:] -"fix ehex"_fix_ehex.html, "fix heat"_fix_heat.html, -"fix ave/spatial"_fix_ave_spatial.html, "fix -viscosity"_fix_viscosity.html, "compute -heat/flux"_compute_heat_flux.html +"fix ehex"_fix_ehex.html, "fix heat"_fix_heat.html, "fix +ave/chunk"_fix_ave_chunk.html, "fix viscosity"_fix_viscosity.html, +"compute heat/flux"_compute_heat_flux.html [Default:] diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 4b9c8174b0..87cc9618e4 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -60,8 +60,8 @@ directions. Over time, this induces a shear velocity profile in the system which can be measured using commands such as the following, which writes the profile to the file tmp.profile: -fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & - file tmp.profile units reduced :pre +compute layers all chunk/atom z lower 0.05 units reduced +fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile :pre Note that by default, Nswap = 1 and vtarget = INF, though this can be changed by the optional {swap} and {vtarget} keywords. When vtarget = @@ -152,7 +152,7 @@ solvent particles. [Related commands:] -"fix ave/spatial"_fix_ave_spatial.html, "fix +"fix ave/chunk"_fix_ave_chunk.html, "fix thermal/conductivity"_fix_thermal_conductivity.html [Default:] diff --git a/doc/src/prd.txt b/doc/src/prd.txt index b4f5184e1d..484e36004c 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -295,9 +295,9 @@ for dephasing. This command cannot be used when any fixes are defined that keep track of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as "fix -ave/spatial"_fix_ave_spatial.html. Also "fix -dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html. +include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html. +Also "fix dt/reset"_fix_dt_reset.html and "fix +deposit"_fix_deposit.html. [Related commands:] diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 6a291d181d..8e93b93c3b 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -284,9 +284,9 @@ restart, but "fix langevin"_fix_langevin.html will not. This command cannot be used when any fixes are defined that keep track of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as "fix -ave/spatial"_fix_ave_spatial.html. Also "fix -dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html. +include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html. +Also "fix dt/reset"_fix_dt_reset.html and "fix +deposit"_fix_deposit.html. [Related commands:] diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 408e4beda9..c84dc8df99 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -1096,7 +1096,7 @@ variable formula. Referencing a variable with a leading "v_" is an optional or required kind of argument for some commands (e.g. the "fix -ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html or +ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html or "thermo_style"_thermo_style.html commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The From 0a01592d0aa3496e755b70e50af013f8224ea930 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:49:26 +0000 Subject: [PATCH 003/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15070 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-MISC/README | 1 - src/USER-MISC/fix_ave_spatial_sphere.cpp | 1063 ---------------------- src/USER-MISC/fix_ave_spatial_sphere.h | 186 ---- 3 files changed, 1250 deletions(-) delete mode 100644 src/USER-MISC/fix_ave_spatial_sphere.cpp delete mode 100644 src/USER-MISC/fix_ave_spatial_sphere.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index dc1a76e014..131befd5ca 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -35,7 +35,6 @@ dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 -fix ave/spatial/sphere, Niall Jackson (Imperial College), niall.jackson at gmail.com, 18 Nov 14 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 diff --git a/src/USER-MISC/fix_ave_spatial_sphere.cpp b/src/USER-MISC/fix_ave_spatial_sphere.cpp deleted file mode 100644 index 77a5d48960..0000000000 --- a/src/USER-MISC/fix_ave_spatial_sphere.cpp +++ /dev/null @@ -1,1063 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Adapted from fix ave/spatial by Niall Jackson -------------------------------------------------------------------------- */ - -#include -#include -#include -#include "fix_ave_spatial_sphere.h" -#include "atom.h" -#include "update.h" -#include "force.h" -#include "domain.h" -#include "region.h" -#include "lattice.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" - -using namespace LAMMPS_NS; -using namespace FixConst; -using namespace MathConst; - -//the different types of variables that we can track -enum{V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE,CONSTANT}; -//normalisation types -enum{SAMPLE,ALL}; -//unit scaling options -enum{BOX,LATTICE,REDUCED}; -//averaging types -enum{ONE,RUNNING,WINDOW}; - -#define INVOKED_SCALAR 1 -#define INVOKED_VECTOR 2 -#define INVOKED_PERATOM 8 -#define BIG 1000000000 - -/* ---------------------------------------------------------------------- */ - -FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) : - Fix(lmp, narg, arg) { - - if (narg < 12) error->all(FLERR, "Illegal fix ave/spatial/sphere command"); - - MPI_Comm_rank(world, &me); - - nevery= force->inumeric(FLERR, arg[3]); - nrepeat= force->inumeric(FLERR, arg[4]); - nfreq= force->inumeric(FLERR, arg[5]); - - global_freq= nfreq; - - for (int iarg = 6; iarg < 9; ++iarg) { - int dim= iarg-6; - origin_ids[dim]= NULL; - if (strncmp(arg[iarg],"c_",2) == 0 || - strncmp(arg[iarg],"v_",2) == 0) { - if(arg[iarg][0] == 'c') { - origin_type[dim]= COMPUTE; - } else { - origin_type[dim]= VARIABLE; - } - - //strip the v_/c_ off the front of the variable name - int n= strlen(arg[iarg]); - char *suffix= new char[n]; - strcpy(suffix, &arg[iarg][2]); - //does the variable name contain a [? - //(in other words, is this an array element?) - char *ptr= strchr(suffix, '['); - if(ptr) { - //if the last character ISN'T ], then the array syntax - //has been used wrongly - if(suffix[strlen(suffix)-1] != ']') { - error->all(FLERR, "Illegal fix ave/spatial/sphere command"); - } - origin_index[dim]= atoi(ptr+1); - *ptr= '\0'; - } else { - origin_index[dim]= 0; - } - //store the name of the variable - n= strlen(suffix)+1; - origin_ids[dim]= new char[n]; - strcpy(origin_ids[dim], suffix); - //tidy up the array we allocated earlier - delete[] suffix; - - if(origin_type[dim] == COMPUTE) { - int icompute= modify->find_compute(origin_ids[dim]); - if(icompute < 0) - error->all(FLERR, - "Compute ID for fix ave/spatial/sphere does not exist"); - - if(origin_index[dim] == 0 && - modify->compute[icompute]->scalar_flag != 0) - error->all(FLERR,"Compute for fix ave/spatial/sphere does not calculate a scalar"); - else if(origin_index[dim] && modify->compute[icompute]->vector_flag == 0) - error->all(FLERR, "Compute for fix ave/spatial/sphere does not calculate a vector"); - else if(origin_index[dim] && origin_index[dim] > modify->compute[icompute]->size_vector) - error->all(FLERR, "Fix ave/spatial/sphere compute vector accessed out of range"); - } else if(origin_type[dim] == VARIABLE) { - int ivariable = input->variable->find(origin_ids[dim]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/spatial/sphere does not exist"); - else if (input->variable->equalstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/spatial/sphere variable is not equal-style variable"); - } - } else { - origin_type[dim]= CONSTANT; - origin[dim]= force->numeric(FLERR, arg[iarg]); - } - } - - //the extrema of the radius - r_min= force->numeric(FLERR, arg[9]); - r_max= force->numeric(FLERR, arg[10]); - - //and finally, the number of spherical bins - nbins= force->inumeric(FLERR, arg[11]); - - if (r_min >= r_max) { - error->all(FLERR, "r_min must be less than r_max in fix ave/spatial/sphere"); - } - - if (nbins <= 0) { - error->all(FLERR, "nbins must be positive in fix ave/spatial/sphere"); - } - - int iarg= 12; - which= new int[narg-12]; - argindex= new int[narg-12]; - ids= new char*[narg-12]; - value2index= new int[narg-12]; - nvalues= 0; - - while(iarg < narg) { - ids[nvalues]= NULL; - - if(strcmp(arg[iarg], "vx") == 0) { - which[nvalues] = V; - argindex[nvalues++]= 0; - } else if(strcmp(arg[iarg], "vy") == 0) { - which[nvalues] = V; - argindex[nvalues++]= 1; - } else if(strcmp(arg[iarg], "vz") == 0) { - which[nvalues] = V; - argindex[nvalues++]= 2; - } else if(strcmp(arg[iarg], "fx") == 0) { - which[nvalues] = F; - argindex[nvalues++]= 0; - } else if(strcmp(arg[iarg], "fy") == 0) { - which[nvalues] = F; - argindex[nvalues++]= 1; - } else if(strcmp(arg[iarg], "fz") == 0) { - which[nvalues] = F; - argindex[nvalues++]= 2; - } else if(strcmp(arg[iarg], "density/number") == 0) { - which[nvalues] = DENSITY_NUMBER; - argindex[nvalues++]= 0; - } else if(strcmp(arg[iarg], "density/mass") == 0) { - which[nvalues] = DENSITY_MASS; - argindex[nvalues++]= 0; - } else if (strncmp(arg[iarg],"c_",2) == 0 || - strncmp(arg[iarg],"f_",2) == 0 || - strncmp(arg[iarg],"v_",2) == 0) { - if(arg[iarg][0] == 'c') which[nvalues] = COMPUTE; - else if(arg[iarg][0] == 'f') which[nvalues] = FIX; - else if(arg[iarg][0] == 'v') which[nvalues] = VARIABLE; - - //strip the v_/c_/f_ off the front of the variable name - int n= strlen(arg[iarg]); - char *suffix= new char[n]; - strcpy(suffix, &arg[iarg][2]); - - //does the variable name contain a [? - //(in other words, is this an array element?) - char *ptr= strchr(suffix, '['); - if(ptr) { - //if the last character ISN'T ], then the array syntax - //has been used wrongly - if(suffix[strlen(suffix)-1] != ']') { - error->all(FLERR, "Illegal fix ave/spatial/sphere command"); - } - argindex[nvalues]= atoi(ptr+1); - *ptr= '\0'; - } else { - argindex[nvalues]= 0; - } - - //store the name of the variable - n= strlen(suffix)+1; - ids[nvalues]= new char[n]; - strcpy(ids[nvalues], suffix); - nvalues++; - //tidy up the array we allocated earlier - delete[] suffix; - } else break; - - iarg++; - } - - //process the optional arguments - normflag= ALL; //normalise the average right at the end - scaleflag= LATTICE; // lattice units are the default - regionflag= 0; //are we restricted to a particular region? - idregion= NULL; //name of the region to sue, if so - fp= NULL; //output file - ave= ONE; //averaging mode - nwindow= 0; //number of averaging windows - overwrite= 0; //continuously overwrite output? - char *title1= NULL; - char *title2= NULL; - char *title3= NULL; - - while (iarg < narg) { - if (strcmp(arg[iarg],"norm") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL; - else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE; - else error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - iarg += 2; - } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX; - else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE; - else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED; - else error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - iarg += 2; - } else if (strcmp(arg[iarg],"region") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - int iregion = domain->find_region(arg[iarg+1]); - if (iregion == -1) - error->all(FLERR,"Region ID for fix ave/spatial does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); - regionflag = 1; - iarg += 2; - } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (me == 0) { - fp = fopen(arg[iarg+1],"w"); - if (fp == NULL) { - char str[128]; - sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]); - error->one(FLERR,str); - } - } - iarg += 2; - } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; - else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; - else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; - else error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (ave == WINDOW) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - nwindow = force->inumeric(FLERR,arg[iarg+2]); - if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - } - iarg += 2; - if (ave == WINDOW) iarg++; - } else if (strcmp(arg[iarg],"overwrite") == 0) { - overwrite = 1; - iarg += 1; - } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - delete [] title1; - int n = strlen(arg[iarg+1]) + 1; - title1 = new char[n]; - strcpy(title1,arg[iarg+1]); - iarg += 2; - } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - delete [] title2; - int n = strlen(arg[iarg+1]) + 1; - title2 = new char[n]; - strcpy(title2,arg[iarg+1]); - iarg += 2; - } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - delete [] title3; - int n = strlen(arg[iarg+1]) + 1; - title3 = new char[n]; - strcpy(title3,arg[iarg+1]); - iarg += 2; - } else error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - } - - //setup and error checking - if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (nfreq % nevery || nrepeat*nevery > nfreq) - error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - if (ave != RUNNING && overwrite) - error->all(FLERR,"Illegal fix ave/spatial/sphere command"); - - //setup the variables that we need to average - for (int i = 0; i < nvalues; i++) { - if (which[i] == COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/spatial/sphere does not exist"); - if (modify->compute[icompute]->peratom_flag == 0) - error->all(FLERR,"Fix ave/spatial/sphere compute does not " - "calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Fix ave/spatial/sphere compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Fix ave/spatial/sphere compute does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Fix ave/spatial/sphere compute vector is accessed out-of-range"); - - } else if (which[i] == FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/spatial/sphere does not exist"); - if (modify->fix[ifix]->peratom_flag == 0) - error->all(FLERR, - "Fix ave/spatial/sphere fix does not calculate per-atom values"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR, - "Fix ave/spatial/spherefix does not calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR, - "Fix ave/spatial/sphere fix does not calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR,"Fix ave/spatial/sphere fix vector is accessed out-of-range"); - } else if (which[i] == VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/spatial/sphere does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/spatial/sphere variable is not atom-style variable"); - } - } - - // setup the scaling - int triclinic= domain->triclinic; - if(scaleflag != REDUCED) { - if (triclinic) { - error->all(FLERR, "Fix ave/spatial/sphere for triclinic boxes requires units reduced"); - } else { - // if not in reduced units, the box must not become triclinic - no_change_box= 1; - } - } - - if(scaleflag == LATTICE) { - scale= domain->lattice->xlattice; - if(domain->lattice->xlattice != domain->lattice->ylattice - && domain->lattice->xlattice != domain->lattice->zlattice) - error->all(FLERR, "Fix ave/spatial/sphere with lattice units requires that the lattice " - "spacing be equal in all dimensions"); - } else if(scaleflag == REDUCED) { - scale= 1.0; - } else { - scale= 1.0; - } - - //apply the scaling factors - origin[0]*= scale; - origin[1]*= scale; - origin[2]*= scale; - r_min*= scale; - r_max*= scale; - r_minsq= r_min*r_min; - r_maxsq= r_max*r_max; - deltar= (r_max-r_min)/nbins; - inv_deltar= 1.0/deltar; - - //print file comment lines - if (fp && me == 0) { - if (title1) { - fprintf(fp,"%s\n",title1); - } else { - fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n", id,arg[1]); - fprintf(fp,"# Spherical bins centred at ("); - for (int i= 0; i < 3; ++i) { - if(origin_type[i] == CONSTANT) fprintf(fp,"%g",origin[i]); - else fprintf(fp,"%s",arg[i+6]); - - if(i != 2) fprintf(fp, ", "); - else fprintf(fp, ")"); - } - if (scaleflag == REDUCED) { - fprintf(fp, " [reduced units]"); - } - fprintf(fp, "\n"); - } - if (title2) fprintf(fp,"%s\n",title2); - else fprintf(fp,"# Timestep Number-of-bins\n"); - if (title3) fprintf(fp,"%s\n",title3); - else { - fprintf(fp,"# Bin r Ncount"); - for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[12+i]); - fprintf(fp,"\n"); - } - filepos = ftell(fp); - } - - delete [] title1; - delete [] title2; - delete [] title3; - - //this fix produces a global array - array_flag= 1; - size_array_rows= BIG; - size_array_cols= 1 + 1 + nvalues; - extarray= 0; //intensive value (don't divide by N when we output this) - - //initialization of remaining variables - irepeat= 0; - iwindow= window_limit= 0; - norm= 0; - maxvar= 0; - varatom= NULL; - maxatom= 0; - bin= NULL; - binvol= NULL; - maxbin= 0; - count_one= count_many= count_sum= count_total= NULL; - coord= NULL; - count_list= NULL; - values_one= values_many= values_sum= values_total= NULL; - values_list= NULL; - - //nvalid = next step on which end_of_step does something - nvalid= nextvalid(); - //make every compute update itself on step nvalid - //since we don't yet know which ones we need - //can correct this when we call end_of_step - modify->addstep_compute_all(nvalid); -} - -/* ---------------------------------------------------------------------- */ - -FixAveSpatialSphere::~FixAveSpatialSphere() -{ - delete [] which; - delete [] argindex; - for (int i = 0; i < nvalues; i++) delete [] ids[i]; - delete [] ids; - delete [] value2index; - delete [] idregion; - for (int i= 0; i < 3; ++i) delete [] origin_ids[i]; - - if (fp && me == 0) fclose(fp); - - memory->destroy(varatom); - memory->destroy(bin); - memory->destroy(binvol); - - memory->destroy(count_one); - memory->destroy(count_many); - memory->destroy(count_sum); - memory->destroy(count_total); - memory->destroy(coord); - memory->destroy(count_list); - memory->destroy(values_one); - memory->destroy(values_many); - memory->destroy(values_sum); - memory->destroy(values_total); - memory->destroy(values_list); -} - -/* ---------------------------------------------------------------------- - tell LAMMPS at which stages in the timestep we want to be called - we only care about running at the end of a step -------------------------------------------------------------------------- */ - -int FixAveSpatialSphere::setmask() -{ - int mask = 0; - mask |= END_OF_STEP; - return mask; -} - -/* ---------------------------------------------------------------------- */ - -void FixAveSpatialSphere::init() -{ - //set up the region and check it's valid - if(regionflag) { - int iregion= domain->find_region(idregion); - if(iregion == -1) - error->all(FLERR,"Region ID for fix ave/spatial/sphere does not exist"); - region = domain->regions[iregion]; - } - - // set indices and check validity of all computes,fixes,variables - // check that fix frequency is acceptable - - for (int m = 0; m < 3; ++m) { - if (origin_type[m] == COMPUTE) { - int icompute = modify->find_compute(origin_ids[m]); - if (icompute < 0) - error->all(FLERR, "Compute ID for fix ave/spatial/sphere does not exist"); - origin_val2idx[m]= icompute; - } else if (origin_type[m] == VARIABLE) { - int ivariable = input->variable->find(origin_ids[m]); - if (ivariable < 0) - error->all(FLERR, "Variable name for fix ave/spatial/sphere does not exist"); - origin_val2idx[m]= ivariable; - } - } - - for (int m = 0; m < nvalues; m++) { - if (which[m] == COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/spatial/sphere does not exist"); - value2index[m] = icompute; - - } else if (which[m] == FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/spatial/sphere does not exist"); - value2index[m] = ifix; - - if (nevery % modify->fix[ifix]->peratom_freq) - error->all(FLERR, - "Fix for fix ave/spatial/sphere not computed at compatible time"); - - } else if (which[m] == VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/spatial/sphere does not exist"); - value2index[m] = ivariable; - - } else value2index[m] = -1; - } - - - // need to reset nvalid if nvalid < ntimestep b/c minimize was performed - if (nvalid < update->ntimestep) { - irepeat = 0; - nvalid = nextvalid(); - modify->addstep_compute_all(nvalid); - } -} - -/* ---------------------------------------------------------------------- - setup initial bins - only does averaging if nvalid = current timestep -------------------------------------------------------------------------- */ - -void FixAveSpatialSphere::setup(int vflag) -{ - setup_bins(); - end_of_step(); -} - -/* ---------------------------------------------------------------------- */ - -void FixAveSpatialSphere::end_of_step() -{ - //skip this step if we don't need to do anything - bigint ntimestep= update->ntimestep; - if(ntimestep != nvalid) return; - - //update region if necessary - if (regionflag) region->prematch(); - - //zero out arrays that accumulate over many samples - if(irepeat == 0) { - for(int m= 0; m < nbins; m++) { - count_many[m]= count_sum[m]= 0.0; - for(int i= 0; i < nvalues; i++) values_many[m][i]= 0.0; - } - } - - //if in reduced units, we need to update the bin volumes - if (scaleflag == REDUCED && domain->box_change) set_bin_volumes(); - - //zero out arrays for one sample - for(int m= 0; m < nbins; m++) { - count_one[m]= 0.0; - for (int i= 0; i < nvalues; i++) values_one[m][i]= 0.0; - } - - //bin each atom - int *mask= atom->mask; - int nlocal= atom->nlocal; - - if (nlocal > maxatom) { - maxatom= atom->nmax; - memory->destroy(bin); - memory->create(bin,maxatom,"ave/spatial/sphere:bin"); - } - - // perform the computation for one sample - // accumulate results of attributes,computes,fixes,variables to local copy - // sum within each bin, only include atoms in fix group - // compute/fix/variable may invoke computes so wrap with clear/add - modify->clearstep_compute(); - - //allocates the bins array - //each atom gets either the number of the bin into which - //it fits, or -1 - bin_atoms(); - - for(int m= 0; m < nvalues; m++) { - int n= value2index[m]; - int j= argindex[m]; - - if(which[m] == V || which[m] == F) { - double **attribute; - if(which[m] == V) attribute= atom->v; - else attribute= atom->f; - - for(int i= 0; i < nlocal; i++) { - if(mask[i] & groupbit && bin[i] > -1) { - values_one[bin[i]][m] += attribute[i][j]; - } - } - } else if(which[m] == DENSITY_NUMBER) { - for(int i= 0; i < nlocal; i++) { - if(mask[i] & groupbit && bin[i] > -1) { - values_one[bin[i]][m] += 1.0; - } - } - // density is additionally normalized by bin volume - for (int j = 0; j < nbins; j++) - values_one[j][m] /= binvol[j]; - } else if(which[m] == DENSITY_MASS) { - int *type = atom->type; - double *mass = atom->mass; - double *rmass = atom->rmass; - for(int i= 0; i < nlocal; i++) { - if(mask[i] & groupbit && bin[i] > -1) { - if (rmass) values_one[bin[i]][m] += rmass[i]; - else values_one[bin[i]][m] += mass[type[i]]; - } - } - // density is additionally normalized by bin volume - for (int j = 0; j < nbins; j++) - values_one[j][m] /= binvol[j]; - } else if(which[m] == COMPUTE) { - Compute *compute = modify->compute[n]; - if (!(compute->invoked_flag & INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= INVOKED_PERATOM; - } - double *vector = compute->vector_atom; - double **array = compute->array_atom; - int jm1 = j - 1; - - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] > -1) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - - } else if(which[m] == FIX) { - double *vector = modify->fix[n]->vector_atom; - double **array = modify->fix[n]->array_atom; - int jm1 = j - 1; - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] > -1) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - } else if(which[m] == VARIABLE) { - if (nlocal > maxvar) { - maxvar = atom->nmax; - memory->destroy(varatom); - memory->create(varatom,maxvar,"ave/spatial:varatom"); - } - - input->variable->compute_atom(n,igroup,varatom,1,0); - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] > -1) - values_one[bin[i]][m] += varatom[i]; - } - } - - // process a single sample - // if normflag = ALL, accumulate values,count separately to many - // if normflag = SAMPLE, one = value/count, accumulate one to many - // exception is SAMPLE density: no normalization by atom count - - if (normflag == ALL) { - for (int m = 0; m < nbins; m++) { - count_many[m] += count_one[m]; - for (int j = 0; j < nvalues; j++) - values_many[m][j] += values_one[m][j]; - } - } else { - MPI_Allreduce(count_one,count_many,nbins,MPI_DOUBLE,MPI_SUM,world); - for (int m = 0; m < nbins; m++) { - if (count_many[m] > 0.0) - for (int j = 0; j < nvalues; j++) { - if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS) - values_many[m][j] += values_one[m][j]; - else values_many[m][j] += values_one[m][j]/count_many[m]; - } - count_sum[m] += count_many[m]; - } - } - - // done if irepeat < nrepeat - // else reset irepeat and nvalid - irepeat++; - if (irepeat < nrepeat) { - nvalid += nevery; - modify->addstep_compute(nvalid); - return; - } - - irepeat++; - if (irepeat < nrepeat) { - nvalid += nevery; - modify->addstep_compute(nvalid); - return; - } - - irepeat = 0; - nvalid = ntimestep+nfreq - (nrepeat-1)*nevery; - modify->addstep_compute(nvalid); - - // time average across samples - // if normflag = ALL, final is total value / total count - // if normflag = SAMPLE, final is sum of ave / repeat - // exception is densities: normalized by repeat, not total count - - double repeat = nrepeat; - double mv2d = force->mv2d; - if (normflag == ALL) { - MPI_Allreduce(count_many,count_sum,nbins,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues, - MPI_DOUBLE,MPI_SUM,world); - for (int m = 0; m < nbins; m++) { - if (count_sum[m] > 0.0) - for (int j = 0; j < nvalues; j++) - if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat; - else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat; - else values_sum[m][j] /= count_sum[m]; - count_sum[m] /= repeat; - } - } else { - MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues, - MPI_DOUBLE,MPI_SUM,world); - for (int m = 0; m < nbins; m++) { - for (int j = 0; j < nvalues; j++) - values_sum[m][j] /= repeat; - count_sum[m] /= repeat; - } - } - - // if ave = ONE, only single Nfreq timestep value is needed - // if ave = RUNNING, combine with all previous Nfreq timestep values - // if ave = WINDOW, comine with nwindow most recent Nfreq timestep values - - if (ave == ONE) { - for (int m = 0; m < nbins; m++) { - for (int i = 0; i < nvalues; i++) - values_total[m][i] = values_sum[m][i]; - count_total[m] = count_sum[m]; - } - norm = 1; - - } else if (ave == RUNNING) { - for (int m = 0; m < nbins; m++) { - for (int i = 0; i < nvalues; i++) - values_total[m][i] += values_sum[m][i]; - count_total[m] += count_sum[m]; - } - norm++; - - } else if (ave == WINDOW) { - for (int m = 0; m < nbins; m++) { - for (int i = 0; i < nvalues; i++) { - values_total[m][i] += values_sum[m][i]; - if (window_limit) values_total[m][i] -= values_list[iwindow][m][i]; - values_list[iwindow][m][i] = values_sum[m][i]; - } - count_total[m] += count_sum[m]; - if (window_limit) count_total[m] -= count_list[iwindow][m]; - count_list[iwindow][m] = count_sum[m]; - } - - iwindow++; - if (iwindow == nwindow) { - iwindow = 0; - window_limit = 1; - } - if (window_limit) norm = nwindow; - else norm = iwindow; - } - - // output result to file - - if (fp && me == 0) { - if (overwrite) fseek(fp,filepos,SEEK_SET); - fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nbins); - for (int m = 0; m < nbins; m++) { - fprintf(fp," %d %g %g",m+1,coord[m], - count_total[m]/norm); - for (int i = 0; i < nvalues; i++) - fprintf(fp," %g",values_total[m][i]/norm); - fprintf(fp,"\n"); - } - - fflush(fp); - if (overwrite) { - long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); - } - } -} - -/* ---------------------------------------------------------------------- - setup the bins - called at setup() -------------------------------------------------------------------------- */ - -void FixAveSpatialSphere::setup_bins() -{ - if(nbins > maxbin) { - maxbin= nbins; - memory->grow(count_one,nbins,"ave/spatial/sphere:count_one"); - memory->grow(count_many,nbins,"ave/spatial/sphere:count_many"); - memory->grow(count_sum,nbins,"ave/spatial/sphere:count_sum"); - memory->grow(count_total,nbins,"ave/spatial/sphere:count_total"); - - memory->grow(coord,nbins,"ave/spatial/sphere:coord"); - memory->grow(binvol,nbins, "ave/spatial/sphere:binvol"); - memory->grow(values_one,nbins,nvalues,"ave/spatial/sphere:values_one"); - memory->grow(values_many,nbins,nvalues,"ave/spatial/sphere:values_many"); - memory->grow(values_sum,nbins,nvalues,"ave/spatial/sphere:values_sum"); - memory->grow(values_total,nbins,nvalues,"ave/spatial/sphere:values_total"); - - //the count and value lists are only relevant for windowed averaging - if(ave == WINDOW) { - memory->create(count_list,nwindow,nbins,"ave/spatial/sphere:count_list"); - memory->create(values_list,nwindow,nbins,nvalues, - "ave/spatial/sphere:values_list"); - } - - //reinitialize the regrown count and values - for(int m= 0; m < nbins; m++) { - for(int i= 0; i < nvalues; i++) values_total[m][i]= 0.0; - count_total[m]= 0.0; - } - } - - //set the bin coordinates - for(int i= 0; i < nbins; i++) - coord[i]= r_min + (i+0.5)*deltar; - - set_bin_volumes(); -} - -/* ---------------------------------------------------------------------- - set the bin volumes - called at setup() and when averaging occurs if box size changes -------------------------------------------------------------------------- */ - -void FixAveSpatialSphere::set_bin_volumes() -{ - double last_vol= THIRD*MY_4PI*r_minsq*r_min; - for(int i= 0; i < nbins; i++) { - double temp_r= r_min + (i+1)*deltar; - double temp_vol= THIRD*MY_4PI*temp_r*temp_r*temp_r; - binvol[i]= temp_vol-last_vol; - last_vol= temp_vol; - } - - //if in reduced co-ordinates, need to adjust the bin volumes appropriately - if (scaleflag == REDUCED) { - double xprd= domain->xprd; - double yprd= domain->yprd; - double zprd= domain->zprd; - for(int i= 0; i < nbins; i++) { - binvol[i]*= xprd*yprd*zprd; - } - } -} - -/* ---------------------------------------------------------------------- - assign atoms to bins -------------------------------------------------------------------------- */ - -void FixAveSpatialSphere::bin_atoms() -{ - //update the origin coordinates if necessary - //unscale the existing coordinates - if(scaleflag == REDUCED) domain->lamda2x(origin, origin); - - for (int i = 0; i < 3; ++i) { - if (origin_type[i] == COMPUTE) { - Compute *compute = modify->compute[origin_val2idx[i]]; - if (origin_index[i] == 0) { - if (!(compute->invoked_flag & INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= INVOKED_SCALAR; - } - origin[i] = compute->scalar; - } else { - if (!(compute->invoked_flag & INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= INVOKED_VECTOR; - } - origin[i] = compute->vector[origin_index[i]-1]; - } - } else if (origin_type[i] == VARIABLE) { - origin[i] = input->variable->compute_equal(origin_val2idx[i]); - } - } - //make sure that the origin point is INSIDE the box - domain->remap(origin); - //rescale if necessary - if(scaleflag == REDUCED) domain->x2lamda(origin, origin); - - double **x= atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double *prd,*prd_half; - //deal with the periodic boundary conditions - if(domain->periodicity[0] || domain->periodicity[1] || domain->periodicity[2]) { - if(scaleflag == REDUCED) { - prd= domain->prd_lamda; - prd_half= domain->prd_half_lamda; - } else { - prd= domain->prd; - prd_half= domain->prd_half; - } - } - - double rsq, tmp; - - if(!regionflag) { - if(scaleflag == REDUCED) { - //convert the atomic coordinates into reduced coordinates - domain->x2lamda(nlocal); - } - for(int i= 0; i < nlocal; i++) { - if(mask[i] & groupbit) { - rsq= 0.0; - for(int dim= 0; dim < 3; dim++) { - tmp= x[i][dim] - origin[dim]; - if(domain->periodicity[dim]) { - if(tmp < -prd_half[dim]) tmp+= prd[dim]; - else if(tmp >= prd_half[dim]) tmp-= prd[dim]; - } - rsq+= tmp*tmp; - } - if(rsq >= r_minsq && rsq <= r_maxsq) { - double r= sqrt(rsq); - int ibin= static_cast((r-r_min)*inv_deltar); - ibin = MAX(ibin,0); - ibin = MIN(ibin,nbins-1); - bin[i]= ibin; - count_one[ibin]+= 1.0; - } else { - bin[i]= -1; - } - } - } - if(scaleflag == REDUCED) { - //convert the atomic coordinates back into "real" coordinates - domain->lamda2x(nlocal); - } - } else { - for(int i= 0; i < nlocal; i++) { - if(mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) { - rsq= 0.0; - for(int dim= 0; dim < 3; dim++) { - tmp= x[i][dim] - origin[dim]; - if(domain->periodicity[dim]) { - if(tmp < -0.5*prd[dim]) tmp+= prd[dim]; - else if(tmp >= 0.5*prd[dim]) tmp-= prd[dim]; - } - rsq+= tmp*tmp; - } - if(rsq >= r_minsq && rsq <= r_maxsq) { - double r= sqrt(rsq); - int ibin= static_cast((r-r_min)*inv_deltar); - ibin = MAX(ibin,0); - ibin = MIN(ibin,nbins-1); - bin[i]= ibin; - count_one[ibin]+= 1.0; - } else { - bin[i]= -1; - } - } - } - } -} - -/* ---------------------------------------------------------------------- - return I,J array value - if I exceeds current bins, return 0.0 instead of generating an error - column 1 = bin coords, next column = count, remaining columns = Nvalues -------------------------------------------------------------------------- */ - -double FixAveSpatialSphere::compute_array(int i, int j) -{ - if (values_total == NULL) return 0.0; - if (i >= nbins || j > nvalues) return 0.0; - if (!norm) return 0.0; - if (j == 0) return coord[i]; - if (j == 1) return count_total[i]/norm; - return values_total[i][j]/norm; -} - - -/* ---------------------------------------------------------------------- - calculate nvalid = next step on which end_of_step does something - can be this timestep if multiple of nfreq and nrepeat = 1 - else backup from next multiple of nfreq -------------------------------------------------------------------------- */ - -bigint FixAveSpatialSphere::nextvalid() -{ - bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq; - if (nvalid-nfreq == update->ntimestep && nrepeat == 1) - nvalid = update->ntimestep; - else - nvalid -= (nrepeat-1)*nevery; - if (nvalid < update->ntimestep) nvalid += nfreq; - return nvalid; -} - -/* ---------------------------------------------------------------------- - memory usage of varatom and bins -------------------------------------------------------------------------- */ - -double FixAveSpatialSphere::memory_usage() -{ - double bytes = maxvar * sizeof(double); // varatom - bytes += maxatom * sizeof(int); // bin - bytes += 4*nbins * sizeof(double); // count one,many,sum,total - bytes += nbins * sizeof(double); // coord - bytes += nvalues*nbins * sizeof(double); // values one,many,sum,total - bytes += nwindow*nbins * sizeof(double); // count_list - bytes += nwindow*nbins*nvalues * sizeof(double); // values_list - return bytes; -} diff --git a/src/USER-MISC/fix_ave_spatial_sphere.h b/src/USER-MISC/fix_ave_spatial_sphere.h deleted file mode 100644 index 1ac550c5e0..0000000000 --- a/src/USER-MISC/fix_ave_spatial_sphere.h +++ /dev/null @@ -1,186 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* Adapted from fix ave/spatial by Niall Jackson */ - -#ifdef FIX_CLASS - -FixStyle(ave/spatial/sphere,FixAveSpatialSphere) - -#else - -#ifndef LMP_FIX_AVE_SPATIAL_SPHERE_H -#define LMP_FIX_AVE_SPATIAL_SPHERE_H - -#include -#include "fix.h" - -namespace LAMMPS_NS { - -class FixAveSpatialSphere : public Fix { - public: - FixAveSpatialSphere(class LAMMPS *, int, char **); - ~FixAveSpatialSphere(); - int setmask(); - void init(); - void setup(int); - void end_of_step(); - double memory_usage(); - double compute_array(int,int); - - private: - int me; //rank of the MPI Process - int nfreq; //fix nfreq parameter - int nrepeat; //fix nrepeat parameter - bigint nvalid; //the next timestep on which I'll be invoked - - //controls for various optional behaviours - int normflag; //what type of normalisation to do - int norm; - int scaleflag; //default units (lattice, box, etc.) - double scale; //coordinate scaling factor - int regionflag; //restricted to a particular region? - char *idregion; //name of the region to use - class Region *region; //pointer to the region - FILE *fp; //pointer for the output file - long int filepos; //file position pointer - int ave; //averaging mode - int nwindow; //number of averaging windows - int iwindow; //current window - int window_limit; - int overwrite; //continuously overwrite the output (requires ave running) - - //used to keep track of which per-atom values we deal with - int nvalues; //number of variables to average - int *argindex; //if the variable is an array, this is the offset in that array - int *value2index; - int *which; //what sort of variable is arg i? Variable, compute, etc? - char **ids; //names of the variables - int maxvar; //current size of the varatom array - double* varatom; //contains the peratom values of a variable - - //details of the sphere and the bins - int maxbin; //current number of bins in memory (relevant if box changes) - int nbins; //number of spherical bins - int maxatom; //current size of the bin array - int *bin; //stores the bin of each atom - double *coord; //values of r at the mid points of the bins - double *binvol; //volumes of the bins - double *count_one, *count_many, *count_sum, *count_total; //bin populations - double **values_one, **values_many, **values_sum, **values_total; //accumulated bin values - double origin[3]; //origin coordinates of the sphere - int origin_type[3]; //are origin coordinates constant or variable? - char *origin_ids[3]; //store the names of variables used to access the origin - int origin_index[3]; //indices for the origin variables - int origin_val2idx[3]; //compute/variable indices - double r_min, r_minsq; //minimum radius, and its square - double r_max, r_maxsq; //maximum radius, and its square - double deltar, inv_deltar; //radial width of a bin, and its inverse (and their squares) - - void setup_bins(); //create the bin arrays - void set_bin_volumes(); //calculate the volume of each bin - void bin_atoms(); //put the atom into bins based on their coordinates - bigint nextvalid(); //return the next timestep on which this is invoked - - //NEED TO BE CATEGORISED - int irepeat; - double **count_list; - double ***values_list; - -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Region ID for fix ave/spatial/spherical does not exist - -Self-explanatory. - -E: Cannot open fix ave/spatial/spherical file %s - -The specified file cannot be opened. Check that the path and name are -correct. - -E: Compute ID for fix ave/spatial/spherical does not exist - -Self-explanatory. - -E: Fix ave/spatial/spherical compute does not calculate per-atom values - -A compute used by fix ave/spatial/spherical must generate per-atom values. - -E: Fix ave/spatial/spherical compute does not calculate a per-atom vector - -A compute used by fix ave/spatial/spherical must generate per-atom values. - -E: Fix ave/spatial/spherical compute does not calculate a per-atom array - -Self-explanatory. - -E: Fix ave/spatial/spherical compute vector is accessed out-of-range - -The index for the vector is out of bounds. - -E: Fix ID for fix ave/spatial/spherical does not exist - -Self-explanatory. - -E: Fix ave/spatial/spherical fix does not calculate per-atom values - -A fix used by fix ave/spatial/spherical must generate per-atom values. - -E: Fix ave/spatial/spherical fix does not calculate a per-atom vector - -A fix used by fix ave/spatial/spherical must generate per-atom values. - -E: Fix ave/spatial/spherical fix does not calculate a per-atom array - -Self-explanatory. - -E: Fix ave/spatial/spherical fix vector is accessed out-of-range - -The index for the vector is out of bounds. - -E: Variable name for fix ave/spatial/spherical does not exist - -Self-explanatory. - -E: Fix ave/spatial/spherical variable is not atom-style variable - -A variable used by fix ave/spatial/spherical must generate per-atom values. - -E: Fix ave/spatial/spherical for triclinic boxes requires units reduced - -Self-explanatory. - -E: Fix ave/spatial/spherical requires reduced units if the box changes size. - -If the box size changes, only the units reduced option can be -used. - -E: Invalid timestep reset for fix ave/spatial/sphere - -Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -*/ From 9d3d6193f39a43984e458cadb9f8204e931f4799 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:49:49 +0000 Subject: [PATCH 004/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15071 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_ave_spatial.cpp | 1522 +-------------------------------------- src/fix_ave_spatial.h | 157 +--- src/pair_table.cpp | 29 +- 3 files changed, 40 insertions(+), 1668 deletions(-) diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp index bf32065e22..ef9e04a373 100644 --- a/src/fix_ave_spatial.cpp +++ b/src/fix_ave_spatial.cpp @@ -11,1528 +11,30 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing author: Pieter in 't Veld (SNL) -------------------------------------------------------------------------- */ - -#include -#include -#include #include "fix_ave_spatial.h" -#include "atom.h" -#include "update.h" -#include "force.h" -#include "domain.h" -#include "region.h" -#include "lattice.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "comm.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace FixConst; - -enum{LOWER,CENTER,UPPER,COORD}; -enum{V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE}; -enum{SAMPLE,ALL}; -enum{BOX,LATTICE,REDUCED}; -enum{ONE,RUNNING,WINDOW}; -enum{NODISCARD,MIXED,YESDISCARD}; - -#define INVOKED_PERATOM 8 /* ---------------------------------------------------------------------- */ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (comm->me == 0) - error->warning(FLERR,"The fix ave/spatial command has been replaced " - "by the more flexible fix ave/chunk and compute chunk/atom " - "commands -- fix ave/spatial will be removed in " - "the summer of 2015"); + const char *message = "\n" + "NOTE: The fix ave/spatial command has been replaced by the\n" + "more general fix ave/chunk and compute chunk/atom commands.\n" + "All ave/spatial functionality is available in the new commands.\n" + "These ave/spatial keywords & options are part of fix ave/chunk:\n" + " Nevery, Nrepeat, Nfreq, input values, norm, ave, file, overwrite, title123\n" + "These ave/spatial keywords & options for binning are part of compute chunk/atom:\n" + " dim, origin, delta, region, bound, discard, units\n\n"; - if (narg < 6) error->all(FLERR,"Illegal fix ave/spatial command"); - - MPI_Comm_rank(world,&me); - - nevery = force->inumeric(FLERR,arg[3]); - nrepeat = force->inumeric(FLERR,arg[4]); - nfreq = force->inumeric(FLERR,arg[5]); - - global_freq = nfreq; - no_change_box = 1; - - ndim = 0; - int iarg = 6; - while (iarg < narg && ndim < 3) { - if (iarg+3 > narg) break; - if (strcmp(arg[iarg],"x") == 0) dim[ndim] = 0; - else if (strcmp(arg[iarg],"y") == 0) dim[ndim] = 1; - else if (strcmp(arg[iarg],"z") == 0) dim[ndim] = 2; - else break; - - if (dim[ndim] == 2 && domain->dimension == 2) - error->all(FLERR,"Cannot use fix ave/spatial z for 2 dimensional model"); - - if (strcmp(arg[iarg+1],"lower") == 0) originflag[ndim] = LOWER; - else if (strcmp(arg[iarg+1],"center") == 0) originflag[ndim] = CENTER; - else if (strcmp(arg[iarg+1],"upper") == 0) originflag[ndim] = UPPER; - else originflag[ndim] = COORD; - if (originflag[ndim] == COORD) - origin[ndim] = force->numeric(FLERR,arg[iarg+1]); - - delta[ndim] = force->numeric(FLERR,arg[iarg+2]); - ndim++; - iarg += 3; + if (comm->me == 0) { + if (screen) fprintf(screen,message); + if (logfile) fprintf(logfile,message); } - if (!ndim) error->all(FLERR,"Illegal fix ave/spatial command"); - if (ndim == 2 && dim[0] == dim[1]) - error->all(FLERR,"Same dimension twice in fix ave/spatial"); - if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2])) - error->all(FLERR,"Same dimension twice in fix ave/spatial"); - - // parse values until one isn't recognized - - which = new int[narg-9]; - argindex = new int[narg-9]; - ids = new char*[narg-9]; - value2index = new int[narg-9]; - nvalues = 0; - - while (iarg < narg) { - ids[nvalues] = NULL; - - if (strcmp(arg[iarg],"vx") == 0) { - which[nvalues] = V; - argindex[nvalues++] = 0; - } else if (strcmp(arg[iarg],"vy") == 0) { - which[nvalues] = V; - argindex[nvalues++] = 1; - } else if (strcmp(arg[iarg],"vz") == 0) { - which[nvalues] = V; - argindex[nvalues++] = 2; - - } else if (strcmp(arg[iarg],"fx") == 0) { - which[nvalues] = F; - argindex[nvalues++] = 0; - } else if (strcmp(arg[iarg],"fy") == 0) { - which[nvalues] = F; - argindex[nvalues++] = 1; - } else if (strcmp(arg[iarg],"fz") == 0) { - which[nvalues] = F; - argindex[nvalues++] = 2; - - } else if (strcmp(arg[iarg],"density/number") == 0) { - which[nvalues] = DENSITY_NUMBER; - argindex[nvalues++] = 0; - } else if (strcmp(arg[iarg],"density/mass") == 0) { - which[nvalues] = DENSITY_MASS; - argindex[nvalues++] = 0; - - } else if (strncmp(arg[iarg],"c_",2) == 0 || - strncmp(arg[iarg],"f_",2) == 0 || - strncmp(arg[iarg],"v_",2) == 0) { - if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; - else if (arg[iarg][0] == 'f') which[nvalues] = FIX; - else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE; - - int n = strlen(arg[iarg]); - char *suffix = new char[n]; - strcpy(suffix,&arg[iarg][2]); - - char *ptr = strchr(suffix,'['); - if (ptr) { - if (suffix[strlen(suffix)-1] != ']') - error->all(FLERR,"Illegal fix ave/spatial command"); - argindex[nvalues] = atoi(ptr+1); - *ptr = '\0'; - } else argindex[nvalues] = 0; - - n = strlen(suffix) + 1; - ids[nvalues] = new char[n]; - strcpy(ids[nvalues],suffix); - nvalues++; - delete [] suffix; - - } else break; - - iarg++; - } - - if (nvalues == 0) error->all(FLERR,"No input values for fix ave/spatial"); - - // optional args - - regionflag = 0; - idregion = NULL; - minflag[0] = LOWER; - minflag[1] = LOWER; - minflag[2] = LOWER; - maxflag[0] = UPPER; - maxflag[1] = UPPER; - maxflag[2] = UPPER; - discard = MIXED; - normflag = ALL; - ave = ONE; - scaleflag = LATTICE; - fp = NULL; - nwindow = 0; - overwrite = 0; - char *title1 = NULL; - char *title2 = NULL; - char *title3 = NULL; - - while (iarg < narg) { - if (strcmp(arg[iarg],"region") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - int iregion = domain->find_region(arg[iarg+1]); - if (iregion == -1) - error->all(FLERR,"Region ID for fix ave/spatial does not exist"); - int n = strlen(arg[iarg+1]) + 1; - idregion = new char[n]; - strcpy(idregion,arg[iarg+1]); - regionflag = 1; - iarg += 2; - } else if (strcmp(arg[iarg],"bound") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - int idim; - if (strcmp(arg[iarg+1],"x") == 0) idim = 0; - else if (strcmp(arg[iarg+1],"y") == 0) idim = 1; - else if (strcmp(arg[iarg+1],"z") == 0) idim = 2; - else error->all(FLERR,"Illegal fix ave/spatial command"); - if (strcmp(arg[iarg+2],"lower") == 0) minflag[idim] = LOWER; - else minflag[idim] = COORD; - if (minflag[idim] == COORD) - minvalue[idim] = force->numeric(FLERR,arg[iarg+2]); - if (strcmp(arg[iarg+3],"upper") == 0) maxflag[idim] = UPPER; - else maxflag[idim] = COORD; - if (maxflag[idim] == COORD) - maxvalue[idim] = force->numeric(FLERR,arg[iarg+3]); - else error->all(FLERR,"Illegal fix ave/spatial command"); - iarg += 4; - } else if (strcmp(arg[iarg],"discard") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - if (strcmp(arg[iarg+1],"mixed") == 0) discard = MIXED; - else if (strcmp(arg[iarg+1],"no") == 0) discard = NODISCARD; - else if (strcmp(arg[iarg+1],"yes") == 0) discard = YESDISCARD; - else error->all(FLERR,"Illegal fix ave/spatial command"); - iarg += 2; - } else if (strcmp(arg[iarg],"norm") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL; - else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE; - else error->all(FLERR,"Illegal fix ave/spatial command"); - iarg += 2; - } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; - else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; - else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; - else error->all(FLERR,"Illegal fix ave/spatial command"); - if (ave == WINDOW) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - nwindow = force->inumeric(FLERR,arg[iarg+2]); - if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command"); - } - iarg += 2; - if (ave == WINDOW) iarg++; - } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX; - else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE; - else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED; - else error->all(FLERR,"Illegal fix ave/spatial command"); - iarg += 2; - } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - if (me == 0) { - fp = fopen(arg[iarg+1],"w"); - if (fp == NULL) { - char str[128]; - sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]); - error->one(FLERR,str); - } - } - iarg += 2; - } else if (strcmp(arg[iarg],"overwrite") == 0) { - overwrite = 1; - iarg += 1; - } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - delete [] title1; - int n = strlen(arg[iarg+1]) + 1; - title1 = new char[n]; - strcpy(title1,arg[iarg+1]); - iarg += 2; - } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - delete [] title2; - int n = strlen(arg[iarg+1]) + 1; - title2 = new char[n]; - strcpy(title2,arg[iarg+1]); - iarg += 2; - } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command"); - delete [] title3; - int n = strlen(arg[iarg+1]) + 1; - title3 = new char[n]; - strcpy(title3,arg[iarg+1]); - iarg += 2; - } else error->all(FLERR,"Illegal fix ave/spatial command"); - } - - // setup and error check - - if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/spatial command"); - if (nfreq % nevery || nrepeat*nevery > nfreq) - error->all(FLERR,"Illegal fix ave/spatial command"); - if (delta[0] <= 0.0) error->all(FLERR,"Illegal fix ave/spatial command"); - if (ndim >= 2 && delta[1] <= 0.0) - error->all(FLERR,"Illegal fix ave/spatial command"); - if (ndim == 3 && delta[2] <= 0.0) - error->all(FLERR,"Illegal fix ave/spatial command"); - if (ave != RUNNING && overwrite) - error->all(FLERR,"Illegal fix ave/spatial command"); - - for (int i = 0; i < nvalues; i++) { - if (which[i] == COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/spatial does not exist"); - if (modify->compute[icompute]->peratom_flag == 0) - error->all(FLERR,"Fix ave/spatial compute does not " - "calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Fix ave/spatial compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Fix ave/spatial compute does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Fix ave/spatial compute vector is accessed out-of-range"); - - } else if (which[i] == FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/spatial does not exist"); - if (modify->fix[ifix]->peratom_flag == 0) - error->all(FLERR, - "Fix ave/spatial fix does not calculate per-atom values"); - if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR, - "Fix ave/spatial fix does not calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR, - "Fix ave/spatial fix does not calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range"); - } else if (which[i] == VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/spatial does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/spatial variable is not atom-style variable"); - } - } - - // print file comment lines - - if (fp && me == 0) { - if (title1) fprintf(fp,"%s\n",title1); - else fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n", - id,arg[1]); - if (title2) fprintf(fp,"%s\n",title2); - else fprintf(fp,"# Timestep Number-of-bins\n"); - if (title3) fprintf(fp,"%s\n",title3); - else { - if (ndim == 1) fprintf(fp,"# Bin Coord Ncount"); - else if (ndim == 2) fprintf(fp,"# Bin Coord1 Coord2 Ncount"); - else if (ndim == 3) fprintf(fp,"# Bin Coord1 Coord2 Coord3 Ncount"); - for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+3*ndim+i]); - fprintf(fp,"\n"); - } - filepos = ftell(fp); - } - - delete [] title1; - delete [] title2; - delete [] title3; - - // this fix produces a global array - // size_array_rows set by setup_bins() - - array_flag = 1; - size_array_cols = 1 + ndim + nvalues; - extarray = 0; - - // setup scaling - - int triclinic = domain->triclinic; - if (triclinic == 1 && scaleflag != REDUCED) - error->all(FLERR, - "Fix ave/spatial for triclinic boxes requires units reduced"); - - if (scaleflag == LATTICE) { - xscale = domain->lattice->xlattice; - yscale = domain->lattice->ylattice; - zscale = domain->lattice->zlattice; - } else xscale = yscale = zscale = 1.0; - - // apply scaling factors - - double scale; - for (int idim = 0; idim < ndim; idim++) { - if (dim[idim] == 0) scale = xscale; - else if (dim[idim] == 1) scale = yscale; - else if (dim[idim] == 2) scale = zscale; - delta[idim] *= scale; - invdelta[idim] = 1.0/delta[idim]; - if (originflag[idim] == COORD) origin[idim] *= scale; - if (minflag[idim] == COORD) minvalue[idim] *= scale; - if (maxflag[idim] == COORD) maxvalue[idim] *= scale; - } - - // initializations - // invoke setup_bins() now to set size_array_rows - // will be reset in setup(), but needed now so Thermo custom can access it - - irepeat = 0; - iwindow = window_limit = 0; - norm = 0; - - maxvar = 0; - varatom = NULL; - - maxatom = 0; - bin = NULL; - - nbins = maxbin = 0; - count_one = count_many = count_sum = count_total = NULL; - coord = NULL; - count_list = NULL; - values_one = values_many = values_sum = values_total = NULL; - values_list = NULL; - - setup_bins(); - - // nvalid = next step on which end_of_step does something - // add nvalid to all computes that store invocation times - // since don't know a priori which are invoked by this fix - // once in end_of_step() can set timestep for ones actually invoked - - nvalid_last = -1; - nvalid = nextvalid(); - modify->addstep_compute_all(nvalid); -} - -/* ---------------------------------------------------------------------- */ - -FixAveSpatial::~FixAveSpatial() -{ - delete [] which; - delete [] argindex; - for (int i = 0; i < nvalues; i++) delete [] ids[i]; - delete [] ids; - delete [] value2index; - delete [] idregion; - - if (fp && me == 0) fclose(fp); - - memory->destroy(varatom); - memory->destroy(bin); - - memory->destroy(count_one); - memory->destroy(count_many); - memory->destroy(count_sum); - memory->destroy(count_total); - memory->destroy(coord); - memory->destroy(count_list); - memory->destroy(values_one); - memory->destroy(values_many); - memory->destroy(values_sum); - memory->destroy(values_total); - memory->destroy(values_list); -} -/* ---------------------------------------------------------------------- */ - -int FixAveSpatial::setmask() -{ - int mask = 0; - mask |= END_OF_STEP; - return mask; -} - -/* ---------------------------------------------------------------------- */ - -void FixAveSpatial::init() -{ - // set and check validity of region - - if (regionflag) { - int iregion = domain->find_region(idregion); - if (iregion == -1) - error->all(FLERR,"Region ID for fix ave/spatial does not exist"); - region = domain->regions[iregion]; - } - - // # of bins cannot vary for ave = RUNNING or WINDOW - - if (ave == RUNNING || ave == WINDOW) { - if (scaleflag != REDUCED && domain->box_change_size) - error->all(FLERR, - "Fix ave/spatial settings invalid with changing box size"); - } - - // set indices and check validity of all computes,fixes,variables - // check that fix frequency is acceptable - - for (int m = 0; m < nvalues; m++) { - if (which[m] == COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/spatial does not exist"); - value2index[m] = icompute; - - } else if (which[m] == FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/spatial does not exist"); - value2index[m] = ifix; - - if (nevery % modify->fix[ifix]->peratom_freq) - error->all(FLERR, - "Fix for fix ave/spatial not computed at compatible time"); - - } else if (which[m] == VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/spatial does not exist"); - value2index[m] = ivariable; - - } else value2index[m] = -1; - } - - // need to reset nvalid if nvalid < ntimestep b/c minimize was performed - - if (nvalid < update->ntimestep) { - irepeat = 0; - nvalid = nextvalid(); - modify->addstep_compute_all(nvalid); - } -} - -/* ---------------------------------------------------------------------- - setup initial bins - only does averaging if nvalid = current timestep -------------------------------------------------------------------------- */ - -void FixAveSpatial::setup(int vflag) -{ - setup_bins(); - end_of_step(); -} - -/* ---------------------------------------------------------------------- */ - -void FixAveSpatial::end_of_step() -{ - int i,j,m,n; - - // skip if not step which requires doing something - // error check if timestep was reset in an invalid manner - - bigint ntimestep = update->ntimestep; - if (ntimestep < nvalid_last || ntimestep > nvalid) - error->all(FLERR,"Invalid timestep reset for fix ave/spatial"); - if (ntimestep != nvalid) return; - nvalid_last = nvalid; - - // update region if necessary - - if (regionflag) region->prematch(); - - // zero out arrays that accumulate over many samples - // if box changes, first re-setup bins - - if (irepeat == 0) { - if (domain->box_change) setup_bins(); - for (m = 0; m < nbins; m++) { - count_many[m] = count_sum[m] = 0.0; - for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0; - } - } - - // zero out arrays for one sample - - for (m = 0; m < nbins; m++) { - count_one[m] = 0.0; - for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0; - } - - // assign each atom to a bin - - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - if (nlocal > maxatom) { - maxatom = atom->nmax; - memory->destroy(bin); - memory->create(bin,maxatom,"ave/spatial:bin"); - } - - if (ndim == 1) atom2bin1d(); - else if (ndim == 2) atom2bin2d(); - else atom2bin3d(); - - // perform the computation for one sample - // accumulate results of attributes,computes,fixes,variables to local copy - // sum within each bin, only include atoms in fix group - // compute/fix/variable may invoke computes so wrap with clear/add - - modify->clearstep_compute(); - - for (m = 0; m < nvalues; m++) { - n = value2index[m]; - j = argindex[m]; - - // V,F adds velocities,forces to values - - if (which[m] == V || which[m] == F) { - double **attribute; - if (which[m] == V) attribute = atom->v; - else attribute = atom->f; - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) - values_one[bin[i]][m] += attribute[i][j]; - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) - values_one[bin[i]][m] += attribute[i][j]; - } - - // DENSITY_NUMBER adds 1 to values - - } else if (which[m] == DENSITY_NUMBER) { - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) - values_one[bin[i]][m] += 1.0; - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) - values_one[bin[i]][m] += 1.0; - } - - // DENSITY_MASS adds mass to values - - } else if (which[m] == DENSITY_MASS) { - int *type = atom->type; - double *mass = atom->mass; - double *rmass = atom->rmass; - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) { - if (rmass) values_one[bin[i]][m] += rmass[i]; - else values_one[bin[i]][m] += mass[type[i]]; - } - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) { - if (rmass) values_one[bin[i]][m] += rmass[i]; - else values_one[bin[i]][m] += mass[type[i]]; - } - } - - // COMPUTE adds its scalar or vector component to values - // invoke compute if not previously invoked - - } else if (which[m] == COMPUTE) { - Compute *compute = modify->compute[n]; - if (!(compute->invoked_flag & INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= INVOKED_PERATOM; - } - double *vector = compute->vector_atom; - double **array = compute->array_atom; - int jm1 = j - 1; - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - } - - // FIX adds its scalar or vector component to values - // access fix fields, guaranteed to be ready - - } else if (which[m] == FIX) { - double *vector = modify->fix[n]->vector_atom; - double **array = modify->fix[n]->array_atom; - int jm1 = j - 1; - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) { - if (j == 0) values_one[bin[i]][m] += vector[i]; - else values_one[bin[i]][m] += array[i][jm1]; - } - } - - // VARIABLE adds its per-atom quantities to values - // evaluate atom-style variable - - } else if (which[m] == VARIABLE) { - if (nlocal > maxvar) { - maxvar = atom->nmax; - memory->destroy(varatom); - memory->create(varatom,maxvar,"ave/spatial:varatom"); - } - - input->variable->compute_atom(n,igroup,varatom,1,0); - - if (!regionflag) { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && bin[i] >= 0) - values_one[bin[i]][m] += varatom[i]; - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) && - bin[i] >= 0) - values_one[bin[i]][m] += varatom[i]; - } - } - } - - // process a single sample - // if normflag = ALL, accumulate values,count separately to many - // if normflag = SAMPLE, one = value/count, accumulate one to many - // exception is SAMPLE density: no normalization by atom count - - if (normflag == ALL) { - for (m = 0; m < nbins; m++) { - count_many[m] += count_one[m]; - for (j = 0; j < nvalues; j++) - values_many[m][j] += values_one[m][j]; - } - } else { - MPI_Allreduce(count_one,count_many,nbins,MPI_DOUBLE,MPI_SUM,world); - for (m = 0; m < nbins; m++) { - if (count_many[m] > 0.0) - for (j = 0; j < nvalues; j++) { - if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS) - values_many[m][j] += values_one[m][j]; - else values_many[m][j] += values_one[m][j]/count_many[m]; - } - count_sum[m] += count_many[m]; - } - } - - // done if irepeat < nrepeat - // else reset irepeat and nvalid - - irepeat++; - if (irepeat < nrepeat) { - nvalid += nevery; - modify->addstep_compute(nvalid); - return; - } - - irepeat = 0; - nvalid = ntimestep+nfreq - (nrepeat-1)*nevery; - modify->addstep_compute(nvalid); - - // time average across samples - // if normflag = ALL, final is total value / total count - // if normflag = SAMPLE, final is sum of ave / repeat - // exception is densities: normalized by repeat, not total count - - double repeat = nrepeat; - double mv2d = force->mv2d; - - if (normflag == ALL) { - MPI_Allreduce(count_many,count_sum,nbins,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues, - MPI_DOUBLE,MPI_SUM,world); - for (m = 0; m < nbins; m++) { - if (count_sum[m] > 0.0) - for (j = 0; j < nvalues; j++) { - if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat; - else if (which[j] == DENSITY_MASS) { - values_sum[m][j] *= mv2d/repeat; - } else values_sum[m][j] /= count_sum[m]; - } - count_sum[m] /= repeat; - } - } else { - MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues, - MPI_DOUBLE,MPI_SUM,world); - for (m = 0; m < nbins; m++) { - for (j = 0; j < nvalues; j++) - values_sum[m][j] /= repeat; - count_sum[m] /= repeat; - } - } - - // density is additionally normalized by bin volume - - for (j = 0; j < nvalues; j++) - if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS) - for (m = 0; m < nbins; m++) - values_sum[m][j] /= bin_volume; - - // if ave = ONE, only single Nfreq timestep value is needed - // if ave = RUNNING, combine with all previous Nfreq timestep values - // if ave = WINDOW, comine with nwindow most recent Nfreq timestep values - - if (ave == ONE) { - for (m = 0; m < nbins; m++) { - for (i = 0; i < nvalues; i++) - values_total[m][i] = values_sum[m][i]; - count_total[m] = count_sum[m]; - } - norm = 1; - - } else if (ave == RUNNING) { - for (m = 0; m < nbins; m++) { - for (i = 0; i < nvalues; i++) - values_total[m][i] += values_sum[m][i]; - count_total[m] += count_sum[m]; - } - norm++; - - } else if (ave == WINDOW) { - for (m = 0; m < nbins; m++) { - for (i = 0; i < nvalues; i++) { - values_total[m][i] += values_sum[m][i]; - if (window_limit) values_total[m][i] -= values_list[iwindow][m][i]; - values_list[iwindow][m][i] = values_sum[m][i]; - } - count_total[m] += count_sum[m]; - if (window_limit) count_total[m] -= count_list[iwindow][m]; - count_list[iwindow][m] = count_sum[m]; - } - - iwindow++; - if (iwindow == nwindow) { - iwindow = 0; - window_limit = 1; - } - if (window_limit) norm = nwindow; - else norm = iwindow; - } - - // output result to file - - if (fp && me == 0) { - if (overwrite) fseek(fp,filepos,SEEK_SET); - fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nbins); - if (ndim == 1) { - for (m = 0; m < nbins; m++) { - fprintf(fp," %d %g %g",m+1,coord[m][0], - count_total[m]/norm); - for (i = 0; i < nvalues; i++) - fprintf(fp," %g",values_total[m][i]/norm); - fprintf(fp,"\n"); - } - } else if (ndim == 2) - for (m = 0; m < nbins; m++) { - fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1], - count_total[m]/norm); - for (i = 0; i < nvalues; i++) - fprintf(fp," %g",values_total[m][i]/norm); - fprintf(fp,"\n"); - } - else - for (m = 0; m < nbins; m++) { - fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2], - count_total[m]/norm); - for (i = 0; i < nvalues; i++) - fprintf(fp," %g",values_total[m][i]/norm); - fprintf(fp,"\n"); - } - - fflush(fp); - if (overwrite) { - long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); - } - } -} - -/* ---------------------------------------------------------------------- - setup 1d, 2d, or 3d bins and their extent and coordinates - called at setup() and when averaging occurs if box size changes -------------------------------------------------------------------------- */ - -void FixAveSpatial::setup_bins() -{ - int i,j,k,m,n,idim; - double lo,hi,coord1,coord2; - - // lo = bin boundary immediately below boxlo or minvalue - // hi = bin boundary immediately above boxhi or maxvalue - // allocate and initialize arrays based on new bin count - - double binlo[3],binhi[3]; - double *prd; - if (scaleflag == REDUCED) { - binlo[0] = domain->boxlo_lamda[0]; - binlo[1] = domain->boxlo_lamda[1]; - binlo[2] = domain->boxlo_lamda[2]; - binhi[0] = domain->boxhi_lamda[0]; - binhi[1] = domain->boxhi_lamda[1]; - binhi[2] = domain->boxhi_lamda[2]; - prd = domain->prd_lamda; - } else { - binlo[0] = domain->boxlo[0]; - binlo[1] = domain->boxlo[1]; - binlo[2] = domain->boxlo[2]; - binhi[0] = domain->boxhi[0]; - binhi[1] = domain->boxhi[1]; - binhi[2] = domain->boxhi[2]; - prd = domain->prd; - } - - if (minflag[0] == COORD) binlo[0] = minvalue[0]; - if (minflag[1] == COORD) binlo[1] = minvalue[1]; - if (minflag[2] == COORD) binlo[2] = minvalue[2]; - if (maxflag[0] == COORD) binhi[0] = maxvalue[0]; - if (maxflag[1] == COORD) binhi[1] = maxvalue[1]; - if (maxflag[2] == COORD) binhi[2] = maxvalue[2]; - - if (domain->dimension == 3) - bin_volume = domain->xprd * domain->yprd * domain->zprd; - else bin_volume = domain->xprd * domain->yprd; - nbins = 1; - - for (m = 0; m < ndim; m++) { - idim = dim[m]; - if (originflag[m] == LOWER) origin[m] = binlo[idim]; - else if (originflag[m] == UPPER) origin[m] = binhi[idim]; - else if (originflag[m] == CENTER) - origin[m] = 0.5 * (binlo[idim] + binhi[idim]); - - if (origin[m] < binlo[idim]) { - n = static_cast ((binlo[idim] - origin[m]) * invdelta[m]); - lo = origin[m] + n*delta[m]; - } else { - n = static_cast ((origin[m] - binlo[idim]) * invdelta[m]); - lo = origin[m] - n*delta[m]; - if (lo > binlo[idim]) lo -= delta[m]; - } - if (origin[m] < binhi[idim]) { - n = static_cast ((binhi[idim] - origin[m]) * invdelta[m]); - hi = origin[m] + n*delta[m]; - if (hi < binhi[idim]) hi += delta[m]; - } else { - n = static_cast ((origin[m] - binhi[idim]) * invdelta[m]); - hi = origin[m] - n*delta[m]; - } - - if (lo > hi) error->all(FLERR,"Invalid bin bounds in fix ave/spatial"); - - offset[m] = lo; - nlayers[m] = static_cast ((hi-lo) * invdelta[m] + 0.5); - nbins *= nlayers[m]; - bin_volume *= delta[m]/prd[idim]; - } - - size_array_rows = nbins; - - // reallocate bin arrays if needed - - if (nbins > maxbin) { - maxbin = nbins; - memory->grow(count_one,nbins,"ave/spatial:count_one"); - memory->grow(count_many,nbins,"ave/spatial:count_many"); - memory->grow(count_sum,nbins,"ave/spatial:count_sum"); - memory->grow(count_total,nbins,"ave/spatial:count_total"); - - memory->grow(coord,nbins,ndim,"ave/spatial:coord"); - memory->grow(values_one,nbins,nvalues,"ave/spatial:values_one"); - memory->grow(values_many,nbins,nvalues,"ave/spatial:values_many"); - memory->grow(values_sum,nbins,nvalues,"ave/spatial:values_sum"); - memory->grow(values_total,nbins,nvalues,"ave/spatial:values_total"); - - // only allocate count and values list for ave = WINDOW - - if (ave == WINDOW) { - memory->create(count_list,nwindow,nbins,"ave/spatial:count_list"); - memory->create(values_list,nwindow,nbins,nvalues, - "ave/spatial:values_list"); - } - - // reinitialize regrown count/values total since they accumulate - - for (m = 0; m < nbins; m++) { - for (i = 0; i < nvalues; i++) values_total[m][i] = 0.0; - count_total[m] = 0.0; - } - } - - // set bin coordinates - - if (ndim == 1) { - for (i = 0; i < nlayers[0]; i++) - coord[i][0] = offset[0] + (i+0.5)*delta[0]; - } else if (ndim == 2) { - m = 0; - for (i = 0; i < nlayers[0]; i++) { - coord1 = offset[0] + (i+0.5)*delta[0]; - for (j = 0; j < nlayers[1]; j++) { - coord[m][0] = coord1; - coord[m][1] = offset[1] + (j+0.5)*delta[1]; - m++; - } - } - } else if (ndim == 3) { - m = 0; - for (i = 0; i < nlayers[0]; i++) { - coord1 = offset[0] + (i+0.5)*delta[0]; - for (j = 0; j < nlayers[1]; j++) { - coord2 = offset[1] + (j+0.5)*delta[1]; - for (k = 0; k < nlayers[2]; k++) { - coord[m][0] = coord1; - coord[m][1] = coord2; - coord[m][2] = offset[2] + (k+0.5)*delta[2]; - m++; - } - } - } - } -} - -/* ---------------------------------------------------------------------- - assign each atom to a 1d bin -------------------------------------------------------------------------- */ - -void FixAveSpatial::atom2bin1d() -{ - int i,ibin; - double *boxlo,*boxhi,*prd; - double xremap; - double lamda[3]; - - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - int idim = dim[0]; - int nlayer1m1 = nlayers[0] - 1; - int periodicity = domain->periodicity[idim]; - - if (periodicity) { - if (scaleflag == REDUCED) { - boxlo = domain->boxlo_lamda; - boxhi = domain->boxhi_lamda; - prd = domain->prd_lamda; - } else { - boxlo = domain->boxlo; - boxhi = domain->boxhi; - prd = domain->prd; - } - } - - // remap each atom's relevant coord back into box via PBC if necessary - // apply discard rule - // if scaleflag = REDUCED, box coords -> lamda coords - - if (!regionflag) { - if (scaleflag == REDUCED) domain->x2lamda(nlocal); - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { - bin[i] = -1; - - xremap = x[i][idim]; - if (periodicity) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - ibin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) ibin--; - - if (discard== MIXED) { - if (!minflag[idim]) ibin = MAX(ibin,0); - else if (ibin < 0) continue; - if (!maxflag[idim]) ibin = MIN(ibin,nlayer1m1); - else if (ibin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - ibin = MAX(ibin,0); - ibin = MIN(ibin,nlayer1m1); - } else { - if (ibin < 0 || ibin > nlayer1m1) continue; - } - - bin[i] = ibin; - count_one[ibin] += 1.0; - } - if (scaleflag == REDUCED) domain->lamda2x(nlocal); - - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { - bin[i] = -1; - - if (scaleflag == REDUCED) { - domain->x2lamda(x[i],lamda); - xremap = lamda[idim]; - } else xremap = x[i][idim]; - if (periodicity) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - ibin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) ibin--; - - if (discard == MIXED) { - if (!minflag[idim]) ibin = MAX(ibin,0); - else if (ibin < 0) continue; - if (!maxflag[idim]) ibin = MIN(ibin,nlayer1m1); - else if (ibin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - ibin = MAX(ibin,0); - ibin = MIN(ibin,nlayer1m1); - } else { - if (ibin < 0 || ibin > nlayer1m1) continue; - } - - bin[i] = ibin; - count_one[ibin] += 1.0; - } - } -} - -/* ---------------------------------------------------------------------- - assign each atom to a 2d bin -------------------------------------------------------------------------- */ - -void FixAveSpatial::atom2bin2d() -{ - int i,ibin,i1bin,i2bin; - double *boxlo,*boxhi,*prd; - double xremap,yremap; - double lamda[3]; - - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - int idim = dim[0]; - int jdim = dim[1]; - int nlayer1m1 = nlayers[0] - 1; - int nlayer2m1 = nlayers[1] - 1; - int* periodicity = domain->periodicity; - - if (periodicity[idim] || periodicity[jdim]) { - if (scaleflag == REDUCED) { - boxlo = domain->boxlo_lamda; - boxhi = domain->boxhi_lamda; - prd = domain->prd_lamda; - } else { - boxlo = domain->boxlo; - boxhi = domain->boxhi; - prd = domain->prd; - } - } - - // remap each atom's relevant coord back into box via PBC if necessary - // apply discard rule - // if scaleflag = REDUCED, box coords -> lamda coords - - if (!regionflag) { - if (scaleflag == REDUCED) domain->x2lamda(nlocal); - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { - bin[i] = -1; - - xremap = x[i][idim]; - if (periodicity[idim]) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - i1bin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) i1bin--; - - if (discard == MIXED) { - if (!minflag[idim]) i1bin = MAX(i1bin,0); - else if (i1bin < 0) continue; - if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1); - else if (i1bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i1bin = MAX(i1bin,0); - i1bin = MIN(i1bin,nlayer1m1); - } else { - if (i1bin < 0 || i1bin > nlayer1m1) continue; - } - - yremap = x[i][jdim]; - if (periodicity[jdim]) { - if (yremap < boxlo[jdim]) yremap += prd[jdim]; - if (yremap >= boxhi[jdim]) yremap -= prd[jdim]; - } - - i2bin = static_cast ((yremap - offset[1]) * invdelta[1]); - if (yremap < offset[1]) i2bin--; - - if (discard == MIXED) { - if (!minflag[jdim]) i2bin = MAX(i2bin,0); - else if (i2bin < 0) continue; - if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1); - else if (i2bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i2bin = MAX(i2bin,0); - i2bin = MIN(i2bin,nlayer2m1); - } else { - if (i2bin < 0 || i2bin > nlayer2m1) continue; - } - - ibin = i1bin*nlayers[1] + i2bin; - bin[i] = ibin; - count_one[ibin] += 1.0; - } - if (scaleflag == REDUCED) domain->lamda2x(nlocal); - - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { - bin[i] = -1; - - if (scaleflag == REDUCED) { - domain->x2lamda(x[i],lamda); - xremap = lamda[idim]; - yremap = lamda[jdim]; - } else { - xremap = x[i][idim]; - yremap = x[i][jdim]; - } - - if (periodicity[idim]) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - i1bin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) i1bin--; - - if (discard == MIXED) { - if (!minflag[idim]) i1bin = MAX(i1bin,0); - else if (i1bin < 0) continue; - if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1); - else if (i1bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i1bin = MAX(i1bin,0); - i1bin = MIN(i1bin,nlayer1m1); - } else { - if (i1bin < 0 || i1bin > nlayer1m1) continue; - } - - if (periodicity[jdim]) { - if (yremap < boxlo[jdim]) yremap += prd[jdim]; - if (yremap >= boxhi[jdim]) yremap -= prd[jdim]; - } - - i2bin = static_cast ((yremap - offset[1]) * invdelta[1]); - if (yremap < offset[1]) i2bin--; - - if (discard == MIXED) { - if (!minflag[jdim]) i2bin = MAX(i2bin,0); - else if (i2bin < 0) continue; - if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1); - else if (i2bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i2bin = MAX(i2bin,0); - i2bin = MIN(i2bin,nlayer2m1); - } else { - if (i2bin < 0 || i2bin > nlayer2m1) continue; - } - - ibin = i1bin*nlayers[1] + i2bin; - bin[i] = ibin; - count_one[ibin] += 1.0; - } - } -} - -/* ---------------------------------------------------------------------- - assign each atom to a 3d bin -------------------------------------------------------------------------- */ - -void FixAveSpatial::atom2bin3d() -{ - int i,ibin,i1bin,i2bin,i3bin; - double *boxlo,*boxhi,*prd; - double xremap,yremap,zremap; - double lamda[3]; - - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - int idim = dim[0]; - int jdim = dim[1]; - int kdim = dim[2]; - int nlayer1m1 = nlayers[0] - 1; - int nlayer2m1 = nlayers[1] - 1; - int nlayer3m1 = nlayers[2] - 1; - int* periodicity = domain->periodicity; - - if (periodicity[idim] || periodicity[jdim] || periodicity[kdim]) { - if (scaleflag == REDUCED) { - boxlo = domain->boxlo_lamda; - boxhi = domain->boxhi_lamda; - prd = domain->prd_lamda; - } else { - boxlo = domain->boxlo; - boxhi = domain->boxhi; - prd = domain->prd; - } - } - - // remap each atom's relevant coord back into box via PBC if necessary - // apply discard rule - // if scaleflag = REDUCED, box coords -> lamda coords - - if (!regionflag) { - if (scaleflag == REDUCED) domain->x2lamda(nlocal); - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { - bin[i] = -1; - - xremap = x[i][idim]; - if (periodicity[idim]) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - i1bin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) i1bin--; - - if (discard == MIXED) { - if (!minflag[idim]) i1bin = MAX(i1bin,0); - else if (i1bin < 0) continue; - if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1); - else if (i1bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i1bin = MAX(i1bin,0); - i1bin = MIN(i1bin,nlayer1m1); - } else { - if (i1bin < 0 || i1bin > nlayer1m1) continue; - } - - yremap = x[i][jdim]; - if (periodicity[jdim]) { - if (yremap < boxlo[jdim]) yremap += prd[jdim]; - if (yremap >= boxhi[jdim]) yremap -= prd[jdim]; - } - - i2bin = static_cast ((yremap - offset[1]) * invdelta[1]); - if (yremap < offset[1]) i2bin--; - - if (discard == MIXED) { - if (!minflag[jdim]) i2bin = MAX(i2bin,0); - else if (i2bin < 0) continue; - if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1); - else if (i2bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i2bin = MAX(i2bin,0); - i2bin = MIN(i2bin,nlayer2m1); - } else { - if (i2bin < 0 || i2bin > nlayer2m1) continue; - } - - zremap = x[i][kdim]; - if (periodicity[kdim]) { - if (zremap < boxlo[kdim]) zremap += prd[kdim]; - if (zremap >= boxhi[kdim]) zremap -= prd[kdim]; - } - - i3bin = static_cast ((zremap - offset[2]) * invdelta[2]); - if (zremap < offset[2]) i3bin--; - - if (discard == MIXED) { - if (!minflag[kdim]) i3bin = MAX(i3bin,0); - else if (i3bin < 0) continue; - if (!maxflag[kdim]) i3bin = MIN(i3bin,nlayer3m1); - else if (i3bin > nlayer3m1) continue; - } else if (discard == NODISCARD) { - i3bin = MAX(i3bin,0); - i3bin = MIN(i3bin,nlayer3m1); - } else { - if (i3bin < 0 || i3bin > nlayer3m1) continue; - } - - ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin; - bin[i] = ibin; - count_one[ibin] += 1.0; - } - if (scaleflag == REDUCED) domain->lamda2x(nlocal); - - } else { - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { - bin[i] = -1; - - if (scaleflag == REDUCED) { - domain->x2lamda(x[i],lamda); - xremap = lamda[idim]; - yremap = lamda[jdim]; - zremap = lamda[kdim]; - } else { - xremap = x[i][idim]; - yremap = x[i][jdim]; - zremap = x[i][kdim]; - } - - if (periodicity[idim]) { - if (xremap < boxlo[idim]) xremap += prd[idim]; - if (xremap >= boxhi[idim]) xremap -= prd[idim]; - } - - i1bin = static_cast ((xremap - offset[0]) * invdelta[0]); - if (xremap < offset[0]) i1bin--; - - if (discard == MIXED) { - if (!minflag[idim]) i1bin = MAX(i1bin,0); - else if (i1bin < 0) continue; - if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1); - else if (i1bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i1bin = MAX(i1bin,0); - i1bin = MIN(i1bin,nlayer1m1); - } else { - if (i1bin < 0 || i1bin > nlayer1m1) continue; - } - - if (periodicity[jdim]) { - if (yremap < boxlo[jdim]) yremap += prd[jdim]; - if (yremap >= boxhi[jdim]) yremap -= prd[jdim]; - } - - i2bin = static_cast ((yremap - offset[1]) * invdelta[1]); - if (yremap < offset[1]) i2bin--; - - if (discard == MIXED) { - if (!minflag[jdim]) i2bin = MAX(i2bin,0); - else if (i2bin < 0) continue; - if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1); - else if (i2bin > nlayer1m1) continue; - } else if (discard == NODISCARD) { - i2bin = MAX(i2bin,0); - i2bin = MIN(i2bin,nlayer2m1); - } else { - if (i2bin < 0 || i2bin > nlayer2m1) continue; - } - - if (periodicity[kdim]) { - if (zremap < boxlo[kdim]) zremap += prd[kdim]; - if (zremap >= boxhi[kdim]) zremap -= prd[kdim]; - } - - i3bin = static_cast ((zremap - offset[2]) * invdelta[2]); - if (zremap < offset[2]) i3bin--; - - if (discard == MIXED) { - if (!minflag[kdim]) i3bin = MAX(i3bin,0); - else if (i3bin < 0) continue; - if (!maxflag[kdim]) i3bin = MIN(i3bin,nlayer3m1); - else if (i3bin > nlayer3m1) continue; - } else if (discard == NODISCARD) { - i3bin = MAX(i3bin,0); - i3bin = MIN(i3bin,nlayer3m1); - } else { - if (i3bin < 0 || i3bin > nlayer3m1) continue; - } - - ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin; - bin[i] = ibin; - count_one[ibin] += 1.0; - } - } -} - -/* ---------------------------------------------------------------------- - return I,J array value - if I exceeds current nbins, return 0.0 instead of generating an error - column 1,2,3 = bin coords, next column = count, remaining columns = Nvalues -------------------------------------------------------------------------- */ - -double FixAveSpatial::compute_array(int i, int j) -{ - if (values_total == NULL) return 0.0; - if (i >= nbins) return 0.0; - if (j < ndim) return coord[i][j]; - j -= ndim+1; - if (!norm) return 0.0; - if (j < 0) return count_total[i]/norm; - return values_total[i][j]/norm; -} - -/* ---------------------------------------------------------------------- - calculate nvalid = next step on which end_of_step does something - can be this timestep if multiple of nfreq and nrepeat = 1 - else backup from next multiple of nfreq -------------------------------------------------------------------------- */ - -bigint FixAveSpatial::nextvalid() -{ - bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq; - if (nvalid-nfreq == update->ntimestep && nrepeat == 1) - nvalid = update->ntimestep; - else - nvalid -= (nrepeat-1)*nevery; - if (nvalid < update->ntimestep) nvalid += nfreq; - return nvalid; -} - -/* ---------------------------------------------------------------------- - memory usage of varatom and bins -------------------------------------------------------------------------- */ - -double FixAveSpatial::memory_usage() -{ - double bytes = maxvar * sizeof(double); // varatom - bytes += maxatom * sizeof(int); // bin - bytes += 4*nbins * sizeof(double); // count one,many,sum,total - bytes += ndim*nbins * sizeof(double); // coord - bytes += nvalues*nbins * sizeof(double); // values one,many,sum,total - bytes += nwindow*nbins * sizeof(double); // count_list - bytes += nwindow*nbins*nvalues * sizeof(double); // values_list - return bytes; + error->all(FLERR,"The fix ave/spatial command has been removed from LAMMPS"); } diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h index 1df4c363b2..de592cbc95 100644 --- a/src/fix_ave_spatial.h +++ b/src/fix_ave_spatial.h @@ -28,56 +28,9 @@ namespace LAMMPS_NS { class FixAveSpatial : public Fix { public: FixAveSpatial(class LAMMPS *, int, char **); - ~FixAveSpatial(); - int setmask(); - void init(); - void setup(int); - void end_of_step(); - double compute_array(int,int); - double memory_usage(); - - private: - int me,nvalues; - int nrepeat,nfreq,irepeat; - bigint nvalid,nvalid_last; - int ndim,normflag,regionflag,overwrite,discard; - char *tstring,*sstring,*idregion; - int *which,*argindex,*value2index; - char **ids; - FILE *fp; - class Region *region; - - int ave,nwindow,scaleflag; - int norm,iwindow,window_limit; - double xscale,yscale,zscale; - double bin_volume; - - long filepos; - int dim[3],originflag[3],nlayers[3]; - double origin[3],delta[3]; - double offset[3],invdelta[3]; - - int maxvar; - double *varatom; - - int maxatom; - int *bin; - - int nbins,maxbin; - double **coord; - double *count_one,*count_many,*count_sum; - double **values_one,**values_many,**values_sum; - double *count_total,**count_list; - double **values_total,***values_list; - - int minflag[3],maxflag[3]; - double minvalue[3],maxvalue[3]; - - void setup_bins(); - void atom2bin1d(); - void atom2bin2d(); - void atom2bin3d(); - bigint nextvalid(); + ~FixAveSpatial() {} + int setmask() {} + void init() {} }; } @@ -87,106 +40,10 @@ class FixAveSpatial : public Fix { /* ERROR/WARNING messages: -W: The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015 +E: The fix ave/spatial command has been removed from LAMMPS -Self-explanatory. - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Cannot use fix ave/spatial z for 2 dimensional model - -Self-explanatory. - -E: Same dimension twice in fix ave/spatial - -Self-explanatory. - -E: No input values for fix ave/spatial - -Self-explanatory. - -E: Region ID for fix ave/spatial does not exist - -Self-explanatory. - -E: Cannot open fix ave/spatial file %s - -The specified file cannot be opened. Check that the path and name are -correct. - -E: Compute ID for fix ave/spatial does not exist - -Self-explanatory. - -E: Fix ave/spatial compute does not calculate per-atom values - -A compute used by fix ave/spatial must generate per-atom values. - -E: Fix ave/spatial compute does not calculate a per-atom vector - -A compute used by fix ave/spatial must generate per-atom values. - -E: Fix ave/spatial compute does not calculate a per-atom array - -Self-explanatory. - -E: Fix ave/spatial compute vector is accessed out-of-range - -The index for the vector is out of bounds. - -E: Fix ID for fix ave/spatial does not exist - -Self-explanatory. - -E: Fix ave/spatial fix does not calculate per-atom values - -A fix used by fix ave/spatial must generate per-atom values. - -E: Fix ave/spatial fix does not calculate a per-atom vector - -A fix used by fix ave/spatial must generate per-atom values. - -E: Fix ave/spatial fix does not calculate a per-atom array - -Self-explanatory. - -E: Fix ave/spatial fix vector is accessed out-of-range - -The index for the vector is out of bounds. - -E: Variable name for fix ave/spatial does not exist - -Self-explanatory. - -E: Fix ave/spatial variable is not atom-style variable - -A variable used by fix ave/spatial must generate per-atom values. - -E: Fix ave/spatial for triclinic boxes requires units reduced - -Self-explanatory. - -E: Fix ave/spatial settings invalid with changing box size - -If the box size changes, only the units reduced option can be -used. - -E: Fix for fix ave/spatial not computed at compatible time - -Fixes generate their values on specific timesteps. Fix ave/spatial is -requesting a value on a non-allowed timestep. - -E: Invalid timestep reset for fix ave/spatial - -Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -E: Invalid bin bounds in fix ave/spatial - -The lo/hi values are inconsistent. +It has been replaced by the more flexible fix ave/chunk and compute +chunk/atom commands. All the fix ave/spatial keywords and options are +available in those two newer commands. */ diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 71b4d49b5f..06afdff78f 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -63,6 +63,7 @@ void PairTable::compute(int eflag, int vflag) int i,j,ii,jj,inum,jnum,itype,jtype,itable; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,factor_lj,fraction,value,a,b; + char estr[128]; int *ilist,*jlist,*numneigh,**firstneigh; Table *tb; @@ -109,25 +110,37 @@ void PairTable::compute(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { tb = &tables[tabindex[itype][jtype]]; - if (rsq < tb->innersq) - error->one(FLERR,"Pair distance < table inner cutoff"); + if (rsq < tb->innersq) { + sprintf(estr,"Pair distance < table inner cutoff: " + "ijtype %d %d dist %g",itype,jtype,sqrt(rsq)); + error->one(FLERR,estr); + } if (tabstyle == LOOKUP) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); - if (itable >= tlm1) - error->one(FLERR,"Pair distance > table outer cutoff"); + if (itable >= tlm1) { + sprintf(estr,"Pair distance > table outer cutoff: " + "ijtype %d %d dist %g",itype,jtype,sqrt(rsq)); + error->one(FLERR,estr); + } fpair = factor_lj * tb->f[itable]; } else if (tabstyle == LINEAR) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); - if (itable >= tlm1) - error->one(FLERR,"Pair distance > table outer cutoff"); + if (itable >= tlm1) { + sprintf(estr,"Pair distance > table outer cutoff: " + "ijtype %d %d dist %g",itype,jtype,sqrt(rsq)); + error->one(FLERR,estr); + } fraction = (rsq - tb->rsq[itable]) * tb->invdelta; value = tb->f[itable] + fraction*tb->df[itable]; fpair = factor_lj * value; } else if (tabstyle == SPLINE) { itable = static_cast ((rsq - tb->innersq) * tb->invdelta); - if (itable >= tlm1) - error->one(FLERR,"Pair distance > table outer cutoff"); + if (itable >= tlm1) { + sprintf(estr,"Pair distance > table outer cutoff: " + "ijtype %d %d dist %g",itype,jtype,sqrt(rsq)); + error->one(FLERR,estr); + } b = (rsq - tb->rsq[itable]) * tb->invdelta; a = 1.0 - b; value = a * tb->f[itable] + b * tb->f[itable+1] + From 402b7a7231750b794b8ef178b19244ef730b088d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:53:34 +0000 Subject: [PATCH 005/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15072 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/fix_ave_spatial.txt | 447 --------------- doc/html/_sources/fix_ave_spatial_sphere.txt | 349 ------------ doc/html/fix_ave_spatial.html | 567 ------------------- doc/html/fix_ave_spatial_sphere.html | 478 ---------------- doc/lammps.book | 2 - 5 files changed, 1843 deletions(-) delete mode 100644 doc/html/_sources/fix_ave_spatial.txt delete mode 100644 doc/html/_sources/fix_ave_spatial_sphere.txt delete mode 100644 doc/html/fix_ave_spatial.html delete mode 100644 doc/html/fix_ave_spatial_sphere.html diff --git a/doc/html/_sources/fix_ave_spatial.txt b/doc/html/_sources/fix_ave_spatial.txt deleted file mode 100644 index 1c7c368503..0000000000 --- a/doc/html/_sources/fix_ave_spatial.txt +++ /dev/null @@ -1,447 +0,0 @@ -.. index:: fix ave/spatial - -fix ave/spatial command -======================= - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... - -* ID, group-ID are documented in :doc:`fix ` command -* ave/spatial = style name of this fix command -* Nevery = use input values every this many timesteps -* Nrepeat = # of times to use input values for calculating averages -* Nfreq = calculate averages every this many timesteps -* dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins -.. parsed-literal:: - - dim = *x* or *y* or *z* - origin = *lower* or *center* or *upper* or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) - -* one or more input values can be listed -* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name -.. parsed-literal:: - - vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) - density/number, density/mass = number or mass density - c_ID = per-atom vector calculated by a compute with ID - c_ID[I] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID[I] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name - -* zero or more keyword/arg pairs may be appended -* keyword = *region* or *bound* or *discard* or *norm* or *ave* or *units* or *file* or *overwrite* or *title1* or *title2* or *title3* -.. parsed-literal:: - - *region* arg = region-ID - *bound* args = x/y/z lo hi - x/y/z = *x* or *y* or *z* to bound bins in this dimension - lo = *lower* or coordinate value (distance units) - hi = *upper* or coordinate value (distance units) - *discard* arg = *mixed* or *no* or *yes* - mixed = discard atoms outside bins only if bin bounds are explicitly set - no = always keep out-of-bounds atoms - yes = always discard out-of-bounds atoms - *norm* arg = *all* or *sample* - region-ID = ID of region atoms must be in to contribute to spatial averaging - *ave* args = *one* or *running* or *window M* - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - *units* arg = *box* or *lattice* or *reduced* - *file* arg = filename - filename = file to write results to - *overwrite* arg = none = overwrite output file with only latest output - *title1* arg = string - string = text to print as 1st line of output file - *title2* arg = string - string = text to print as 2nd line of output file - *title3* arg = string - string = text to print as 3rd line of output file - - - -Examples -"""""""" - -.. parsed-literal:: - - fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced & - title1 "My output values" - fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile - fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running - fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running - -**NOTE:** - -The fix ave/spatial command has been replaced by the more flexible -:doc:`fix ave/chunk ` and :doc:`compute chunk/atom ` commands. The fix ave/spatial -command will be removed from LAMMPS sometime in the summer of 2015. - -Any fix ave/spatial command can be replaced by the two new commands. -You simply need to split the fix ave/spatial arguments across the two -new commands. For example, this command: - -.. parsed-literal:: - - fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile - -could be replaced by: - -.. parsed-literal:: - - compute cc1 flow chunk/atom bin/1d y 0.0 1.0 - fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile - -Description -""""""""""" - -Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into 1d, 2d, or 3d bins based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. - -The group specified with the command means only atoms within the group -contribute to bin averages. If the *region* keyword is used, the atom -must be in both the specified group and the specified geometric -:doc:`region ` in order to contribute to bin averages. - -Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -:doc:`compute ` or :doc:`fix ` or the evaluation of an -atom-style :doc:`variable `. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the :doc:`fix ave/time ` command. - -:doc:`Computes ` that produce per-atom quantities are those -which have the word *atom* in their style name. See the doc pages for -individual :doc:`fixes ` to determine which ones produce per-atom -quantities. :doc:`Variables ` of style *atom* are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. - -The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. - -The size and dimensionality of the bins (1d = layers or slabs, 2d = -pencils, 3d = boxes) are determined by the *dim*\ , *origin*\ , and -*delta* settings and how many times they are specified (1, 2, or 3). -See details below. - -.. note:: - - This fix works by creating an array of size Nbins by Nvalues on - each processor. Nbins is the total number of bins; Nvalues is the - number of input values specified. Each processor loops over its - atoms, tallying its values to the appropriate bin. Then the entire - array is summed across all processors. This means that using a large - number of bins (easy to do for 2d or 3d bins) will incur an overhead - in memory and computational cost (summing across processors), so be - careful to use reasonable numbers of bins. - - ----------- - - -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of *Nfreq*\ . The average is over *Nrepeat* -quantities, computed in the preceding portion of the simulation every -*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and -*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - - ----------- - - -Each per-atom property is also averaged over atoms in each bin. The -way the averaging is one across the *Nrepeat* timesteps to produce -output on the *Nfreq* timesteps, and across multiple *Nfreq* outputs, -is determined by the *norm* and *av* keyword settings, as discussed -below. - -Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends -on how many times (1, 2, or 3) the *dim*\ , *origin*\ , and *delta* -settings are specified in the fix ave/spatial command. For 2d or 3d -bins, there is no restriction on specifying dim = x before dim = y, or -dim = y before dim = z. Bins in a particular *dim* have a bin size in -that dimension given by *delta*\ . Every Nfreq steps, when averaging is -being performed and the per-atom property is calculated for the first -time, the number of bins and the bin sizes and boundaries are -computed. Thus if the simulation box changes size during a -simulation, the number of bins and their boundaries may also change. -In each dimension, bins are defined relative to a specified *origin*\ , -which may be the lower/upper edge of the simulation box in that -dimension, or its center point, or a specified coordinate value. -Starting at the origin, sufficient bins are created in both directions -to completely span the bin extent in that dimension. By default the -bin extent is the entire simulation box. - -The *bound* keyword can be used one or more times to limit the extent -of bin coverage in specified dimensions, i.e. to only bin a portion of -the box. If the *lo* setting is *lower* or the *hi* setting is -*upper*\ , the bin extent in that direction extends to the box boundary. -If a numeric value is used for *lo* and/or *hi*\ , then the bin extent -in the *lo* or *hi* direction extends only to that value, which is -assumed to be inside (or at least near) the simulation box boundaries, -though LAMMPS does not check for this. - -On each sampling timestep, each atom is mapped to the bin it currently -belongs to, based on its current position. Note that the group-ID and -region keyword can exclude specific atoms from this operation, as -discussed above. Note that between reneighboring timesteps, atoms can -move outside the current simulation box. If the box is periodic (in -that dimension) the atom is remapping into the periodic box for -purposes of binning. If the box in not periodic, the atom may have -moved outside the bounds of any bin. - -The *discard* keyword determines what is done with any atom which is -outside the bounds of any bin. If *discard* is set to *yes*\ , the atom -will be ignored and not contribute to any bin averages. If *discard* -is set to *no*\ , the atom will be counted as if it were in the first or -last bin in that dimension. If (discard* is set to *mixed*\ , which is -the default, it will only be counted in the first or last bin if bins -extend to the box boundary in that dimension. This is the case if the -*bound* keyword settings are *lower* and *upper*\ , which is the -default. If the *bound* keyword settings are numeric values, then the -atom will be ignored if it is outside the bounds of any bin. Note -that in this case, it is possible that the first or last bin extends -beyond the numeric *bounds* settings, depending on the specified -*origin*\ . If this is the case, the atom is only ignored if it is -outside the first or last bin, not if it is simply outside the numeric -*bounds* setting. - -For orthogonal simulation boxes, the bins are also layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bins are so that they are -parallel to the tilted faces of the simulation box. See :ref:`this section ` of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" -direction. Bins in y have faces normal to the "a" cross "c" -direction. And bins in z have faces normal to the "a" cross "b" -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the *units* option must be set -to *reduced* when using a triclinic simulation box, as noted below. - - ----------- - - -The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying -an input value from that compute. - -The *density/number* value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The *density/mass* -value means the mass density is computed in each bind, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the :doc:`units ` command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and :doc:`add them to LAMMPS `. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -*Nevery*\ , else an error results. Users can also write code for their -own fix styles and :doc:`add them to LAMMPS `. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -*atom* can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. - - ----------- - - -Additional optional keywords also affect the operation of this fix. -The *region*\ , *bound*\ , and *discard* keywords were discussed above. - -The *norm* keyword affects how averaging is done for the output -produced every *Nfreq* timesteps. For an *all* setting, a bin -quantity is summed over all atoms in all *Nrepeat* samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire *Nfreq* timescale. - -For a *sample* setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the *Nrepeat* "average sample values", In -other words it is an average of an average. - -The *ave* keyword determines how the bin values produced every *Nfreq* -steps are averaged with bin values produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output -command or written to a file. - -If the *ave* setting is *one*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are independent of each other; -they are output as-is without further averaging. - -If the *ave* setting is *running*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the :doc:`unfix ` command, or re-defining the fix by -re-specifying it. - -If the *ave* setting is *window*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. - -The *units* keyword determines the meaning of the distance units used -for the bin size *delta* and for *origin* and *bounds* values if they -are coordinate value. For orthogonal simulation boxes, any of the 3 -options may be used. For non-orthogonal (triclinic) simulation boxes, -only the *reduced* option may be used. - -A *box* value selects standard distance units as defined by the -:doc:`units ` command, e.g. Angstroms for units = real or metal. -A *lattice* value means the distance units are in lattice spacings. -The :doc:`lattice ` command must have been previously used to -define the lattice spacing. A *reduced* value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an *origin* value of -0.5 means the center of the box in any dimension. A *delta* value of -0.1 means 10 bins span the box in that dimension. - -Consider a non-orthogonal box, with bins that are 1d layers or slabs -in the x dimension. No matter how the box is tilted, an *origin* of -0.0 means start layers at the lower "b" cross "c" plane of the -simulation box and an *origin* of 1.0 means to start layers at the -upper "b" cross "c" face of the box. A *delta* value of 0.1 means -there will be 10 layers from 0.0 to 1.0, regardless of the current -size or shape of the simulation box. - -The *file* keyword allows a filename to be specified. Every *Nfreq* -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms -in the bin, and one or more calculated values. The number of values -in each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the *units* keyword is *box* or -*lattice*\ , the "coord" is printed in box units. If the value of the -*units* keyword is *reduced*\ , the "coord" is printed in reduced units -(0-1). - -The *overwrite* keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the *ave running* setting. - -The *title1* and *title2* and *title3* keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the *file* keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -.. parsed-literal:: - - # Spatial-averaged data for fix ID and group name - # Timestep Number-of-bins - # Bin Coord1 Coord2 Coord3 Count value1 value2 ... - -In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. - - ----------- - - -Restart, fix_modify, output, run start/stop, minimize info -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various :ref:`output commands `. The values can -only be accessed on timesteps that are multiples of *Nfreq* since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for -1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates -(center of the bin) in the appropriate dimensions, the next column has -the count of atoms in that bin, and the remaining columns are the -Nvalue quantities. When the array is accessed with an I that exceeds -the current number of bins, than a 0.0 is returned by the fix instead -of an error, since the number of bins can vary as a simulation runs, -depending on the simulation box size. 2d or 3d bins are ordered so -that the last dimension(s) vary fastest. The array values calculated -by this fix are "intensive", since they are already normalized by the -count of atoms in each bin. - -No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - -Restrictions -"""""""""""" - - -When the *ave* keyword is set to *running* or *window* then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the *units* keyword is set to -*reduced*\ . - -Related commands -"""""""""""""""" - -:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/time `, -:doc:`variable `, :doc:`fix ave/correlate `, -:doc:`fix ave/spatial/sphere ` - -Default -""""""" - -The option defaults are bound = lower and upper in all dimensions, -discard = mixed, norm = all, ave = one, units = lattice, no file -output, and title 1,2,3 = strings as described above. - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/fix_ave_spatial_sphere.txt b/doc/html/_sources/fix_ave_spatial_sphere.txt deleted file mode 100644 index 17da5e45a8..0000000000 --- a/doc/html/_sources/fix_ave_spatial_sphere.txt +++ /dev/null @@ -1,349 +0,0 @@ -.. index:: fix ave/spatial/sphere - -fix ave/spatial/sphere command -============================== - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ... - -* ID, group-ID are documented in :doc:`fix ` command -* ave/spatial = style name of this fix command -* Nevery = use input values every this many timesteps -* Nrepeat = # of times to use input values for calculating averages -* Nfreq = calculate averages every this many timesteps -* origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) -* r_min = radial distance at which binning begins -* r_max = radial distance at which binning ends -* nbins = number of spherical shells to create between r_min and r_max -* one or more input values can be listed -* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name -.. parsed-literal:: - - vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) - density/number, density/mass = number or mass density - c_ID = per-atom vector calculated by a compute with ID - c_ID[I] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID[I] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name - -* zero or more keyword/arg pairs may be appended -* keyword = *region* or *norm* or *units* or *ave* or *file* or *overwrite* or *title1* or *title2* or *title3* -.. parsed-literal:: - - *region* arg = region-ID - region-ID = ID of region atoms must be in to contribute to spatial averaging - *norm* arg = *all* or *sample* - *units* arg = *box* or *lattice* or *reduced* - *ave* args = *one* or *running* or *window M* - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - *file* arg = filename - filename = file to write results to - *overwrite* arg = none = overwrite output file with only latest output - *title1* arg = string - string = text to print as 1st line of output file - *title2* arg = string - string = text to print as 2nd line of output file - *title3* arg = string - string = text to print as 3rd line of output file - - - -Examples -"""""""" - -.. parsed-literal:: - - fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values" - fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile - -Description -""""""""""" - -Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into spherical shells based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. - -The group specified with the command means only atoms within the group -contribute to bin averages. If the *region* keyword is used, the atom -must be in both the group and the specified geometric -:doc:`region ` in order to contribute to bin averages. - -Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -:doc:`compute ` or :doc:`fix ` or the evaluation of an -atom-style :doc:`variable `. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the :doc:`fix ave/time ` command. - -:doc:`Computes ` that produce per-atom quantities are those -which have the word *atom* in their style name. See the doc pages for -individual :doc:`fixes ` to determine which ones produce per-atom -quantities. :doc:`Variables ` of style *atom* are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. - -The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. - -*Nbins* specifies the number of spherical shells which will be created -between r_min and r_max centered at (origin_x, origin_y, origin_z). - -.. note:: - - This fix works by creating an array of size Nbins by Nvalues on - each processor. Nbins is the total number of bins; Nvalues is the - number of input values specified. Each processor loops over its - atoms, tallying its values to the appropriate bin. Then the entire - array is summed across all processors. This means that using a large - number of bins will incur an overhead in memory and computational cost - (summing across processors), so be careful to use reasonable numbers - of bins. - - ----------- - - -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of *Nfreq*\ . The average is over *Nrepeat* -quantities, computed in the preceding portion of the simulation every -*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and -*Nevery* must be non-zero even if *Nrepeat* is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - - ----------- - - -The *origin_x*\ , *origin_y*\ , and *origin_z* parameters may be specified -by either a compute or a variable. This allows, for example, the -center of the spherical bins to be attached to the center of mass of a -group of atoms. If a variable origin is used and periodic boundary -conditions are in effect, then the origin will be wrapped across -periodic boundaries whenever it changes so that it is always inside -the simulation box. - - ----------- - - -The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying -an input value from that compute. - -The *density/number* value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The *density/mass* -value means the mass density is computed in each bin, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the :doc:`units ` command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. -The bin volume will always be calculated in box units, independent -of the use of the *units* keyword in this command. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and :doc:`add them to LAMMPS `. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -*Nevery*\ , else an error results. Users can also write code for their -own fix styles and :doc:`add them to LAMMPS `. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -*atom* can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. - - ----------- - - -Additional optional keywords also affect the operation of this fix. -The *region* keyword was discussed above. - -The *norm* keyword affects how averaging is done for the output -produced every *Nfreq* timesteps. For an *all* setting, a bin -quantity is summed over all atoms in all *Nrepeat* samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire *Nfreq* timescale. - -For a *sample* setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the *Nrepeat* "average sample values", In -other words it is an average of an average. - -The *ave* keyword determines how the bin values produced every *Nfreq* -steps are averaged with bin values produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output -command or written to a file. - -If the *ave* setting is *one*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are independent of each other; -they are output as-is without further averaging. - -If the *ave* setting is *running*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the :doc:`unfix ` command, or re-defining the fix by -re-specifying it. - -If the *ave* setting is *window*\ , then the bin values produced on -timesteps that are multiples of *Nfreq* are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. - -The *units* keyword determines the meaning of the distance units used -for the sphere origin and the two radial lengths. For orthogonal -simulation boxes, any of the 3 options may be used. For -non-orthogonal (triclinic) simulation boxes, only the *reduced* option -may be used. - -A *box* value selects standard distance units as defined by the -:doc:`units ` command, e.g. Angstroms for units = real or metal. -A *lattice* value means the distance units are in lattice spacings. -The :doc:`lattice ` command must have been previously used to -define the lattice spacing. - -.. note:: - - The *lattice* style may only be used if the lattice spacing is - the same in each direction. - -A *reduced* value means normalized unitless values between 0 and 1, -which represent the lower and upper faces of the simulation box -respectively. Thus an *origin* value of 0.5 means the center of the -box in any dimension. - -The *file* keyword allows a filename to be specified. Every *Nfreq* -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms in -the bin, and one or more calculated values. The number of values in -each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the *units* keyword is *box* or -*lattice*\ , the "coord" is printed in box units. If the value of the -*units* keyword is *reduced*\ , the "coord" is printed in reduced units -(0-1). - -The *overwrite* keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the *ave running* setting. - -The *title1* and *title2* and *title3* keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the *file* keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -.. parsed-literal:: - - # Spatial-averaged data for fix ID and group name - # Timestep Number-of-bins - # Bin r Count value1 value2 ... - -In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. - - ----------- - - -Restart, fix_modify, output, run start/stop, minimize info -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various :ref:`output commands `. The values can -only be accessed on timesteps that are multiples of *Nfreq* since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = 2+Nvalues. The first column contains the -radius at the center of the shell. For units *reduced*\ , this is in -reduced units, while for units *box* and *lattice* this is in box -units. The next column has the count of atoms in that bin, and the -remaining columns are the Nvalue quantities. When the array is -accessed with an I that exceeds the current number of bins, than a 0.0 -is returned by the fix instead of an error. The array values -calculated by this fix are "intensive", since they are already -normalized by the count of atoms in each bin. - -No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - -Restrictions -"""""""""""" - - -When the *ave* keyword is set to *running* or *window* then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the *units* keyword is set to -*reduced*\ . - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the :ref:`Making of LAMMPS <3>` section for more info. - -Related commands -"""""""""""""""" - -:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/time `, -:doc:`variable `, :doc:`fix ave/correlate `, -:doc:`fix ave/spatial `, - -Default -""""""" - -The option defaults are norm = all, ave = one, units = lattice, no -file output, and title 1,2,3 = strings as described above. - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/html/fix_ave_spatial.html b/doc/html/fix_ave_spatial.html deleted file mode 100644 index a435667770..0000000000 --- a/doc/html/fix_ave_spatial.html +++ /dev/null @@ -1,567 +0,0 @@ - - - - - - - - - - - fix ave/spatial command — LAMMPS documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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fix ave/spatial command

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Syntax

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fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ...
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  • ID, group-ID are documented in fix command
    • -
  • ave/spatial = style name of this fix command
    • -
  • Nevery = use input values every this many timesteps
    • -
  • Nrepeat = # of times to use input values for calculating averages
    • -
  • Nfreq = calculate averages every this many timesteps
    • -
  • dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins
    • -
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-dim = x or y or z
-origin = lower or center or upper or coordinate value (distance units)
-delta = thickness of spatial bins in dim (distance units)
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  • one or more input values can be listed
    • -
  • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
    • -
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vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-density/number, density/mass = number or mass density
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-v_name = per-atom vector calculated by an atom-style variable with name
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  • zero or more keyword/arg pairs may be appended
    • -
  • keyword = region or bound or discard or norm or ave or units or file or overwrite or title1 or title2 or title3
    • -
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-region arg = region-ID
-bound args = x/y/z lo hi
-  x/y/z = x or y or z to bound bins in this dimension
-  lo = lower or coordinate value (distance units)
-  hi = upper or coordinate value (distance units)
-discard arg = mixed or no or yes
-  mixed = discard atoms outside bins only if bin bounds are explicitly set
-  no = always keep out-of-bounds atoms
-  yes = always discard out-of-bounds atoms
-norm arg = all or sample
-  region-ID = ID of region atoms must be in to contribute to spatial averaging
-ave args = one or running or window M
-  one = output new average value every Nfreq steps
-  running = output cumulative average of all previous Nfreq steps
-  window M = output average of M most recent Nfreq steps
-units arg = box or lattice or reduced
-file arg = filename
-  filename = file to write results to
-overwrite arg = none = overwrite output file with only latest output
-title1 arg = string
-  string = text to print as 1st line of output file
-title2 arg = string
-  string = text to print as 2nd line of output file
-title3 arg = string
-  string = text to print as 3rd line of output file
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Examples

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fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
-                      title1 "My output values"
-fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
-fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
-fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running
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NOTE:

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The fix ave/spatial command has been replaced by the more flexible -fix ave/chunk and compute chunk/atom commands. The fix ave/spatial -command will be removed from LAMMPS sometime in the summer of 2015.

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Any fix ave/spatial command can be replaced by the two new commands. -You simply need to split the fix ave/spatial arguments across the two -new commands. For example, this command:

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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
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could be replaced by:

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compute cc1 flow chunk/atom bin/1d y 0.0 1.0
-fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
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Description

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Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into 1d, 2d, or 3d bins based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other output commands such as thermo_style custom, and can also be written to a file.

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The group specified with the command means only atoms within the group -contribute to bin averages. If the region keyword is used, the atom -must be in both the specified group and the specified geometric -region in order to contribute to bin averages.

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Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -compute or fix or the evaluation of an -atom-style variable. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the fix ave/time command.

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Computes that produce per-atom quantities are those -which have the word atom in their style name. See the doc pages for -individual fixes to determine which ones produce per-atom -quantities. Variables of style atom are the only -ones that can be used with this fix since all other styles of variable -produce global quantities.

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The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors.

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The size and dimensionality of the bins (1d = layers or slabs, 2d = -pencils, 3d = boxes) are determined by the dim, origin, and -delta settings and how many times they are specified (1, 2, or 3). -See details below.

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Note

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This fix works by creating an array of size Nbins by Nvalues on -each processor. Nbins is the total number of bins; Nvalues is the -number of input values specified. Each processor loops over its -atoms, tallying its values to the appropriate bin. Then the entire -array is summed across all processors. This means that using a large -number of bins (easy to do for 2d or 3d bins) will incur an overhead -in memory and computational cost (summing across processors), so be -careful to use reasonable numbers of bins.

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The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq.

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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc.

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Each per-atom property is also averaged over atoms in each bin. The -way the averaging is one across the Nrepeat timesteps to produce -output on the Nfreq timesteps, and across multiple Nfreq outputs, -is determined by the norm and av keyword settings, as discussed -below.

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Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends -on how many times (1, 2, or 3) the dim, origin, and delta -settings are specified in the fix ave/spatial command. For 2d or 3d -bins, there is no restriction on specifying dim = x before dim = y, or -dim = y before dim = z. Bins in a particular dim have a bin size in -that dimension given by delta. Every Nfreq steps, when averaging is -being performed and the per-atom property is calculated for the first -time, the number of bins and the bin sizes and boundaries are -computed. Thus if the simulation box changes size during a -simulation, the number of bins and their boundaries may also change. -In each dimension, bins are defined relative to a specified origin, -which may be the lower/upper edge of the simulation box in that -dimension, or its center point, or a specified coordinate value. -Starting at the origin, sufficient bins are created in both directions -to completely span the bin extent in that dimension. By default the -bin extent is the entire simulation box.

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The bound keyword can be used one or more times to limit the extent -of bin coverage in specified dimensions, i.e. to only bin a portion of -the box. If the lo setting is lower or the hi setting is -upper, the bin extent in that direction extends to the box boundary. -If a numeric value is used for lo and/or hi, then the bin extent -in the lo or hi direction extends only to that value, which is -assumed to be inside (or at least near) the simulation box boundaries, -though LAMMPS does not check for this.

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On each sampling timestep, each atom is mapped to the bin it currently -belongs to, based on its current position. Note that the group-ID and -region keyword can exclude specific atoms from this operation, as -discussed above. Note that between reneighboring timesteps, atoms can -move outside the current simulation box. If the box is periodic (in -that dimension) the atom is remapping into the periodic box for -purposes of binning. If the box in not periodic, the atom may have -moved outside the bounds of any bin.

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The discard keyword determines what is done with any atom which is -outside the bounds of any bin. If discard is set to yes, the atom -will be ignored and not contribute to any bin averages. If discard -is set to no, the atom will be counted as if it were in the first or -last bin in that dimension. If (discard* is set to mixed, which is -the default, it will only be counted in the first or last bin if bins -extend to the box boundary in that dimension. This is the case if the -bound keyword settings are lower and upper, which is the -default. If the bound keyword settings are numeric values, then the -atom will be ignored if it is outside the bounds of any bin. Note -that in this case, it is possible that the first or last bin extends -beyond the numeric bounds settings, depending on the specified -origin. If this is the case, the atom is only ignored if it is -outside the first or last bin, not if it is simply outside the numeric -bounds setting.

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For orthogonal simulation boxes, the bins are also layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bins are so that they are -parallel to the tilted faces of the simulation box. See this section of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the “b” cross “c” -direction. Bins in y have faces normal to the “a” cross “c” -direction. And bins in z have faces normal to the “a” cross “b” -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the units option must be set -to reduced when using a triclinic simulation box, as noted below.

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The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the compute property/atom command and then specifying -an input value from that compute.

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The density/number value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The density/mass -value means the mass density is computed in each bind, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the units command doc page for the -definition of density for each choice of units, e.g. gram/cm^3.

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If a value begins with “c_”, a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS.

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If a value begins with “f_”, a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS.

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If a value begins with “v_”, a variable name must follow which has -been previously defined in the input script. Variables of style -atom can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average.

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Additional optional keywords also affect the operation of this fix. -The region, bound, and discard keywords were discussed above.

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The norm keyword affects how averaging is done for the output -produced every Nfreq timesteps. For an all setting, a bin -quantity is summed over all atoms in all Nrepeat samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire Nfreq timescale.

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For a sample setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a “average sample value” is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the Nrepeat “average sample values”, In -other words it is an average of an average.

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The ave keyword determines how the bin values produced every Nfreq -steps are averaged with bin values produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file.

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If the ave setting is one, then the bin values produced on -timesteps that are multiples of Nfreq are independent of each other; -they are output as-is without further averaging.

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If the ave setting is running, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the unfix command, or re-defining the fix by -re-specifying it.

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If the ave setting is window, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving “window” of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available.

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The units keyword determines the meaning of the distance units used -for the bin size delta and for origin and bounds values if they -are coordinate value. For orthogonal simulation boxes, any of the 3 -options may be used. For non-orthogonal (triclinic) simulation boxes, -only the reduced option may be used.

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A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacing. A reduced value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an origin value of -0.5 means the center of the box in any dimension. A delta value of -0.1 means 10 bins span the box in that dimension.

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Consider a non-orthogonal box, with bins that are 1d layers or slabs -in the x dimension. No matter how the box is tilted, an origin of -0.0 means start layers at the lower “b” cross “c” plane of the -simulation box and an origin of 1.0 means to start layers at the -upper “b” cross “c” face of the box. A delta value of 0.1 means -there will be 10 layers from 0.0 to 1.0, regardless of the current -size or shape of the simulation box.

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The file keyword allows a filename to be specified. Every Nfreq -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms -in the bin, and one or more calculated values. The number of values -in each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the units keyword is box or -lattice, the “coord” is printed in box units. If the value of the -units keyword is reduced, the “coord” is printed in reduced units -(0-1).

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The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting.

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The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified.

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By default, these header lines are as follows:

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# Spatial-averaged data for fix ID and group name
-# Timestep Number-of-bins
-# Bin Coord1 Coord2 Coord3 Count value1 value2 ...
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In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord.

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Restart, fix_modify, output, run start/stop, minimize info

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No information about this fix is written to binary restart files. None of the fix_modify options -are relevant to this fix.

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This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for -1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates -(center of the bin) in the appropriate dimensions, the next column has -the count of atoms in that bin, and the remaining columns are the -Nvalue quantities. When the array is accessed with an I that exceeds -the current number of bins, than a 0.0 is returned by the fix instead -of an error, since the number of bins can vary as a simulation runs, -depending on the simulation box size. 2d or 3d bins are ordered so -that the last dimension(s) vary fastest. The array values calculated -by this fix are “intensive”, since they are already normalized by the -count of atoms in each bin.

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No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy minimization.

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Restrictions

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When the ave keyword is set to running or window then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn’t change or if the units keyword is set to -reduced.

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Default

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The option defaults are bound = lower and upper in all dimensions, -discard = mixed, norm = all, ave = one, units = lattice, no file -output, and title 1,2,3 = strings as described above.

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/doc/html/fix_ave_spatial_sphere.html b/doc/html/fix_ave_spatial_sphere.html deleted file mode 100644 index 109f9aa98d..0000000000 --- a/doc/html/fix_ave_spatial_sphere.html +++ /dev/null @@ -1,478 +0,0 @@ - - - - - - - - - - - fix ave/spatial/sphere command — LAMMPS documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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fix ave/spatial/sphere command

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Syntax

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fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ...
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-
-
    -
  • ID, group-ID are documented in fix command
    • -
  • ave/spatial = style name of this fix command
    • -
  • Nevery = use input values every this many timesteps
    • -
  • Nrepeat = # of times to use input values for calculating averages
    • -
  • Nfreq = calculate averages every this many timesteps
    • -
  • origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below)
    • -
  • r_min = radial distance at which binning begins
    • -
  • r_max = radial distance at which binning ends
    • -
  • nbins = number of spherical shells to create between r_min and r_max
    • -
  • one or more input values can be listed
    • -
  • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
    • -
-
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-density/number, density/mass = number or mass density
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-v_name = per-atom vector calculated by an atom-style variable with name
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-
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    -
  • zero or more keyword/arg pairs may be appended
    • -
  • keyword = region or norm or units or ave or file or overwrite or title1 or title2 or title3
    • -
-
-region arg = region-ID
-  region-ID = ID of region atoms must be in to contribute to spatial averaging
-norm arg = all or sample
-units arg = box or lattice or reduced
-ave args = one or running or window M
-  one = output new average value every Nfreq steps
-  running = output cumulative average of all previous Nfreq steps
-  window M = output average of M most recent Nfreq steps
-file arg = filename
-  filename = file to write results to
-overwrite arg = none = overwrite output file with only latest output
-title1 arg = string
-  string = text to print as 1st line of output file
-title2 arg = string
-  string = text to print as 2nd line of output file
-title3 arg = string
-  string = text to print as 3rd line of output file
-
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Examples

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fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values"
-fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile
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Description

-

Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into spherical shells based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other output commands such as thermo_style custom, and can also be written to a file.

-

The group specified with the command means only atoms within the group -contribute to bin averages. If the region keyword is used, the atom -must be in both the group and the specified geometric -region in order to contribute to bin averages.

-

Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -compute or fix or the evaluation of an -atom-style variable. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the fix ave/time command.

-

Computes that produce per-atom quantities are those -which have the word atom in their style name. See the doc pages for -individual fixes to determine which ones produce per-atom -quantities. Variables of style atom are the only -ones that can be used with this fix since all other styles of variable -produce global quantities.

-

The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors.

-

Nbins specifies the number of spherical shells which will be created -between r_min and r_max centered at (origin_x, origin_y, origin_z).

-
-

Note

-

This fix works by creating an array of size Nbins by Nvalues on -each processor. Nbins is the total number of bins; Nvalues is the -number of input values specified. Each processor loops over its -atoms, tallying its values to the appropriate bin. Then the entire -array is summed across all processors. This means that using a large -number of bins will incur an overhead in memory and computational cost -(summing across processors), so be careful to use reasonable numbers -of bins.

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-
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The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq.

-

For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc.

-
-

The origin_x, origin_y, and origin_z parameters may be specified -by either a compute or a variable. This allows, for example, the -center of the spherical bins to be attached to the center of mass of a -group of atoms. If a variable origin is used and periodic boundary -conditions are in effect, then the origin will be wrapped across -periodic boundaries whenever it changes so that it is always inside -the simulation box.

-
-

The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the compute property/atom command and then specifying -an input value from that compute.

-

The density/number value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The density/mass -value means the mass density is computed in each bin, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the units command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. -The bin volume will always be calculated in box units, independent -of the use of the units keyword in this command.

-

If a value begins with “c_”, a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS.

-

If a value begins with “f_”, a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS.

-

If a value begins with “v_”, a variable name must follow which has -been previously defined in the input script. Variables of style -atom can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average.

-
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Additional optional keywords also affect the operation of this fix. -The region keyword was discussed above.

-

The norm keyword affects how averaging is done for the output -produced every Nfreq timesteps. For an all setting, a bin -quantity is summed over all atoms in all Nrepeat samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire Nfreq timescale.

-

For a sample setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a “average sample value” is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the Nrepeat “average sample values”, In -other words it is an average of an average.

-

The ave keyword determines how the bin values produced every Nfreq -steps are averaged with bin values produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file.

-

If the ave setting is one, then the bin values produced on -timesteps that are multiples of Nfreq are independent of each other; -they are output as-is without further averaging.

-

If the ave setting is running, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the unfix command, or re-defining the fix by -re-specifying it.

-

If the ave setting is window, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving “window” of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available.

-

The units keyword determines the meaning of the distance units used -for the sphere origin and the two radial lengths. For orthogonal -simulation boxes, any of the 3 options may be used. For -non-orthogonal (triclinic) simulation boxes, only the reduced option -may be used.

-

A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacing.

-
-

Note

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The lattice style may only be used if the lattice spacing is -the same in each direction.

-
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A reduced value means normalized unitless values between 0 and 1, -which represent the lower and upper faces of the simulation box -respectively. Thus an origin value of 0.5 means the center of the -box in any dimension.

-

The file keyword allows a filename to be specified. Every Nfreq -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms in -the bin, and one or more calculated values. The number of values in -each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the units keyword is box or -lattice, the “coord” is printed in box units. If the value of the -units keyword is reduced, the “coord” is printed in reduced units -(0-1).

-

The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting.

-

The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified.

-

By default, these header lines are as follows:

-
# Spatial-averaged data for fix ID and group name
-# Timestep Number-of-bins
-# Bin r Count value1 value2 ...
-
-
-

In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord.

-
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Restart, fix_modify, output, run start/stop, minimize info

-

No information about this fix is written to binary restart files. None of the fix_modify options -are relevant to this fix.

-

This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = 2+Nvalues. The first column contains the -radius at the center of the shell. For units reduced, this is in -reduced units, while for units box and lattice this is in box -units. The next column has the count of atoms in that bin, and the -remaining columns are the Nvalue quantities. When the array is -accessed with an I that exceeds the current number of bins, than a 0.0 -is returned by the fix instead of an error. The array values -calculated by this fix are “intensive”, since they are already -normalized by the count of atoms in each bin.

-

No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy minimization.

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Restrictions

-

When the ave keyword is set to running or window then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn’t change or if the units keyword is set to -reduced.

-

This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the Making of LAMMPS section for more info.

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Default

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The option defaults are norm = all, ave = one, units = lattice, no -file output, and title 1,2,3 = strings as described above.

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- © Copyright 2013 Sandia Corporation. -

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- Built with Sphinx using a theme provided by Read the Docs. - -
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/doc/lammps.book b/doc/lammps.book index 2f5dda57ed..e93e9b8dcf 100644 --- a/doc/lammps.book +++ b/doc/lammps.book @@ -118,8 +118,6 @@ fix_ave_correlate.html fix_ave_correlate_long.html fix_ave_chunk.html fix_ave_histo.html -fix_ave_spatial.html -fix_ave_spatial_sphere.html fix_ave_time.html fix_aveforce.html fix_balance.html From 6f75d4389cb9ed56a45f02667f3184d474363017 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:55:17 +0000 Subject: [PATCH 006/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15073 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Section_commands.html | 92 ++++++++-------- doc/html/Section_howto.html | 10 +- doc/html/_sources/Section_commands.txt | 100 +++++++++--------- doc/html/_sources/change_box.txt | 11 +- doc/html/_sources/compute.txt | 12 +-- doc/html/_sources/compute_property_atom.txt | 4 +- doc/html/_sources/compute_temp_deform.txt | 2 +- doc/html/_sources/fix.txt | 10 +- doc/html/_sources/fix_ave_atom.txt | 4 +- doc/html/_sources/fix_ave_chunk.txt | 4 +- doc/html/_sources/fix_ave_correlate.txt | 9 +- doc/html/_sources/fix_ave_histo.txt | 2 +- doc/html/_sources/fix_ave_time.txt | 4 +- doc/html/_sources/fix_deform.txt | 2 +- .../_sources/fix_thermal_conductivity.txt | 8 +- doc/html/_sources/fix_viscosity.txt | 6 +- doc/html/_sources/prd.txt | 3 +- doc/html/_sources/tad.txt | 3 +- doc/html/_sources/variable.txt | 2 +- doc/html/_static/basic.css | 4 - doc/html/_static/doctools.js | 26 ++++- doc/html/change_box.html | 11 +- doc/html/compute.html | 12 +-- doc/html/compute_property_atom.html | 4 +- doc/html/compute_temp_deform.html | 2 +- doc/html/fix.html | 10 +- doc/html/fix_ave_atom.html | 4 +- doc/html/fix_ave_chunk.html | 4 +- doc/html/fix_ave_correlate.html | 9 +- doc/html/fix_ave_histo.html | 2 +- doc/html/fix_ave_time.html | 4 +- doc/html/fix_deform.html | 2 +- doc/html/fix_thermal_conductivity.html | 8 +- doc/html/fix_viscosity.html | 6 +- doc/html/genindex.html | 12 +-- doc/html/prd.html | 3 +- doc/html/searchindex.js | 2 +- doc/html/tad.html | 3 +- doc/html/variable.html | 2 +- 39 files changed, 213 insertions(+), 205 deletions(-) diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index cbd6a70e59..e041f81de4 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -618,13 +618,13 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

-+ @@ -639,129 +639,129 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + +
ave/histo ave/histo/weightave/spatial ave/time balance bond/break bond/create bond/swapbox/relax
box/relaxdeform (k)
deform (k) deposit drag dt/reset efield ehex enforce2d (c)evaporate
evaporateexternal
external freeze (c) gcmc gld gravity (co) heat indentlangevin (k)
langevin (k)lineforce
lineforce momentum move msst neb nph (ko) nphug (o)nph/asphere (o)
nph/asphere (o)nph/body
nph/body nph/sphere (o) npt (ckio) npt/asphere (o) npt/body npt/sphere (o) nve (ckio)nve/asphere (i)
nve/asphere (i)nve/asphere/noforce
nve/asphere/noforce nve/body nve/limit nve/line nve/noforce nve/sphere (o) nve/trinvt (ciko)
nvt (ciko)nvt/asphere (o)
nvt/asphere (o) nvt/body nvt/sllod (io) nvt/sphere (o) oneway orient/fcc planeforcepoems
poemspour
pour press/berendsen print property/atom qeq/comb (o) qeq/dynamic qeq/fireqeq/point
qeq/pointqeq/shielded
qeq/shielded qeq/slater rattle reax/bonds recenter restrain rigid (o)rigid/nph (o)
rigid/nph (o)rigid/npt (o)
rigid/npt (o) rigid/nve (o) rigid/nvt (o) rigid/small (o) rigid/small/nph rigid/small/npt rigid/small/nverigid/small/nvt
rigid/small/nvtsetforce (ck)
setforce (ck) shake (c) spring spring/rg spring/self srd store/forcestore/state
store/statetemp/berendsen (c)
temp/berendsen (c) temp/csld temp/csvr temp/rescale (c) tfmc thermal/conductivity tmdttm
ttmtune/kspace
tune/kspace vector viscosity viscous (c) wall/colloid wall/gran wall/harmonicwall/lj1043
wall/lj1043wall/lj126
wall/lj126 wall/lj93 wall/piston wall/reflect (k) wall/region wall/srd   
@@ -771,74 +771,74 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- + adapt/fep addtorque atc ave/correlate/long -ave/spatial/sphere colvars +drude -drude -drude/transform/direct +drude/transform/direct drude/transform/reverse eos/cv eos/table gle +imd -imd -ipi +ipi langevin/drude langevin/eff lb/fluid lb/momentum +lb/pc -lb/pc -lb/rigid/pc/sphere +lb/rigid/pc/sphere lb/viscous meso manifoldforce meso/stationary +nve/manifold/rattle -nve/manifold/rattle -nvt/manifold/rattle +nvt/manifold/rattle nph/eff npt/eff nve/eff nvt/eff +nvt/sllod/eff -nvt/sllod/eff -phonon +phonon pimd qbmsst qeq/reax qmmm +qtb -qtb -reax/c/bonds +reax/c/bonds reax/c/species saed/vtk shardlow smd +smd/adjust/dt -smd/adjust/dt -smd/integrate/tlsph +smd/integrate/tlsph smd/integrate/ulsph smd/move/triangulated/surface smd/setvel smd/tlsph/reference/configuration +smd/wall/surface -smd/wall/surface -temp/rescale/eff +temp/rescale/eff ti/rs ti/spring ttm/mod   +  diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index 1fe9224652..307539d233 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -1086,7 +1086,7 @@ the sheared fluid and integrate the SLLOD equations of motion for the system. Fix nvt/sllod uses compute temp/deform to compute a thermal temperature by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via -the fix ave/spatial command.

+the fix ave/spatial command.

As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by LAMMPS for computational efficiency to be 1/2 of the parallel box @@ -2011,13 +2011,13 @@ on each of two regions to add/subtract specified amounts of energy to both regions. In both cases, the resulting temperatures of the two regions can be monitored with the “compute temp/region” command and the temperature profile of the intermediate region can be monitored -with the fix ave/spatial and compute ke/atom commands.

+with the fix ave/spatial and compute ke/atom commands.

The third method is to perform a reverse non-equilibrium MD simulation using the fix thermal/conductivity command which implements the rNEMD algorithm of Muller-Plathe. Kinetic energy is swapped between atoms in two different layers of the simulation box. This induces a temperature gradient between the two -layers which can be monitored with the fix ave/spatial and compute ke/atom commands. The fix tallies the +layers which can be monitored with the fix ave/spatial and compute ke/atom commands. The fix tallies the cumulative energy transfer that it performs. See the fix thermal/conductivity command for details.

The fourth method is based on the Green-Kubo (GK) formula which @@ -2060,7 +2060,7 @@ used to shear the fluid in between them, again with some kind of thermostat that modifies only the thermal (non-shearing) components of velocity to prevent the fluid from heating up.

In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the fix ave/spatial command, which determines +procedure can be monitored by the fix ave/spatial command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress @@ -2073,7 +2073,7 @@ using the fix ave/spatial command. +monitored with the fix ave/spatial command. The fix tallies the cummulative momentum transfer that it performs. See the fix viscosity command for details.

The fourth method is based on the Green-Kubo (GK) formula which diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt index 6612704b81..5b5632f5d1 100644 --- a/doc/html/_sources/Section_commands.txt +++ b/doc/html/_sources/Section_commands.txt @@ -457,60 +457,60 @@ with the :doc:`appropriate accelerated package `. This is indicated by additional letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`adapt ` | :doc:`addforce (c) ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce (c) ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/spatial ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`box/relax ` | :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`ehex ` | :doc:`enforce2d (c) ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`evaporate ` | :doc:`external ` | :doc:`freeze (c) ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (co) ` | :doc:`heat ` | :doc:`indent ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`langevin (k) ` | :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nph/asphere (o) ` | :doc:`nph/body ` | :doc:`nph/sphere (o) ` | :doc:`npt (ckio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/body ` | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nve/asphere (i) ` | :doc:`nve/asphere/noforce ` | :doc:`nve/body ` | :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nvt (ciko) ` | :doc:`nvt/asphere (o) ` | :doc:`nvt/body ` | :doc:`nvt/sllod (io) ` | :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/fcc ` | :doc:`planeforce ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`poems ` | :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` | :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`qeq/point ` | :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`rattle ` | :doc:`reax/bonds ` | :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`rigid/nph (o) ` | :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` | :doc:`rigid/small (o) ` | :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`rigid/small/nvt ` | :doc:`setforce (ck) ` | :doc:`shake (c) ` | :doc:`spring ` | :doc:`spring/rg ` | :doc:`spring/self ` | :doc:`srd ` | :doc:`store/force ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`store/state ` | :doc:`temp/berendsen (c) ` | :doc:`temp/csld ` | :doc:`temp/csvr ` | :doc:`temp/rescale (c) ` | :doc:`tfmc ` | :doc:`thermal/conductivity ` | :doc:`tmd ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`ttm ` | :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` | :doc:`viscous (c) ` | :doc:`wall/colloid ` | :doc:`wall/gran ` | :doc:`wall/harmonic ` | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`wall/lj1043 ` | :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` | :doc:`wall/reflect (k) ` | :doc:`wall/region ` | :doc:`wall/srd ` | | -+------------------------------------------+------------------------------------------------------+----------------------------------------------+---------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+------------------------------------------+ ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`adapt ` | :doc:`addforce (c) ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce (c) ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` | :doc:`box/relax ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`ehex ` | :doc:`enforce2d (c) ` | :doc:`evaporate ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`external ` | :doc:`freeze (c) ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (co) ` | :doc:`heat ` | :doc:`indent ` | :doc:`langevin (k) ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | :doc:`nph/asphere (o) ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`nph/body ` | :doc:`nph/sphere (o) ` | :doc:`npt (ckio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/body ` | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) ` | :doc:`nve/asphere (i) ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`nve/asphere/noforce ` | :doc:`nve/body ` | :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | :doc:`nvt (ciko) ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`nvt/asphere (o) ` | :doc:`nvt/body ` | :doc:`nvt/sllod (io) ` | :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/fcc ` | :doc:`planeforce ` | :doc:`poems ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` | :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | :doc:`qeq/point ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`rattle ` | :doc:`reax/bonds ` | :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | :doc:`rigid/nph (o) ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` | :doc:`rigid/small (o) ` | :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | :doc:`rigid/small/nvt ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`setforce (ck) ` | :doc:`shake (c) ` | :doc:`spring ` | :doc:`spring/rg ` | :doc:`spring/self ` | :doc:`srd ` | :doc:`store/force ` | :doc:`store/state ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`temp/berendsen (c) ` | :doc:`temp/csld ` | :doc:`temp/csvr ` | :doc:`temp/rescale (c) ` | :doc:`tfmc ` | :doc:`thermal/conductivity ` | :doc:`tmd ` | :doc:`ttm ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` | :doc:`viscous (c) ` | :doc:`wall/colloid ` | :doc:`wall/gran ` | :doc:`wall/harmonic ` | :doc:`wall/lj1043 ` | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ +| :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` | :doc:`wall/reflect (k) ` | :doc:`wall/region ` | :doc:`wall/srd ` | | | ++------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+ These are additional fix styles in USER packages, which can be used if :ref:`LAMMPS is built with the appropriate package `. -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`adapt/fep ` | :doc:`addtorque ` | :doc:`atc ` | :doc:`ave/correlate/long ` | :doc:`ave/spatial/sphere ` | :doc:`colvars ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`drude ` | :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`gle ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`imd ` | :doc:`ipi ` | :doc:`langevin/drude ` | :doc:`langevin/eff ` | :doc:`lb/fluid ` | :doc:`lb/momentum ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`lb/pc ` | :doc:`lb/rigid/pc/sphere ` | :doc:`lb/viscous ` | :doc:`meso ` | :doc:`manifoldforce ` | :doc:`meso/stationary ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`nve/manifold/rattle ` | :doc:`nvt/manifold/rattle ` | :doc:`nph/eff ` | :doc:`npt/eff ` | :doc:`nve/eff ` | :doc:`nvt/eff ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`nvt/sllod/eff ` | :doc:`phonon ` | :doc:`pimd ` | :doc:`qbmsst ` | :doc:`qeq/reax ` | :doc:`qmmm ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`qtb ` | :doc:`reax/c/bonds ` | :doc:`reax/c/species ` | :doc:`saed/vtk ` | :doc:`shardlow ` | :doc:`smd ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`smd/adjust/dt ` | :doc:`smd/integrate/tlsph ` | :doc:`smd/integrate/ulsph ` | :doc:`smd/move/triangulated/surface ` | :doc:`smd/setvel ` | :doc:`smd/tlsph/reference/configuration ` | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ -| :doc:`smd/wall/surface ` | :doc:`temp/rescale/eff ` | :doc:`ti/rs ` | :doc:`ti/spring ` | :doc:`ttm/mod ` | | -+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+ ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`adapt/fep ` | :doc:`addtorque ` | :doc:`atc ` | :doc:`ave/correlate/long ` | :doc:`colvars ` | :doc:`drude ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`gle ` | :doc:`imd ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`ipi ` | :doc:`langevin/drude ` | :doc:`langevin/eff ` | :doc:`lb/fluid ` | :doc:`lb/momentum ` | :doc:`lb/pc ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`lb/rigid/pc/sphere ` | :doc:`lb/viscous ` | :doc:`meso ` | :doc:`manifoldforce ` | :doc:`meso/stationary ` | :doc:`nve/manifold/rattle ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`nvt/manifold/rattle ` | :doc:`nph/eff ` | :doc:`npt/eff ` | :doc:`nve/eff ` | :doc:`nvt/eff ` | :doc:`nvt/sllod/eff ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`phonon ` | :doc:`pimd ` | :doc:`qbmsst ` | :doc:`qeq/reax ` | :doc:`qmmm ` | :doc:`qtb ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`reax/c/bonds ` | :doc:`reax/c/species ` | :doc:`saed/vtk ` | :doc:`shardlow ` | :doc:`smd ` | :doc:`smd/adjust/dt ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`smd/integrate/tlsph ` | :doc:`smd/integrate/ulsph ` | :doc:`smd/move/triangulated/surface ` | :doc:`smd/setvel ` | :doc:`smd/tlsph/reference/configuration ` | :doc:`smd/wall/surface ` | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ +| :doc:`temp/rescale/eff ` | :doc:`ti/rs ` | :doc:`ti/spring ` | :doc:`ttm/mod ` | | | ++------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ ---------- diff --git a/doc/html/_sources/change_box.txt b/doc/html/_sources/change_box.txt index f3763ba4ec..c84d4804cc 100644 --- a/doc/html/_sources/change_box.txt +++ b/doc/html/_sources/change_box.txt @@ -359,11 +359,12 @@ Restrictions If you use the *ortho* or *triclinic* keywords, then at the point in the input script when this command is issued, no :doc:`dumps ` can -be active, nor can a :doc:`fix ave/spatial ` or :doc:`fix deform ` be active. This is because these commands -test whether the simulation box is orthogonal when they are first -issued. Note that these commands can be used in your script before a -change_box command is issued, so long as an :doc:`undump ` or -:doc:`unfix ` command is also used to turn them off. +be active, nor can a :doc:`fix deform ` be active. This is +because these commands test whether the simulation box is orthogonal +when they are first issued. Note that these commands can be used in +your script before a change_box command is issued, so long as an +:doc:`undump ` or :doc:`unfix ` command is also used to +turn them off. Related commands """""""""""""""" diff --git a/doc/html/_sources/compute.txt b/doc/html/_sources/compute.txt index 40efa31bc4..89eb05f16a 100644 --- a/doc/html/_sources/compute.txt +++ b/doc/html/_sources/compute.txt @@ -106,11 +106,10 @@ ways: * Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. Or the values can be referenced in a :doc:`variable equal ` or :doc:`variable atom ` command. -* Per-atom values can be output via the :doc:`dump custom ` command - or the :doc:`fix ave/spatial ` command. Or they can be - time-averaged via the :doc:`fix ave/atom ` command or - reduced by the :doc:`compute reduce ` command. Or the - per-atom values can be referenced in an :doc:`atom-style variable `. +* Per-atom values can be output via the :doc:`dump custom ` command. + Or they can be time-averaged via the :doc:`fix ave/atom ` + command or reduced by the :doc:`compute reduce ` + command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command, or output by the :doc:`dump local ` command. The results of computes that calculate global quantities can be either "intensive" or "extensive" values. Intensive means the value is @@ -261,8 +260,7 @@ Restrictions Related commands """""""""""""""" -:doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, -:doc:`fix ave/time `, :doc:`fix ave/histo ` +:doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` **Default:** none diff --git a/doc/html/_sources/compute_property_atom.txt b/doc/html/_sources/compute_property_atom.txt index 11f811e2bd..15c972ffaa 100644 --- a/doc/html/_sources/compute_property_atom.txt +++ b/doc/html/_sources/compute_property_atom.txt @@ -107,7 +107,7 @@ in the group. This is useful so that the values can be used by other :ref:`output commands ` that take computes as inputs. See for example, the :doc:`compute reduce `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, -:doc:`fix ave/spatial `, and :doc:`atom-style variable ` commands. +:doc:`fix ave/chunk `, and :doc:`atom-style variable ` commands. The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning, with some additional quantities that are only defined for certain :doc:`atom styles `. Basically, this augmented list gives an @@ -171,7 +171,7 @@ Restrictions Related commands """""""""""""""" -:doc:`dump custom `, :doc:`compute reduce `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, +:doc:`dump custom `, :doc:`compute reduce `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix property/atom ` **Default:** none diff --git a/doc/html/_sources/compute_temp_deform.txt b/doc/html/_sources/compute_temp_deform.txt index 54eb1dba76..ddb6b15e4d 100644 --- a/doc/html/_sources/compute_temp_deform.txt +++ b/doc/html/_sources/compute_temp_deform.txt @@ -90,7 +90,7 @@ fixes that work in this way include :doc:`fix nvt `, :doc:`fix temp/resc off an incorrect stream velocity, yielding a bogus thermal temperature. You should NOT assume that your atoms are streaming at the same rate the box is deforming. Rather, you should monitor their - velocity profile, e.g. via the :doc:`fix ave/spatial ` + velocity profile, e.g. via the :doc:`fix ave/chunk ` command. And you can compare the results of this compute to :doc:`compute temp/profile `, which actually calculates the stream profile before subtracting it. If the two computes do not give roughly the same temperature, then your atoms are not streaming diff --git a/doc/html/_sources/fix.txt b/doc/html/_sources/fix.txt index 5480dfe26b..9259c93f07 100644 --- a/doc/html/_sources/fix.txt +++ b/doc/html/_sources/fix.txt @@ -131,11 +131,10 @@ In LAMMPS, the values generated by a fix can be used in several ways: * Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. Or the values can be referenced in a :doc:`variable equal ` or :doc:`variable atom ` command. -* Per-atom values can be output via the :doc:`dump custom ` command - or the :doc:`fix ave/spatial ` command. Or they can be - time-averaged via the :doc:`fix ave/atom ` command or - reduced by the :doc:`compute reduce ` command. Or the - per-atom values can be referenced in an :doc:`atom-style variable `. +* Per-atom values can be output via the :doc:`dump custom ` command. + Or they can be time-averaged via the :doc:`fix ave/atom ` + command or reduced by the :doc:`compute reduce ` + command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command. See this :ref:`howto section ` for a summary of various LAMMPS output options, many of which involve fixes. @@ -176,7 +175,6 @@ of :ref:`this page `. * :doc:`ave/chunk ` - compute per-chunk time-averaged quantities * :doc:`ave/correlate ` - compute/output time correlations * :doc:`ave/histo ` - compute/output time-averaged histograms -* :doc:`ave/spatial ` - compute/output time-averaged per-atom quantities by layer * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`balance ` - perform dynamic load-balancing * :doc:`bond/break ` - break bonds on the fly diff --git a/doc/html/_sources/fix_ave_atom.txt b/doc/html/_sources/fix_ave_atom.txt index a0fcb44d4b..1f6fc6e1cb 100644 --- a/doc/html/_sources/fix_ave_atom.txt +++ b/doc/html/_sources/fix_ave_atom.txt @@ -41,7 +41,7 @@ Description Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting -per-atom averages can be used by other :ref:`output commands ` such as the :doc:`fix ave/spatial ` or :doc:`dump custom ` commands. +per-atom averages can be used by other :ref:`output commands ` such as the :doc:`fix ave/chunk ` or :doc:`dump custom ` commands. The group specified with the command means only atoms within the group have their averages computed. Results are set to 0.0 for atoms not in @@ -152,7 +152,7 @@ Restrictions Related commands """""""""""""""" -:doc:`compute `, :doc:`fix ave/histo `, :doc:`fix ave/spatial `, :doc:`fix ave/time `, +:doc:`compute `, :doc:`fix ave/histo `, :doc:`fix ave/chunk `, :doc:`fix ave/time `, :doc:`variable `, **Default:** none diff --git a/doc/html/_sources/fix_ave_chunk.txt b/doc/html/_sources/fix_ave_chunk.txt index f5f8bd28a6..2d3c28c251 100644 --- a/doc/html/_sources/fix_ave_chunk.txt +++ b/doc/html/_sources/fix_ave_chunk.txt @@ -73,8 +73,8 @@ Examples **NOTE:** -If you are trying to replace an older fix ave/spatial command with the -newer, more flexible fix ave/chunk and :doc:`compute chunk/atom ` commands, you simply need to split +If you are trying to replace a deprectated fix ave/spatial command +with the newer, more flexible fix ave/chunk and :doc:`compute chunk/atom ` commands, you simply need to split the fix ave/spatial arguments across the two new commands. For example, this command: diff --git a/doc/html/_sources/fix_ave_correlate.txt b/doc/html/_sources/fix_ave_correlate.txt index 509bef995d..d2cd327d3a 100644 --- a/doc/html/_sources/fix_ave_correlate.txt +++ b/doc/html/_sources/fix_ave_correlate.txt @@ -87,10 +87,9 @@ Each listed value can be the result of a :doc:`compute ` or :doc:`variable `. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. If you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the :doc:`fix ave/spatial `, :doc:`fix ave/atom `, -or :doc:`fix ave/histo ` commands. If you wish to -convert a per-atom quantity into a single global value, see the -:doc:`compute reduce ` command. +from a compute, fix, or variable, then see the :doc:`fix ave/chunk `, :doc:`fix ave/atom `, or +:doc:`fix ave/histo ` commands. If you wish to convert a +per-atom quantity into a single global value, see the :doc:`compute reduce ` command. :doc:`Computes ` that produce global quantities are those which do not have the word *atom* in their style name. Only a few @@ -340,7 +339,7 @@ Related commands """""""""""""""" :doc:`fix ave/correlate/long `, -:doc:`compute `, :doc:`fix ave/time `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, +:doc:`compute `, :doc:`fix ave/time `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix ave/histo `, :doc:`variable ` **Default:** none diff --git a/doc/html/_sources/fix_ave_histo.txt b/doc/html/_sources/fix_ave_histo.txt index f47f040857..afe9768630 100644 --- a/doc/html/_sources/fix_ave_histo.txt +++ b/doc/html/_sources/fix_ave_histo.txt @@ -346,7 +346,7 @@ Restrictions Related commands """""""""""""""" -:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, :doc:`fix ave/time `, +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix ave/time `, :doc:`variable `, :doc:`fix ave/correlate `, **Default:** none diff --git a/doc/html/_sources/fix_ave_time.txt b/doc/html/_sources/fix_ave_time.txt index 2d6641e8f0..eb86e81cf7 100644 --- a/doc/html/_sources/fix_ave_time.txt +++ b/doc/html/_sources/fix_ave_time.txt @@ -85,7 +85,7 @@ Each listed value can be the result of a :doc:`compute ` or :doc:`variable `. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. If you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the :doc:`fix ave/spatial `, :doc:`fix ave/atom `, +from a compute, fix, or variable, then see the :doc:`fix ave/chunk `, :doc:`fix ave/atom `, or :doc:`fix ave/histo ` commands. If you wish to sum a per-atom quantity into a single global quantity, see the :doc:`compute reduce ` command. @@ -337,7 +337,7 @@ Restrictions Related commands """""""""""""""" -:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, :doc:`fix ave/histo `, +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix ave/histo `, :doc:`variable `, :doc:`fix ave/correlate `, Default diff --git a/doc/html/_sources/fix_deform.txt b/doc/html/_sources/fix_deform.txt index 12ffa21160..a4712e62ed 100644 --- a/doc/html/_sources/fix_deform.txt +++ b/doc/html/_sources/fix_deform.txt @@ -524,7 +524,7 @@ box without explicit remapping of their coordinates. box. E.g. for a shearing system the box deformation velocity may vary from 0 at the bottom to 10 at the top of the box. But the stream velocity profile of the atoms may vary from -5 at the bottom to +5 at - the top. You can monitor these effects using the :doc:`fix ave/spatial `, :doc:`compute temp/deform `, and :doc:`compute temp/profile ` commands. One way to induce + the top. You can monitor these effects using the :doc:`fix ave/chunk `, :doc:`compute temp/deform `, and :doc:`compute temp/profile ` commands. One way to induce atoms to stream consistent with the box deformation is to give them an initial velocity profile, via the :doc:`velocity ramp ` command, that matches the box deformation rate. This also typically diff --git a/doc/html/_sources/fix_thermal_conductivity.txt b/doc/html/_sources/fix_thermal_conductivity.txt index 1623e43656..ae30853a3e 100644 --- a/doc/html/_sources/fix_thermal_conductivity.txt +++ b/doc/html/_sources/fix_thermal_conductivity.txt @@ -68,8 +68,8 @@ temperature profile (assuming z = edim) to the file tmp.profile: compute ke all ke/atom variable temp atom c_ke/1.5 - fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp & - file tmp.profile units reduced + compute layers all chunk/atom bin/1d z lower 0.05 units reduced + fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile Note that by default, Nswap = 1, though this can be changed by the optional *swap* keyword. Setting this parameter appropriately, in @@ -154,8 +154,8 @@ bewteen solvent particles. Related commands """""""""""""""" -:doc:`fix ehex `, :doc:`fix heat `, -:doc:`fix ave/spatial `, :doc:`fix viscosity `, :doc:`compute heat/flux ` +:doc:`fix ehex `, :doc:`fix heat `, :doc:`fix ave/chunk `, :doc:`fix viscosity `, +:doc:`compute heat/flux ` Default """"""" diff --git a/doc/html/_sources/fix_viscosity.txt b/doc/html/_sources/fix_viscosity.txt index 25b0ee705b..a4e93cf9af 100644 --- a/doc/html/_sources/fix_viscosity.txt +++ b/doc/html/_sources/fix_viscosity.txt @@ -65,8 +65,8 @@ which writes the profile to the file tmp.profile: .. parsed-literal:: - fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & - file tmp.profile units reduced + compute layers all chunk/atom z lower 0.05 units reduced + fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile Note that by default, Nswap = 1 and vtarget = INF, though this can be changed by the optional *swap* and *vtarget* keywords. When vtarget = @@ -158,7 +158,7 @@ solvent particles. Related commands """""""""""""""" -:doc:`fix ave/spatial `, :doc:`fix thermal/conductivity ` +:doc:`fix ave/chunk `, :doc:`fix thermal/conductivity ` Default """"""" diff --git a/doc/html/_sources/prd.txt b/doc/html/_sources/prd.txt index c594766ac9..23daecbb14 100644 --- a/doc/html/_sources/prd.txt +++ b/doc/html/_sources/prd.txt @@ -312,7 +312,8 @@ for dephasing. This command cannot be used when any fixes are defined that keep track of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as :doc:`fix ave/spatial `. Also :doc:`fix dt/reset ` and :doc:`fix deposit `. +include the "ave" fixes such as :doc:`fix ave/chunk `. +Also :doc:`fix dt/reset ` and :doc:`fix deposit `. Related commands """""""""""""""" diff --git a/doc/html/_sources/tad.txt b/doc/html/_sources/tad.txt index ad558e2ad2..2d028b693d 100644 --- a/doc/html/_sources/tad.txt +++ b/doc/html/_sources/tad.txt @@ -293,7 +293,8 @@ restart, but :doc:`fix langevin ` will not. This command cannot be used when any fixes are defined that keep track of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as :doc:`fix ave/spatial `. Also :doc:`fix dt/reset ` and :doc:`fix deposit `. +include the "ave" fixes such as :doc:`fix ave/chunk `. +Also :doc:`fix dt/reset ` and :doc:`fix deposit `. Related commands """""""""""""""" diff --git a/doc/html/_sources/variable.txt b/doc/html/_sources/variable.txt index 4a1adebcc1..bb95afd0b0 100644 --- a/doc/html/_sources/variable.txt +++ b/doc/html/_sources/variable.txt @@ -1189,7 +1189,7 @@ command evaluates the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v_" is an optional or required -kind of argument for some commands (e.g. the :doc:`fix ave/spatial ` or :doc:`dump custom ` or +kind of argument for some commands (e.g. the :doc:`fix ave/chunk ` or :doc:`dump custom ` or :doc:`thermo_style ` commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css index 65dfd7dfda..2b513f0c96 100644 --- a/doc/html/_static/basic.css +++ b/doc/html/_static/basic.css @@ -85,10 +85,6 @@ div.sphinxsidebar #searchbox input[type="text"] { width: 170px; } -div.sphinxsidebar #searchbox input[type="submit"] { - width: 30px; -} - img { border: 0; max-width: 100%; diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js index e2e70cc287..8163495635 100644 --- a/doc/html/_static/doctools.js +++ b/doc/html/_static/doctools.js @@ -124,6 +124,7 @@ var Documentation = { this.fixFirefoxAnchorBug(); this.highlightSearchWords(); this.initIndexTable(); + }, /** @@ -252,6 +253,29 @@ var Documentation = { }); var url = parts.join('/'); return path.substring(url.lastIndexOf('/') + 1, path.length - 1); + }, + + initOnKeyListeners: function() { + $(document).keyup(function(event) { + var activeElementType = document.activeElement.tagName; + // don't navigate when in search box or textarea + if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { + switch (event.keyCode) { + case 37: // left + var prevHref = $('link[rel="prev"]').prop('href'); + if (prevHref) { + window.location.href = prevHref; + return false; + } + case 39: // right + var nextHref = $('link[rel="next"]').prop('href'); + if (nextHref) { + window.location.href = nextHref; + return false; + } + } + } + }); } }; @@ -260,4 +284,4 @@ _ = Documentation.gettext; $(document).ready(function() { Documentation.init(); -}); +}); \ No newline at end of file diff --git a/doc/html/change_box.html b/doc/html/change_box.html index d7aa07bbc1..fc034cbe2f 100644 --- a/doc/html/change_box.html +++ b/doc/html/change_box.html @@ -419,11 +419,12 @@ been previously used to define the lattice spacing.

Restrictions

If you use the ortho or triclinic keywords, then at the point in the input script when this command is issued, no dumps can -be active, nor can a fix ave/spatial or fix deform be active. This is because these commands -test whether the simulation box is orthogonal when they are first -issued. Note that these commands can be used in your script before a -change_box command is issued, so long as an undump or -unfix command is also used to turn them off.

+be active, nor can a fix deform be active. This is +because these commands test whether the simulation box is orthogonal +when they are first issued. Note that these commands can be used in +your script before a change_box command is issued, so long as an +undump or unfix command is also used to +turn them off.

diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html index 417c581ce8..9fdc98e352 100644 --- a/doc/html/compute_property_atom.html +++ b/doc/html/compute_property_atom.html @@ -221,7 +221,7 @@ in the group. This is useful so that the values can be used by other output commands that take computes as inputs. See for example, the compute reduce, fix ave/atom, fix ave/histo, -fix ave/spatial, and atom-style variable commands.

+fix ave/chunk, and atom-style variable commands.

The list of possible attributes is the same as that used by the dump custom command, which describes their meaning, with some additional quantities that are only defined for certain atom styles. Basically, this augmented list gives an input script access to any per-atom quantity stored by LAMMPS.

@@ -273,7 +273,7 @@ units for q, etc.

diff --git a/doc/html/compute_temp_deform.html b/doc/html/compute_temp_deform.html index 2922d5ce4a..6989e26bf1 100644 --- a/doc/html/compute_temp_deform.html +++ b/doc/html/compute_temp_deform.html @@ -205,7 +205,7 @@ matches the box deformation. If not, then the compute will subtract off an incorrect stream velocity, yielding a bogus thermal temperature. You should NOT assume that your atoms are streaming at the same rate the box is deforming. Rather, you should monitor their -velocity profile, e.g. via the fix ave/spatial +velocity profile, e.g. via the fix ave/chunk command. And you can compare the results of this compute to compute temp/profile, which actually calculates the stream profile before subtracting it. If the two computes do not give roughly the same temperature, then your atoms are not streaming diff --git a/doc/html/fix.html b/doc/html/fix.html index c0cb063015..8f21357c51 100644 --- a/doc/html/fix.html +++ b/doc/html/fix.html @@ -242,11 +242,10 @@ various commands explain the details.

  • Global values can be output via the thermo_style custom or fix ave/time command. Or the values can be referenced in a variable equal or variable atom command.
    • -
  • Per-atom values can be output via the dump custom command -or the fix ave/spatial command. Or they can be -time-averaged via the fix ave/atom command or -reduced by the compute reduce command. Or the -per-atom values can be referenced in an atom-style variable.
    • +
  • Per-atom values can be output via the dump custom command. +Or they can be time-averaged via the fix ave/atom +command or reduced by the compute reduce +command. Or the per-atom values can be referenced in an atom-style variable.
  • Local values can be reduced by the compute reduce command, or histogrammed by the fix ave/histo command.

    • See this howto section for a summary of @@ -282,7 +281,6 @@ of ave/chunk - compute per-chunk time-averaged quantities

  • ave/correlate - compute/output time correlations
  • ave/histo - compute/output time-averaged histograms
    • -
  • ave/spatial - compute/output time-averaged per-atom quantities by layer
  • ave/time - compute/output global time-averaged quantities
  • balance - perform dynamic load-balancing
  • bond/break - break bonds on the fly
    • diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html index a6a6ba9826..713d147446 100644 --- a/doc/html/fix_ave_atom.html +++ b/doc/html/fix_ave_atom.html @@ -160,7 +160,7 @@ one or more input values can be listed

    Description

    Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting -per-atom averages can be used by other output commands such as the fix ave/spatial or dump custom commands.

    +per-atom averages can be used by other output commands such as the fix ave/chunk or dump custom commands.

    The group specified with the command means only atoms within the group have their averages computed. Results are set to 0.0 for atoms not in the group.

    @@ -249,7 +249,7 @@ the run diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index b636808101..dc2732aafd 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -192,8 +192,8 @@

    NOTE:

    -

    If you are trying to replace an older fix ave/spatial command with the -newer, more flexible fix ave/chunk and compute chunk/atom commands, you simply need to split +

    If you are trying to replace a deprectated fix ave/spatial command +with the newer, more flexible fix ave/chunk and compute chunk/atom commands, you simply need to split the fix ave/spatial arguments across the two new commands. For example, this command:

    fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
diff --git a/doc/html/fix_ave_correlate.html b/doc/html/fix_ave_correlate.html
index c6d918b444..a949f45708 100644
--- a/doc/html/fix_ave_correlate.html
+++ b/doc/html/fix_ave_correlate.html
@@ -205,10 +205,9 @@ fixes which store their own “group” definitions.
    
 variable.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the fix ave/spatial, fix ave/atom,
-or fix ave/histo commands.  If you wish to
-convert a per-atom quantity into a single global value, see the
-compute reduce command.
    
+from a compute, fix, or variable, then see the fix ave/chunk, fix ave/atom, or
+fix ave/histo commands.  If you wish to convert a
+per-atom quantity into a single global value, see the compute reduce command.
    
 
    Computes that produce global quantities are those which
 do not have the word atom in their style name.  Only a few
 fixes produce global quantities.  See the doc pages for
@@ -414,7 +413,7 @@ the run
 
    Related commands
    
 
    fix ave/correlate/long,
-compute, fix ave/time, fix ave/atom, fix ave/spatial,
+compute, fix ave/time, fix ave/atom, fix ave/chunk,
 fix ave/histo, variable
    
 
    Default: none
    
 
    The option defaults are ave = one, type = auto, start = 0, no file
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html
index 3930842458..48a236b5b0 100644
--- a/doc/html/fix_ave_histo.html
+++ b/doc/html/fix_ave_histo.html
@@ -419,7 +419,7 @@ the run
    -
    compute 5 defects voronoi/atom occupation
-
    -
    -

    compute 6 all voronoi/atom neighbors yes

    Description

    diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html index 2c21674c50..984513a2c2 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -176,7 +176,7 @@ created to be used in place of that fix, to integrate the equations of motion of spherical rigid bodies when a lattice-Boltzmann fluid is present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in     Mackay et al. to update the positions, velocities, and orientations of +The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of a set of spherical rigid bodies experiencing velocity dependent hydrodynamic forces. The spherical bodies are assumed to rotate as solid, uniform density spheres, with moments of inertia calculated @@ -207,7 +207,7 @@ assumes the constituent atoms are point particles); see

    Restart, fix_modify, output, run start/stop, minimize info

    No information about the rigid and rigid/nve fixes are written to binary restart files.

    -

    Similar to the fix rigid command: &quot; The rigid +

    Similar to the fix rigid command: The rigid fix computes a global scalar which can be accessed by various output commands. The scalar value calculated by these fixes is “intensive”. The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid @@ -217,8 +217,8 @@ mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the force and torque keywords are -removed from this calculation.&quot;

    -

    &quot;All of these fixes compute a global array of values which can be +removed from this calculation.

    +

    All of these fixes compute a global array of values which can be accessed by various output commands. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 @@ -239,7 +239,7 @@ of bodies.

    they are independent of the number of atoms in the simulation.

    No parameter of these fixes can be used with the start/stop keywords of the run command. These fixes are not invoked during -energy minimization. &quot;

    +energy minimization.

    Restrictions

    diff --git a/doc/html/pair_coeff.html b/doc/html/pair_coeff.html index eac6bd4a7e..1689bf6047 100644 --- a/doc/html/pair_coeff.html +++ b/doc/html/pair_coeff.html @@ -223,7 +223,7 @@ for

    Windows:

    -% set LAMMPS_POTENTIALS="C:Path to LAMMPSPotentials"
+% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"

    The alphabetic list of pair styles defined in LAMMPS is given on the diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html index 86eceae04c..bac9a4aa44 100644 --- a/doc/html/pair_morse.html +++ b/doc/html/pair_morse.html @@ -141,21 +141,38 @@

    pair_style morse/smooth/linear/omp command

    +
    +
    +

    pair_style morse/soft command

    Syntax

    -
    pair_style morse cutoff
+
    pair_style style args
 
    
 
    
 
      
-
    • cutoff = global cutoff for Morse interactions (distance units)
      • 
+
    • style = morse or morse/smooth/linear or morse/soft
      • 
+
    • args = list of arguments for a particular style
      • 
 
    
+
    +morse args = cutoff
+  cutoff = global cutoff for Morse interactions (distance units)
+morse/smooth/linear args = cutoff
+  cutoff = global cutoff for Morse interactions (distance units)
+morse/soft args = n lf cutoff
+  n = soft-core parameter
+  lf      = transformation range is lf < lambda < 1
+  cutoff  = global cutoff for Morse interactions (distance units)
+

    Examples

    -
    pair_style morse 2.5
-pair_style morse/smooth/linear 2.5
-pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0
+
    pair_style morse 2.5
+pair_style morse/smooth/linear 2.5
+pair_coeff * * 100.0 2.0 1.5
+pair_coeff 1 1 100.0 2.0 1.5 3.0
    
+
    pair_style morse/soft 4 0.9 10.0
+pair_coeff * * 100.0 2.0 1.5 1.0
+pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
    @@ -174,17 +191,34 @@ commands:

  • alpha (1/distance units)
  • r0 (distance units)
  • cutoff (distance units)
    • -
  • The last coefficient is optional. If not specified, the global morse
    • -
  • cutoff is used.
    • +

    The last coefficient is optional. If not specified, the global morse +cutoff is used.

    -

    The smooth/linear variant is similar to the lj/smooth/linear variant -in that it adds to the potential a shift and a linear term to make both -the potential energy and force go to zero at the cut-off:

    +

    The morse/smooth/linear variant is similar to the lj/smooth/linear +variant in that it adds to the potential a shift and a linear term +so that both, potential energy and force, go to zero at the cut-off:

    _images/pair_morse_smooth_linear.jpg

    The syntax of the pair_style and pair_coeff commands are the same for the morse and morse/smooth/linear styles.

    +

    The morse/soft variant is similar to the lj/cut/soft pair style +in that it modifies the potential at short range to have a soft core. +This helps to avoid singularities during free energy calculation in +which sites are created or anihilated. The formula differs from that +of lj/cut/soft, and is instead given by:

    +_images/pair_morse_soft.jpg +

    The morse/soft style requires the following pair coefficients:

    +
      +
    • D0 (energy units)
      • +
    • alpha (1/distance units)
      • +
    • r0 (distance units)
      • +
    • lamda (unitless, between 0.0 and 1.0)
      • +
    • cutoff (distance units)
      • +
    +

    The last coefficient is optional. If not specified, the global morse +cutoff is used.

    +

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -222,6 +256,8 @@ to be specified in an input script that reads a restart file.

    Restrictions

    The morse/smooth/linear pair style is only enabled if LAMMPS was built with the USER-MISC package. See the Making LAMMPS section for more info.

    +

    The morse/soft pair style is only enabled if LAMMPS was built with +the USER-FEP package. See the Making LAMMPS section for more info.

    (Lamoureux) Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)

    -

    (Schroeder) Schr&ouml;der and Steinhauser, J Chem Phys, 133, +

    (Schroeder) Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).

    (Jiang) Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
    diff --git a/doc/html/tutorial_github.html b/doc/html/tutorial_github.html index 1071d78768..5f6c9e69ba 100644 --- a/doc/html/tutorial_github.html +++ b/doc/html/tutorial_github.html @@ -132,9 +132,11 @@

    This document briefly describes how to use GitHub to merge changes into LAMMPS using GitHub. It assumes that you are familiar with git. You may want to have a look at the Git book to reacquaint yourself.

    +
    +
    -

    Making an account

    +

    Making an account

    First of all, you need a GitHub account. This is fairly simple, just go to GitHub and create an account by clicking the ``Sign up for GitHub’’ button. Once your account is created, you @@ -143,7 +145,7 @@ username or e-mail address and password.

    -

    Forking the repository

    +

    Forking the repository

    To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to LAMMPS on GitHub and make sure branch is set to ``lammps-icms’‘, see the figure below.

    @@ -158,11 +160,9 @@ can include changes from upstream into your repository.

    -

    Adding changes to your own fork

    +

    Adding changes to your own fork

    Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch.

    -
    -

    Feature branches

    Since LAMMPS is such a big project and most user contributions come in @@ -210,6 +210,8 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt

    The “-m” switch is used to add a message to the commit. Use this to indicate what type of change was commited.

    +
    +

    Wisdom by Axel:

    “Do not use “git commit -a”. the -a flag will automatically include *all modified or new files. mercurial does that and it find it hugely annoying and often leading to accidental commits of files you @@ -260,16 +262,19 @@ is now up to the maintainer(s) of the upstream repository to incorporate the changes into the repository and to close the pull request.

    _images/tutorial_pull_request4.png +
    +
    +
    -

    Additional changes

    +

    Additional changes

    Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull request.

    -

    After a merge

    +

    After a merge

    When everything is fine the feature branch is merged into the LAMMPS repositories:

    _images/tutorial_merged.png @@ -293,8 +298,6 @@ to your remote(s) as well:

    $ git push origin :add-user-manifold
    -
    - diff --git a/doc/html/variable.html b/doc/html/variable.html index f3fdbd8b64..1250ca06d3 100644 --- a/doc/html/variable.html +++ b/doc/html/variable.html @@ -168,7 +168,7 @@ constants = PI, version, on, off, true, false, yes, no thermo keywords = vol, ke, press, etc from thermo_style math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, - x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x + x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) @@ -536,36 +536,33 @@ references, and references to other variables.

    vol, pe, ebond, etc Math operators -(), -x, x+y, x-y, x*y, x/y, x^y, x%y, +(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x -Math operators -(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x - -Math functions +Math functions sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) -Group functions +Group functions count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) -Region functions +Region functions count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) -Special functions +Special functions sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) -Atom values +Atom values id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] -Atom vectors +Atom vectors id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q -Compute references +Compute references c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] -Fix references +Fix references f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] -Other variables +Other variables v_name, v_name[i] From 0c89f3524346202675bce785414504410fb1997f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Jun 2016 14:10:24 +0000 Subject: [PATCH 043/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15102 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_images/pair_morse_soft.jpg | Bin 0 -> 20988 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 doc/html/_images/pair_morse_soft.jpg diff --git a/doc/html/_images/pair_morse_soft.jpg b/doc/html/_images/pair_morse_soft.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9c8321eba798943de9ad293f80e95d946e872f95 GIT binary patch literal 20988 zcmd?RcQo8l*ET$Q@4XX5m*_+h>n<^k3@>$jwYkDsWT}PzaO&}#L7Q9V@}56 zac~S0Rou)XAg67a**JrhS1=Diw0yWLYvxjN`ga9D`j3&+0e{BPB47ye|L!d=O4I_sADtcRO=Uh>e_+E{2Sd{iYwq?1}f&-v%)%K*DZq3*zK{ z7!bTkR-MPZ_y{aG0yC0ciRQjzmWDHatgEZ{oO7-Uf?|Hy#~2=G7hYegk7TxS#Wyc4 zas&4sX28kQiOn${0tuIOaC8cW*yL$|DFy+(q&!a;{c3DTs zgxE${h1$mcpO}H?(Zf97c(R{0;}PO@c0Cjv(RiL8lmnLN@p@Ii4TAq+0Mw-Rp`OnG z{LJgE;%W=ws};`}$*jQ|J{DFFNIHO~6!8M4|4&0zV1+)U?U!sFJXEcsa3-?CQYPBxM{IF!!pL|Q##f;tfbV)0TvbCQYu>cA zzE<+#d(Lr;F(qVzU_KEb0ZJGF01_fJ0GW_VlcP&dhrz|%*45&VezA#&{ykrezg`Z( zFz@A0_U)akAzTV!;Q70d0-6qPJ-y9zKVknQpc7UDD$Wd22mQd%+r`LOaR7 zHIM^erM?V7kOK*b0}lu}2%MnF8>L6m2w3#^FV9Am8Gy` zeQdSZVG^=&#iV#5U|oETL%>ffq|NBeUjRt#P5Dn{$5u=V(tMYc;qxX9njd3{&9hNM zGu7-Lf{dSXp!!ydQfiCe1+?B%>_5bBK)eui5@~r3X`!*5UaAv!6o*TG3phM`s~}i& zxzZd@b1b)RkTU~kxvOnZnvegvPgA|_?G4Q1k4*fZ8}+lgnX-OF(@X4DSCO=~HxaG6 zg-eIi$zm&&UJbX^OE>#Zn7*keCH+BOFylRy#8siiXIu!W!bSLc>>~ARmAu;d?TPl) z=enF(C4CyLJrDwI(v8d*O{>Z7$4GPlqF>rYnOz?knr&jTtPqVB$~`9*SfH2+%nbYR{H4vut$^LR$))leP*pG5Mfx zM2L>d_zLM`1O19Mx%z*>Z`*INsXF|)Po?x=@+`#_{1i>YyXn=Yq@ARe4306UDF#-p zXFb~Xh%8w434kCcGFb0EHa$)v6{L>-zK(L)v9-P3oMIDyGP8l0$hiGVtcw(1Kk0C4 zwjKENdO&(5O0C$4;HpZ12En;h^ud$5r>KO8dxQ{j6p%0=w0)RXZqB#{70vM3Z3W_{yqiG?QH#e|rRq%#5

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z3(I>2b7&ox<%|~Qd+RqvzM2Bk{PwT$pIN(ou!Czf5~;P#d;C;`EVmS9l$<`pdxln_ z_1N^OyD+D?0T?PwNkfh!=a~kK_?@bW2d@>@uJz!)?x=T(m=IKy z0xw$@^Yq~#b&U~yK!S{to3nv0z2P7jc7!xK!eTC*dPDP=xzckTE-Mi6+E7^clMJE>t{vB39gKf3?fOg& f3<5*c)IqATM*Tkl$Nov1|Bm`k{Qo#=`uX->6xEgr literal 0 HcmV?d00001 From 10be4c06bd3cf678fac5cb58c37cdf8f6ab4d862 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Jun 2016 14:12:27 +0000 Subject: [PATCH 044/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15103 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/utils/converters/lammpsdoc/txt2html.py | 6 ++++ doc/utils/converters/lammpsdoc/txt2rst.py | 12 +++++-- doc/utils/converters/tests/test_txt2rst.py | 38 +++++++++++++++++++--- 3 files changed, 50 insertions(+), 6 deletions(-) diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py index ddb1b1978e..ab132a380d 100755 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -138,12 +138,18 @@ class Formatting(object): elif command == "dl": return self.definition_list(paragraph) elif command == "l": + if "olb" in commands: + self.current_list_mode = Formatting.ORDERED_LIST_MODE + elif "ulb" in commands: + self.current_list_mode = Formatting.UNORDERED_LIST_MODE + return self.list_item(paragraph) elif command == "dt": return self.definition_term(paragraph) elif command == "dd": return self.definition_description(paragraph) elif command == "ulb": + self.current_list_mode = Formatting.UNORDERED_LIST_MODE return self.unordered_list_begin(paragraph) elif command == "ule": return self.unordered_list_end(paragraph) diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index ba3864008a..f9ceb9b7ae 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -165,7 +165,7 @@ class RSTFormatting(Formatting): return paragraph def unordered_list_end(self, paragraph): - return paragraph + return paragraph.rstrip() + '\n' def ordered_list_begin(self, paragraph): if paragraph.startswith('* '): @@ -179,7 +179,15 @@ class RSTFormatting(Formatting): return paragraph def ordered_list_end(self, paragraph): - return paragraph + return paragraph.rstrip() + '\n' + + def ordered_list(self, paragraph): + paragraph = super().ordered_list(paragraph) + return paragraph.rstrip() + '\n' + + def unordered_list(self, paragraph): + paragraph = super().unordered_list(paragraph) + return paragraph.rstrip() + '\n' def all_breaks(self, paragraph): indented = "" diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py index 1be59ac714..e2c20434be 100644 --- a/doc/utils/converters/tests/test_txt2rst.py +++ b/doc/utils/converters/tests/test_txt2rst.py @@ -222,7 +222,7 @@ class TestListFormatting(unittest.TestCase): "three :ule,l\n") self.assertEqual("* one\n" "* two\n" - "* three\n", s) + "* three\n\n", s) def test_multi_line_unordered_list_elements(self): s = self.txt2rst.convert("one :ulb,l\n" @@ -232,7 +232,7 @@ class TestListFormatting(unittest.TestCase): self.assertEqual("* one\n" "* two\n" " words\n" - "* three\n", s) + "* three\n\n", s) def test_ordered_list(self): s = self.txt2rst.convert("one\n" @@ -248,7 +248,7 @@ class TestListFormatting(unittest.TestCase): "three :ole,l\n") self.assertEqual("#. one\n" "#. two\n" - "#. three\n", s) + "#. three\n\n", s) def test_multi_line_ordered_list_elements(self): s = self.txt2rst.convert("one :olb,l\n" @@ -258,7 +258,37 @@ class TestListFormatting(unittest.TestCase): self.assertEqual("#. one\n" "#. two\n" " words\n" - "#. three\n", s) + "#. three\n\n", s) + + def test_paragraphs_ordered_list(self): + s = self.txt2rst.convert("first\n" + "paragraph :olb,l\n" + "second\n" + "paragraph :l\n" + "third\n" + "paragraph :ole,l\n") + self.assertEqual("#. first\n" + " paragraph\n" + "#. second\n" + " paragraph\n" + "#. third\n" + " paragraph\n\n", s) + + def test_paragraphs_unordered_list(self): + s = self.txt2rst.convert("first\n" + "paragraph :ulb,l\n" + "second\n" + "paragraph :l\n" + "third\n" + "paragraph :ule,l\n") + self.assertEqual("* first\n" + " paragraph\n" + "* second\n" + " paragraph\n" + "* third\n" + " paragraph\n\n", s) + + def test_definition_list(self): s = self.txt2rst.convert("A\n" From 195c521b8a8c830371aa4762c675e564bd0dd666 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Jun 2016 14:14:17 +0000 Subject: [PATCH 045/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15104 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_deprecated.cpp | 42 ++++++++++++++++++++++++++++++++++ src/fix_deprecated.h | 51 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 src/fix_deprecated.cpp create mode 100644 src/fix_deprecated.h diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp new file mode 100644 index 0000000000..8139a14d9d --- /dev/null +++ b/src/fix_deprecated.cpp @@ -0,0 +1,42 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "fix_deprecated.h" +#include "comm.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (strncmp(style,"ave/spatial",11) == 0) { + const char *message = "\n" + "NOTE: The fix styles 'ave/spatial' and 'ave/spatial/sphere' have been replaced\n" + "by the more general fix ave/chunk and compute chunk/atom commands.\n" + "All ave/spatial and ave/spatial/sphere functionality is available in these\n" + "new commands. These ave/spatial keywords & options are part of fix ave/chunk:\n" + " Nevery, Nrepeat, Nfreq, input values, norm, ave, file, overwrite, title123\n" + "These ave/spatial keywords & options for binning are part of compute chunk/atom:\n" + " dim, origin, delta, region, bound, discard, units\n\n"; + + if (comm->me == 0) { + if (screen) fprintf(screen,message); + if (logfile) fprintf(logfile,message); + } + } + error->all(FLERR,"This fix command has been removed from LAMMPS"); +} diff --git a/src/fix_deprecated.h b/src/fix_deprecated.h new file mode 100644 index 0000000000..dcfe75358f --- /dev/null +++ b/src/fix_deprecated.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +// list all deprecated and removed fix styles here + +FixStyle(ave/spatial,FixDeprecated) +FixStyle(ave/spatial/sphere,FixDeprecated) + +#else + +#ifndef LMP_FIX_DEPRECATED_H +#define LMP_FIX_DEPRECATED_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixDeprecated : public Fix { + public: + FixDeprecated(class LAMMPS *, int, char **); + ~FixDeprecated() {} + int setmask() {return 0;} + void init() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: The fix ave/spatial command has been removed from LAMMPS + +It has been replaced by the more flexible fix ave/chunk and compute +chunk/atom commands. All the fix ave/spatial keywords and options are +available in those two newer commands. + +*/ From bb45a5e492ca59a4af7437f54ebcf5ea55ada00b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Jun 2016 14:14:28 +0000 Subject: [PATCH 046/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15105 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_ave_spatial.cpp | 40 --------------------------------- src/fix_ave_spatial.h | 49 ----------------------------------------- 2 files changed, 89 deletions(-) delete mode 100644 src/fix_ave_spatial.cpp delete mode 100644 src/fix_ave_spatial.h diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp deleted file mode 100644 index ef9e04a373..0000000000 --- a/src/fix_ave_spatial.cpp +++ /dev/null @@ -1,40 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "fix_ave_spatial.h" -#include "comm.h" -#include "error.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) -{ - const char *message = "\n" - "NOTE: The fix ave/spatial command has been replaced by the\n" - "more general fix ave/chunk and compute chunk/atom commands.\n" - "All ave/spatial functionality is available in the new commands.\n" - "These ave/spatial keywords & options are part of fix ave/chunk:\n" - " Nevery, Nrepeat, Nfreq, input values, norm, ave, file, overwrite, title123\n" - "These ave/spatial keywords & options for binning are part of compute chunk/atom:\n" - " dim, origin, delta, region, bound, discard, units\n\n"; - - if (comm->me == 0) { - if (screen) fprintf(screen,message); - if (logfile) fprintf(logfile,message); - } - - error->all(FLERR,"The fix ave/spatial command has been removed from LAMMPS"); -} diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h deleted file mode 100644 index de592cbc95..0000000000 --- a/src/fix_ave_spatial.h +++ /dev/null @@ -1,49 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef FIX_CLASS - -FixStyle(ave/spatial,FixAveSpatial) - -#else - -#ifndef LMP_FIX_AVE_SPATIAL_H -#define LMP_FIX_AVE_SPATIAL_H - -#include -#include "fix.h" - -namespace LAMMPS_NS { - -class FixAveSpatial : public Fix { - public: - FixAveSpatial(class LAMMPS *, int, char **); - ~FixAveSpatial() {} - int setmask() {} - void init() {} -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: The fix ave/spatial command has been removed from LAMMPS - -It has been replaced by the more flexible fix ave/chunk and compute -chunk/atom commands. All the fix ave/spatial keywords and options are -available in those two newer commands. - -*/ From a9b7c62a060206de598075a27a4059195d111577 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 01:55:19 -0400 Subject: [PATCH 047/111] bugfix for fix_modify temp issue in fix_rigid_nh.cpp and fix_rigid_nh_small.cpp reported by reese jones. also rename pflag/tflag to pcomputeflag/tcomputeflag consistently across all nose-hoover fixes and document them in the header. also plug some minor memory leaks and consistently intialize flags and pointers. --- src/ASPHERE/fix_nph_asphere.cpp | 4 ++-- src/ASPHERE/fix_npt_asphere.cpp | 4 ++-- src/ASPHERE/fix_nvt_asphere.cpp | 2 +- src/BODY/fix_nph_body.cpp | 4 ++-- src/BODY/fix_npt_body.cpp | 4 ++-- src/BODY/fix_nvt_body.cpp | 2 +- src/KOKKOS/fix_nph_kokkos.cpp | 4 ++-- src/KOKKOS/fix_npt_kokkos.cpp | 4 ++-- src/KOKKOS/fix_nvt_kokkos.cpp | 2 +- src/RIGID/fix_rigid_nh.cpp | 10 +++++----- src/RIGID/fix_rigid_nh.h | 2 +- src/RIGID/fix_rigid_nh_small.cpp | 10 +++++----- src/RIGID/fix_rigid_nh_small.h | 2 +- src/SHOCK/fix_nphug.cpp | 4 ++-- src/USER-EFF/fix_nph_eff.cpp | 4 ++-- src/USER-EFF/fix_npt_eff.cpp | 4 ++-- src/USER-EFF/fix_nvt_eff.cpp | 2 +- src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +- src/USER-INTEL/fix_npt_intel.cpp | 4 ++-- src/USER-INTEL/fix_nvt_intel.cpp | 2 +- src/USER-INTEL/fix_nvt_sllod_intel.cpp | 2 +- src/USER-OMP/fix_nph_asphere_omp.cpp | 4 ++-- src/USER-OMP/fix_nph_omp.cpp | 4 ++-- src/USER-OMP/fix_nph_sphere_omp.cpp | 4 ++-- src/USER-OMP/fix_nphug_omp.cpp | 4 ++-- src/USER-OMP/fix_npt_asphere_omp.cpp | 4 ++-- src/USER-OMP/fix_npt_omp.cpp | 4 ++-- src/USER-OMP/fix_npt_sphere_omp.cpp | 4 ++-- src/USER-OMP/fix_nvt_asphere_omp.cpp | 2 +- src/USER-OMP/fix_nvt_omp.cpp | 2 +- src/USER-OMP/fix_nvt_sllod_omp.cpp | 2 +- src/USER-OMP/fix_nvt_sphere_omp.cpp | 2 +- src/fix_nh.cpp | 17 +++++++++++------ src/fix_nh.h | 2 +- src/fix_nph.cpp | 4 ++-- src/fix_nph_sphere.cpp | 4 ++-- src/fix_npt.cpp | 4 ++-- src/fix_npt_sphere.cpp | 4 ++-- src/fix_nvt.cpp | 2 +- src/fix_nvt_sllod.cpp | 2 +- src/fix_nvt_sphere.cpp | 2 +- 41 files changed, 80 insertions(+), 75 deletions(-) diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 10549ca1b8..9444da77b3 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -46,7 +46,7 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 2625bc6391..205630376a 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -46,7 +46,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 5b8b943ab4..f43e731c23 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -45,5 +45,5 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1808b9ade8..99e33a3d22 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -50,7 +50,7 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -68,5 +68,5 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 17014ba17c..077a7babd4 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -50,7 +50,7 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -68,5 +68,5 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index d6601f4966..464f42eae9 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -49,5 +49,5 @@ FixNVTBody::FixNVTBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 350832a3d7..f3f7c271d6 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -47,7 +47,7 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -65,7 +65,7 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : newarg[3] = this->id_temp; this->modify->add_compute(4,newarg); delete [] newarg; - this->pflag = 1; + this->pcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 3832fb3e57..bbc26b8e88 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -47,7 +47,7 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -65,7 +65,7 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : newarg[3] = this->id_temp; this->modify->add_compute(4,newarg); delete [] newarg; - this->pflag = 1; + this->pcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index bf6ce0de2b..c479251c33 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -46,7 +46,7 @@ FixNVTKokkos::FixNVTKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 5db799e9f0..a2c6c338b7 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -148,6 +148,9 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; + + id_temp = NULL; + id_press = NULL; } /* ---------------------------------------------------------------------- */ @@ -162,10 +165,8 @@ FixRigidNH::~FixRigidNH() if (rfix) delete [] rfix; - if (tcomputeflag) { - modify->delete_compute(id_temp); - delete [] id_temp; - } + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; // delete pressure if fix created it @@ -1265,7 +1266,6 @@ int FixRigidNH::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); if (tcomputeflag) { modify->delete_compute(id_temp); tcomputeflag = 0; diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index 684579b8af..08208e5aac 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -69,7 +69,7 @@ class FixRigidNH : public FixRigid { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tcomputeflag,pcomputeflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external void couple(); void remap(); diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5708bb6602..d8ec174f72 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -163,6 +163,9 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; + + id_temp = NULL; + id_press = NULL; } /* ---------------------------------------------------------------------- */ @@ -176,10 +179,8 @@ FixRigidNHSmall::~FixRigidNHSmall() if (rfix) delete [] rfix; - if (tcomputeflag) { - modify->delete_compute(id_temp); - delete [] id_temp; - } + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; // delete pressure if fix created it @@ -1374,7 +1375,6 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); if (tcomputeflag) { modify->delete_compute(id_temp); tcomputeflag = 0; diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index f771b8c41b..07510a59e3 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -68,7 +68,7 @@ class FixRigidNHSmall : public FixRigidSmall { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tcomputeflag,pcomputeflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external void couple(); void remap(); diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 480b667254..7fc0f8a381 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -135,7 +135,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -153,7 +153,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; // create a new compute potential energy compute diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp index dc6bfe20d5..0fe8c8e6db 100644 --- a/src/USER-EFF/fix_nph_eff.cpp +++ b/src/USER-EFF/fix_nph_eff.cpp @@ -46,7 +46,7 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp index 36a6f87cba..02f09839b1 100644 --- a/src/USER-EFF/fix_npt_eff.cpp +++ b/src/USER-EFF/fix_npt_eff.cpp @@ -46,7 +46,7 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 36a9ff3293..ab82f9e0f8 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -46,5 +46,5 @@ FixNVTEff::FixNVTEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 1f6dea658f..1b4ec1f3fb 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -58,7 +58,7 @@ FixNVTSllodEff::FixNVTSllodEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp index 150464413e..2bfbd5e735 100644 --- a/src/USER-INTEL/fix_npt_intel.cpp +++ b/src/USER-INTEL/fix_npt_intel.cpp @@ -46,7 +46,7 @@ FixNPTIntel::FixNPTIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTIntel::FixNPTIntel(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp index 65854b07a8..3fe712c9ab 100644 --- a/src/USER-INTEL/fix_nvt_intel.cpp +++ b/src/USER-INTEL/fix_nvt_intel.cpp @@ -45,6 +45,6 @@ FixNVTIntel::FixNVTIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index 5505abb9ce..bab748ad74 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -59,7 +59,7 @@ FixNVTSllodIntel::FixNVTSllodIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp index 3e0a6c9df0..dfcbc87e6f 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.cpp +++ b/src/USER-OMP/fix_nph_asphere_omp.cpp @@ -46,7 +46,7 @@ FixNPHAsphereOMP::FixNPHAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHAsphereOMP::FixNPHAsphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index be21da2eed..f2a4e66f55 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -46,7 +46,7 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp index a5626f9d1c..670009de2f 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.cpp +++ b/src/USER-OMP/fix_nph_sphere_omp.cpp @@ -46,7 +46,7 @@ FixNPHSphereOMP::FixNPHSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHSphereOMP::FixNPHSphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp index 7721781769..b652cf563a 100644 --- a/src/USER-OMP/fix_nphug_omp.cpp +++ b/src/USER-OMP/fix_nphug_omp.cpp @@ -135,7 +135,7 @@ FixNPHugOMP::FixNPHugOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -153,7 +153,7 @@ FixNPHugOMP::FixNPHugOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; // create a new compute potential energy compute diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp index 00bafe661a..1db62d40c0 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.cpp +++ b/src/USER-OMP/fix_npt_asphere_omp.cpp @@ -46,7 +46,7 @@ FixNPTAsphereOMP::FixNPTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTAsphereOMP::FixNPTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index c4af48542a..5610f62f36 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -46,7 +46,7 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp index 6baee93cb4..d71d1380b9 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.cpp +++ b/src/USER-OMP/fix_npt_sphere_omp.cpp @@ -46,7 +46,7 @@ FixNPTSphereOMP::FixNPTSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTSphereOMP::FixNPTSphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index 23cc2e9581..bb1e784a37 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -45,5 +45,5 @@ FixNVTAsphereOMP::FixNVTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index 18d02bff4d..f8f3c15b76 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -45,5 +45,5 @@ FixNVTOMP::FixNVTOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index 416a28856b..a829d49c0f 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -65,7 +65,7 @@ FixNVTSllodOMP::FixNVTSllodOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp index 6db9ad849a..22eda99883 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp @@ -45,5 +45,5 @@ FixNVTSphereOMP::FixNVTSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index b300fd2d46..2f1081216b 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -80,6 +80,11 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) flipflag = 1; dipole_flag = 0; + tcomputeflag = 0; + pcomputeflag = 0; + id_temp = NULL; + id_press = NULL; + // turn on tilt factor scaling, whenever applicable dimension = domain->dimension; @@ -558,7 +563,7 @@ FixNH::~FixNH() // delete temperature and pressure if fix created them - if (tflag) modify->delete_compute(id_temp); + if (tcomputeflag) modify->delete_compute(id_temp); delete [] id_temp; if (tstat_flag) { @@ -569,7 +574,7 @@ FixNH::~FixNH() } if (pstat_flag) { - if (pflag) modify->delete_compute(id_press); + if (pcomputeflag) modify->delete_compute(id_press); delete [] id_press; if (mpchain) { delete [] etap; @@ -1347,9 +1352,9 @@ int FixNH::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (tflag) { + if (tcomputeflag) { modify->delete_compute(id_temp); - tflag = 0; + tcomputeflag = 0; } delete [] id_temp; int n = strlen(arg[1]) + 1; @@ -1381,9 +1386,9 @@ int FixNH::modify_param(int narg, char **arg) } else if (strcmp(arg[0],"press") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); - if (pflag) { + if (pcomputeflag) { modify->delete_compute(id_press); - pflag = 0; + pcomputeflag = 0; } delete [] id_press; int n = strlen(arg[1]) + 1; diff --git a/src/fix_nh.h b/src/fix_nh.h index 7227a22968..e468d49817 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -76,7 +76,7 @@ class FixNH : public Fix { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tflag,pflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external double *eta,*eta_dot; // chain thermostat for particles double *eta_dotdot; diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 6f3678ed3a..a331a07d24 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -46,7 +46,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 93d9bf8af2..852234074f 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -46,7 +46,7 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 0326c06c77..e14200f6a2 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -46,7 +46,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 6e7c074d5e..d3773e0d17 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -46,7 +46,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index a86f46c3b5..35ee085da1 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -45,5 +45,5 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 8257afae05..87e86f2351 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -63,7 +63,7 @@ FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index c886935f12..b65b3adfae 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -45,5 +45,5 @@ FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } From d6bbf15efd91c81335cf2edce53b350181856911 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 11:59:01 -0400 Subject: [PATCH 048/111] use fputs() instead of fprintf() to get past "hardened" gcc settings on fedora rpm builds --- src/fix_deprecated.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 8139a14d9d..9c0b6686d1 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -34,8 +34,8 @@ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : " dim, origin, delta, region, bound, discard, units\n\n"; if (comm->me == 0) { - if (screen) fprintf(screen,message); - if (logfile) fprintf(logfile,message); + if (screen) fputs(message,screen); + if (logfile) fputs(message,logfile); } } error->all(FLERR,"This fix command has been removed from LAMMPS"); From 150d7df7ba6dc036f9189f621ec98a916cf233eb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 3 Jun 2016 17:08:25 -0400 Subject: [PATCH 049/111] Removed unnecessary files from theme --- .../_themes/lammps_theme/static/css/badge_only.css.map | 7 ------- .../_themes/lammps_theme/static/css/theme.css.map | 7 ------- 2 files changed, 14 deletions(-) delete mode 100644 doc/utils/sphinx-config/_themes/lammps_theme/static/css/badge_only.css.map delete mode 100644 doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css.map diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/static/css/badge_only.css.map b/doc/utils/sphinx-config/_themes/lammps_theme/static/css/badge_only.css.map deleted file mode 100644 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-"names": [], -"file": "theme.css" -} From dfda0bc667867b777707c7ce413f4ce34983bdbf Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 3 Jun 2016 17:34:23 -0400 Subject: [PATCH 050/111] Fix tutorial_drude.txt --- doc/src/tutorial_drude.txt | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index 987f580aa2..3ab8afcae3 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -5,6 +5,14 @@ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } }); +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + Tutorial for Thermalized Drude oscillators in LAMMPS :h3 This tutorial explains how to use Drude oscillators in LAMMPS to @@ -52,14 +60,14 @@ constant \(k_D\) = 4184 kJ/(mol Ang \(\{\}^2\)) - for all types of \ core-Drude bond, a global mass \(m_D\) = 0.4 g/mol (or u) for all types \ of Drude particles, and to calculate the Drude charges for individual \ atom types from the atom polarizabilities using equation (1). This \ -choice is followed in the polarizable CHARMM force field. :olb,l +choice is followed in the polarizable CHARMM force field. :ulb,l Alternately "Schroeder and Steinhauser"_#Schroeder suggest adopting a global \ charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u) \ for all Drude particles, and to calculate the force constant for each \ type of core-Drude bond from equation (1). The timesteps used by these \ authors are between 0.5 and 2 fs, with the degrees of freedom of the \ Drude oscillators kept cold at 1 K. :l -In both these force fields hydrogen atoms are treated as non-polarizable. :ole,l +In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l The motion of of the Drude particles can be calculated by minimizing From 732f2113ed9331ab4f854e20bc16689b68c6ba67 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 19:16:11 -0400 Subject: [PATCH 051/111] Correct off-by-one indexing errors and incorrect biasing functions in compute temp/chunk Closes #74 --- src/compute_temp_chunk.cpp | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 5a5853514f..87d6e11864 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -472,9 +472,13 @@ void ComputeTempChunk::vcm_compute() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); for (i = 0; i < nchunk; i++) { - vcmall[i][0] /= masstotal[i]; - vcmall[i][1] /= masstotal[i]; - vcmall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + vcmall[i][0] /= masstotal[i]; + vcmall[i][1] /= masstotal[i]; + vcmall[i][2] /= masstotal[i]; + } else { + vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0; + } } } @@ -689,7 +693,7 @@ void ComputeTempChunk::internal(int icol) void ComputeTempChunk::remove_bias(int i, double *v) { - int index = cchunk->ichunk[i]; + int index = cchunk->ichunk[i]-1; if (index < 0) return; v[0] -= vcmall[index][0]; v[1] -= vcmall[index][1]; @@ -711,11 +715,11 @@ void ComputeTempChunk::remove_bias_all() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - index = ichunk[i]; + index = ichunk[i]-1; if (index < 0) continue; - v[i][0] -= vbias[0]; - v[i][1] -= vbias[1]; - v[i][2] -= vbias[2]; + v[i][0] -= vcmall[index][0]; + v[i][1] -= vcmall[index][1]; + v[i][2] -= vcmall[index][2]; } } @@ -726,7 +730,7 @@ void ComputeTempChunk::remove_bias_all() void ComputeTempChunk::restore_bias(int i, double *v) { - int index = cchunk->ichunk[i]; + int index = cchunk->ichunk[i]-1; if (index < 0) return; v[0] += vcmall[index][0]; v[1] += vcmall[index][1]; @@ -749,11 +753,11 @@ void ComputeTempChunk::restore_bias_all() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - index = ichunk[i]; + index = ichunk[i]-1; if (index < 0) continue; - v[i][0] += vbias[0]; - v[i][1] += vbias[1]; - v[i][2] += vbias[2]; + v[i][0] += vcmall[index][0]; + v[i][1] += vcmall[index][1]; + v[i][2] += vcmall[index][2]; } } From d89388fd5ea48b35893ff1694d0447d542ef76c0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 20:53:00 -0400 Subject: [PATCH 052/111] make files safe against division by zero when computing center of mass for a collection of atoms this closes #75 --- src/MC/fix_tfmc.cpp | 9 ++++++--- src/compute_angmom_chunk.cpp | 8 +++++--- src/compute_dipole_chunk.cpp | 9 +++++---- src/compute_gyration.cpp | 5 +++-- src/compute_gyration_chunk.cpp | 20 +++++++++++++------- src/compute_inertia_chunk.cpp | 8 +++++--- src/compute_msd_chunk.cpp | 8 +++++--- src/compute_omega_chunk.cpp | 8 +++++--- src/compute_torque_chunk.cpp | 8 +++++--- src/compute_vcm_chunk.cpp | 8 +++++--- src/fix_heat.cpp | 2 ++ src/fix_spring.cpp | 24 +++++++++++++++--------- src/fix_spring_rg.cpp | 10 ++++++---- src/fix_tmd.cpp | 7 +++---- src/molecule.cpp | 8 +++++--- 15 files changed, 88 insertions(+), 54 deletions(-) diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index eea0a0bf31..8ce1308694 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -229,9 +229,12 @@ void FixTFMC::initial_integrate(int vflag) // zero com motion if (comflag == 1 && group->count(igroup) != 0) { MPI_Allreduce(xcm_d,xcm_dall,3,MPI_DOUBLE,MPI_SUM,world); - xcm_dall[0] /= masstotal; - xcm_dall[1] /= masstotal; - xcm_dall[2] /= masstotal; + if (masstotal > 0.0) { + xcm_dall[0] /= masstotal; + xcm_dall[1] /= masstotal; + xcm_dall[2] /= masstotal; + } else xcm_dall[0] = xcm_dall[1] = xcm_dall[2] = 0.0; + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { if (xflag) x[i][0] -= xcm_dall[0]; diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 93a843ac31..5e88f5bc25 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -136,9 +136,11 @@ void ComputeAngmomChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute angmom for each chunk diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 449fb002b6..cb618055f6 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -159,10 +159,11 @@ void ComputeDipoleChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - if (masstotal[i] == 0.0) masstotal[i] = 1.0; - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute dipole for each chunk diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0c1c58a4fd..7f06df9103 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -109,6 +109,7 @@ void ComputeGyration::compute_vector() } MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world); - if (masstotal == 0.0) return; - for (int i = 0; i < 6; i++) vector[i] = vector[i]/masstotal; + if (masstotal > 0.0) + for (int i = 0; i < 6; i++) + vector[i] /= masstotal; } diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index e006a82299..58fe33bc3c 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -143,7 +143,8 @@ void ComputeGyrationChunk::compute_vector() MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) - rgall[i] = sqrt(rgall[i]/masstotal[i]); + if (masstotal[i] > 0.0) + rgall[i] = sqrt(rgall[i]/masstotal[i]); } /* ---------------------------------------------------------------------- */ @@ -191,9 +192,12 @@ void ComputeGyrationChunk::compute_array() if (nchunk) MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world); - for (i = 0; i < nchunk; i++) - for (j = 0; j < 6; j++) - rgtall[i][j] = rgtall[i][j]/masstotal[i]; + for (i = 0; i < nchunk; i++) { + if (masstotal[i] > 0.0) { + for (j = 0; j < 6; j++) + rgtall[i][j] = rgtall[i][j]/masstotal[i]; + } + } } @@ -253,9 +257,11 @@ void ComputeGyrationChunk::com_chunk() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } } diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 33660b839f..c4e83fa4a1 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -136,9 +136,11 @@ void ComputeInertiaChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute inertia tensor for each chunk diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 9d9ddcb3bd..30eee1d64a 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -201,9 +201,11 @@ void ComputeMSDChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // MSD is difference between current and initial COM diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index c437dd66b3..54e0b8f906 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -138,9 +138,11 @@ void ComputeOmegaChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute inertia tensor for each chunk diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 41ae0c628c..5462debcfc 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -136,9 +136,11 @@ void ComputeTorqueChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute torque on each chunk diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index a3751fa13a..cd864b2aa8 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -146,9 +146,11 @@ void ComputeVCMChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - vcmall[i][0] /= masstotal[i]; - vcmall[i][1] /= masstotal[i]; - vcmall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + vcmall[i][0] /= masstotal[i]; + vcmall[i][1] /= masstotal[i]; + vcmall[i][2] /= masstotal[i]; + } else vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0; } } diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 0609d45efb..5da405ae3f 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -133,6 +133,8 @@ void FixHeat::init() if (group->count(igroup) == 0) error->all(FLERR,"Fix heat group has no atoms"); masstotal = group->mass(igroup); + if (masstotal <= 0.0) + error->all(FLERR,"Fix heat group has invalid mass"); } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index ddc161e50d..0a4b72f79c 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -192,9 +192,11 @@ void FixSpring::spring_tether() if (dr < 0.0) ftotal[3] = -ftotal[3]; espring = 0.5*k_spring * dr*dr; - fx /= masstotal; - fy /= masstotal; - fz /= masstotal; + if (masstotal > 0.0) { + fx /= masstotal; + fy /= masstotal; + fz /= masstotal; + } // apply restoring force to atoms in group @@ -259,12 +261,16 @@ void FixSpring::spring_couple() if (dr < 0.0) ftotal[3] = -ftotal[3]; espring = 0.5*k_spring * dr*dr; - fx2 = fx/masstotal2; - fy2 = fy/masstotal2; - fz2 = fz/masstotal2; - fx /= masstotal; - fy /= masstotal; - fz /= masstotal; + if (masstotal2 > 0.0) { + fx2 = fx/masstotal2; + fy2 = fy/masstotal2; + fz2 = fz/masstotal2; + } + if (masstotal > 0.0) { + fx /= masstotal; + fy /= masstotal; + fz /= masstotal; + } // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 5e267340c1..5f27fc1eb5 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -120,10 +120,12 @@ void FixSpringRG::post_force(int vflag) dy = unwrap[1] - xcm[1]; dz = unwrap[2] - xcm[2]; term1 = 2.0 * k * (1.0 - rg0/rg); - massfrac = mass[type[i]]/masstotal; - f[i][0] -= term1*dx*massfrac; - f[i][1] -= term1*dy*massfrac; - f[i][2] -= term1*dz*massfrac; + if (masstotal > 0.0) { + massfrac = mass[type[i]]/masstotal; + f[i][0] -= term1*dx*massfrac; + f[i][1] -= term1*dy*massfrac; + f[i][2] -= term1*dz*massfrac; + } } } diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 4be97a816e..d326685368 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -85,6 +85,8 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) } masstotal = group->mass(igroup); + if (masstotal == 0.0) + error->all(FLERR,"Cannot use fix TMD on massless group"); // rho_start = initial rho // xold = initial x or 0.0 if not in group @@ -155,10 +157,7 @@ void FixTMD::init() int flag = 0; for (int i = 0; i < modify->nfix; i++) { if (strcmp(modify->fix[i]->style,"tmd") == 0) flag = 1; - if (flag && strcmp(modify->fix[i]->style,"nve") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"nvt") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"npt") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"nph") == 0) flag = 2; + if (flag && modify->fix[i]->time_integrate) flag = 2; } if (flag == 2) error->all(FLERR,"Fix tmd must come after integration fixes"); diff --git a/src/molecule.cpp b/src/molecule.cpp index 99b5718133..91557b32ba 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -245,9 +245,11 @@ void Molecule::compute_com() com[1] += x[i][1]*onemass; com[2] += x[i][2]*onemass; } - com[0] /= masstotal; - com[1] /= masstotal; - com[2] /= masstotal; + if (masstotal > 0.0) { + com[0] /= masstotal; + com[1] /= masstotal; + com[2] /= masstotal; + } } memory->destroy(dxcom); From f49064ea5835fd178916b9196f29213487320084 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 20:53:22 -0400 Subject: [PATCH 053/111] add support for dynamic groups to a few more fixes --- src/fix_recenter.cpp | 4 ++++ src/fix_spring.cpp | 12 ++++++++++++ src/fix_spring_rg.cpp | 4 ++++ 3 files changed, 20 insertions(+) diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 7d30c2f865..e10edcb2d9 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -52,6 +52,7 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 1; global_freq = 1; + dynamic_group_allow = 1; /* ---------------------------------------------------------------------- */ @@ -186,6 +187,9 @@ void FixRecenter::initial_integrate(int vflag) // current COM double xcm[3]; + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + group->xcm(igroup,masstotal,xcm); // shift coords by difference between actual COM and requested COM diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 0a4b72f79c..fb2b21b71d 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -47,6 +47,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; extscalar = 1; extvector = 1; + dynamic_group_allow = 1; group2 = NULL; @@ -166,6 +167,10 @@ void FixSpring::post_force(int vflag) void FixSpring::spring_tether() { double xcm[3]; + + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + group->xcm(igroup,masstotal,xcm); // fx,fy,fz = components of k * (r-r0) / masstotal @@ -233,6 +238,13 @@ void FixSpring::spring_tether() void FixSpring::spring_couple() { double xcm[3],xcm2[3]; + + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + + if (group->dynamic[igroup2]) + masstotal2 = group->mass(igroup2); + group->xcm(igroup,masstotal,xcm); group->xcm(igroup2,masstotal2,xcm2); diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 5f27fc1eb5..2fe1c81681 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -42,6 +42,8 @@ FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) : rg0_flag = 0; if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1; else rg0 = force->numeric(FLERR,arg[4]); + + dynamic_group_allow = 1; } /* ---------------------------------------------------------------------- */ @@ -94,6 +96,8 @@ void FixSpringRG::post_force(int vflag) // compute current Rg and center-of-mass double xcm[3]; + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); group->xcm(igroup,masstotal,xcm); double rg = group->gyration(igroup,masstotal,xcm); From 2992c46bdf10fee420d4f5154609e9453ee349be Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Jun 2016 21:17:36 -0400 Subject: [PATCH 054/111] make fix sprint/rg compatible with per atom masses. closes #76 --- src/fix_spring_rg.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 2fe1c81681..b29562cec5 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -125,7 +125,9 @@ void FixSpringRG::post_force(int vflag) dz = unwrap[2] - xcm[2]; term1 = 2.0 * k * (1.0 - rg0/rg); if (masstotal > 0.0) { - massfrac = mass[type[i]]/masstotal; + if (rmass) massfrac = rmass[i]/masstotal; + else massfrac = mass[type[i]]/masstotal; + f[i][0] -= term1*dx*massfrac; f[i][1] -= term1*dy*massfrac; f[i][2] -= term1*dz*massfrac; From 547b1c868f5428d9a3064f4e0769d5f8e609a6bf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Jun 2016 00:25:08 -0400 Subject: [PATCH 055/111] add missing variable declaration --- src/fix_spring_rg.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index b29562cec5..4145e01047 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -112,6 +112,7 @@ void FixSpringRG::post_force(int vflag) int *type = atom->type; imageint *image = atom->image; double *mass = atom->mass; + double *rmass = atom->rmass; int nlocal = atom->nlocal; double massfrac; From f5f45e5ee03c2e2a2577d70fb5f8ed0ceecd8f2a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 15:47:55 -0400 Subject: [PATCH 056/111] plug some memory leaks in USER-TALLY computes that hold per-atom data --- src/USER-TALLY/compute_force_tally.cpp | 1 + src/USER-TALLY/compute_pe_tally.cpp | 1 + src/USER-TALLY/compute_stress_tally.cpp | 1 + 3 files changed, 3 insertions(+) diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 90464d7949..e9ecedd5ab 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -56,6 +56,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : ComputeForceTally::~ComputeForceTally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(fatom); delete[] vector; } diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index f18a58e44e..68c00b6d2e 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -55,6 +55,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : ComputePETally::~ComputePETally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(eatom); delete[] vector; } diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 2a5f522636..2575bd372a 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -56,6 +56,7 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : ComputeStressTally::~ComputeStressTally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(stress); delete[] vector; } From afb6f64578dcb04f40b827e3863671cb397d49f9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 16:26:44 -0400 Subject: [PATCH 057/111] enable exceptions and type info when compiling voro++ --- lib/voronoi/Makefile.32-bit | 2 +- lib/voronoi/Makefile.g++ | 2 +- lib/voronoi/Makefile.mingw32-cross | 2 +- lib/voronoi/Makefile.mingw64-cross | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/voronoi/Makefile.32-bit b/lib/voronoi/Makefile.32-bit index 555948105b..b164085f78 100644 --- a/lib/voronoi/Makefile.32-bit +++ b/lib/voronoi/Makefile.32-bit @@ -4,7 +4,7 @@ CXX = g++ -m32 CXXFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \ - -fno-rtti -fno-exceptions -finline-functions \ + -finline-functions \ -ffast-math -funroll-loops -fstrict-aliasing \ -Wall -W -Wno-uninitialized ARCHIVE = ar diff --git a/lib/voronoi/Makefile.g++ b/lib/voronoi/Makefile.g++ index 5e62c8e75b..1573645046 100644 --- a/lib/voronoi/Makefile.g++ +++ b/lib/voronoi/Makefile.g++ @@ -3,7 +3,7 @@ # ------ SETTINGS ------ CXX = g++ -CXXFLAGS = -O2 -g -fno-rtti -fno-exceptions -fPIC -funroll-loops -Isrc +CXXFLAGS = -O2 -g -fPIC -funroll-loops -Isrc ARCHIVE = ar ARCHFLAG = -rscv SHELL = /bin/sh diff --git a/lib/voronoi/Makefile.mingw32-cross b/lib/voronoi/Makefile.mingw32-cross index 8a930feaef..55d54fd121 100644 --- a/lib/voronoi/Makefile.mingw32-cross +++ b/lib/voronoi/Makefile.mingw32-cross @@ -4,7 +4,7 @@ CXX = i686-w64-mingw32-g++ CXXFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \ - -fno-rtti -fno-exceptions -finline-functions \ + -finline-functions \ -ffast-math -funroll-loops -fstrict-aliasing \ -Wall -W -Wno-uninitialized ARCHIVE = i686-w64-mingw32-ar diff --git a/lib/voronoi/Makefile.mingw64-cross b/lib/voronoi/Makefile.mingw64-cross index 67ed466874..5c821e54ad 100644 --- a/lib/voronoi/Makefile.mingw64-cross +++ b/lib/voronoi/Makefile.mingw64-cross @@ -4,7 +4,7 @@ CXX = x86_64-w64-mingw32-g++ CXXFLAGS = -O2 -march=core2 -mtune=core2 -mpc64 -msse2 \ - -fno-rtti -fno-exceptions -finline-functions \ + -finline-functions \ -ffast-math -funroll-loops -fstrict-aliasing \ -Wall -W -Wno-uninitialized ARCHIVE = x86_64-w64-mingw32-ar From 55b5c0f272fc3bff009f35d8f2159dab1be08862 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 16:27:39 -0400 Subject: [PATCH 058/111] avoid division by zero when setting up parameters for vashishta pair style --- src/MANYBODY/pair_vashishta.cpp | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 7456c08791..aa030540f4 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -488,13 +488,16 @@ void PairVashishta::setup_params() // set cutsq using shortcut to reduce neighbor list for accelerated // calculations. cut must remain unchanged as it is a potential parameter + double tmp_par; for (m = 0; m < nparams; m++) { params[m].cutsq = params[m].cut * params[m].cut; params[m].cutsq2 = params[m].r0 * params[m].r0; - params[m].lam1inv = 1.0/params[m].lambda1; - params[m].lam4inv = 1.0/params[m].lambda4; + tmp_par = params[m].lambda1; + params[m].lam1inv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; + tmp_par = params[m].lambda4; + params[m].lam4inv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; params[m].zizj = params[m].zi*params[m].zj * force->qqr2e; // note that bigd does not have 1/2 factor params[m].mbigd = params[m].bigd; @@ -502,8 +505,9 @@ void PairVashishta::setup_params() params[m].big2b = 2.0*params[m].bigb; params[m].big6w = 6.0*params[m].bigw; - params[m].rcinv = 1.0/params[m].cut; - params[m].rc2inv = 1.0/params[m].cutsq; + tmp_par = params[m].cut; + params[m].rcinv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; + params[m].rc2inv = params[m].rcinv*params[m].rcinv; params[m].rc4inv = params[m].rc2inv*params[m].rc2inv; params[m].rc6inv = params[m].rc2inv*params[m].rc4inv; params[m].rceta = pow(params[m].rcinv,params[m].eta); From 1d2b1e8df81b6a6a3e24db2254037815f04e6bdb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 16:28:41 -0400 Subject: [PATCH 059/111] handle creating a Lattice instance before Force is initialized --- src/lattice.cpp | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/src/lattice.cpp b/src/lattice.cpp index e851760792..484ce27972 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -53,7 +53,16 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (style == NONE) { if (narg != 2) error->all(FLERR,"Illegal lattice command"); - xlattice = ylattice = zlattice = force->numeric(FLERR,arg[1]); + + // Domain defines a default lattice of style "none" with + // spacing 1.0 before the force class is initialized, so + // we have to fall back to using atof() in that case. + + if (force) + xlattice = ylattice = zlattice = force->numeric(FLERR,arg[1]); + else + xlattice = ylattice = zlattice = atof(arg[1]); + if (xlattice <= 0.0) error->all(FLERR,"Illegal lattice command"); return; } From 184dd6c258ea858f769b6b4b22f2e50270e6a8f8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 16:29:30 -0400 Subject: [PATCH 060/111] clean up illegal "upcasting" for non-KOKKOS runs --- src/replicate.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/replicate.cpp b/src/replicate.cpp index 941ec32492..e2ed718f65 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -116,9 +116,9 @@ void Replicate::command(int narg, char **arg) // also set atomKK for Kokkos version of Atom class Atom *old = atom; - if (lmp->kokkos) atom = new AtomKokkos(lmp); + atomKK = NULL; + if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp); else atom = new Atom(lmp); - atomKK = (AtomKokkos*) atom; atom->settings(old); atom->create_avec(old->atom_style,old->avec->nargcopy,old->avec->argcopy,0); From 252eb5ba342461600e764e57f6158cf9362d2132 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Jun 2016 17:23:09 -0400 Subject: [PATCH 061/111] avoid communication on NULL pointers in setups without data --- src/comm.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/comm.cpp b/src/comm.cpp index 825460720d..f29d1bf7df 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -688,6 +688,10 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag, int maxbytes; MPI_Allreduce(&nbytes,&maxbytes,1,MPI_INT,MPI_MAX,world); + // no need to communicate without data + + if (maxbytes == 0) return; + char *buf,*bufcopy; memory->create(buf,maxbytes,"comm:buf"); memory->create(bufcopy,maxbytes,"comm:bufcopy"); From 2d2a54c8d25758ec62d432ebaf8756138b07a07c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Jun 2016 17:55:17 -0400 Subject: [PATCH 062/111] fix uninitialized variable bug in fix spring spotted by coverity --- src/fix_spring.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index fb2b21b71d..88be8a3145 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -277,12 +277,13 @@ void FixSpring::spring_couple() fx2 = fx/masstotal2; fy2 = fy/masstotal2; fz2 = fz/masstotal2; - } + } else fx2 = fy2 = fz2 = 0.0 + if (masstotal > 0.0) { fx /= masstotal; fy /= masstotal; fz /= masstotal; - } + } else fx = fy = fz = 0.0 // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal From 1a52795e1d14a72bae8764d0f06ba13401dc85e3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Jun 2016 23:17:05 +0000 Subject: [PATCH 063/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15108 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/tutorial_drude.txt | 23 ++++++++++++++++++++--- doc/html/searchindex.js | 2 +- doc/html/tutorial_drude.html | 25 ++++++++++++++++++------- doc/src/tutorial_drude.txt | 12 ++++++++++-- 4 files changed, 49 insertions(+), 13 deletions(-) diff --git a/doc/html/_sources/tutorial_drude.txt b/doc/html/_sources/tutorial_drude.txt index 4a72b8d157..494cd9f153 100644 --- a/doc/html/_sources/tutorial_drude.txt +++ b/doc/html/_sources/tutorial_drude.txt @@ -1,3 +1,18 @@ +Tutorial for Thermalized Drude oscillators in LAMMPS +==================================================== + +This tutorial explains how to use Drude oscillators in LAMMPS to +simulate polarizable systems using the USER-DRUDE package. As an +illustration, the input files for a simulation of 250 phenol molecules +are documented. First of all, LAMMPS has to be compiled with the +USER-DRUDE package activated. Then, the data file and input scripts +have to be modified to include the Drude dipoles and how to handle +them. + + +---------- + + **Overview of Drude induced dipoles** Polarizable atoms acquire an induced electric dipole moment under the @@ -29,9 +44,10 @@ charge, and force constant can be chosen following different strategies, as in the following examples of polarizable force fields: -#. :ref:`Lamoureux and Roux ` suggest adopting a global half-stiffness, :math:`K_D` = 500 kcal/(mol Ang :math:`{}^2`) - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol Ang :math:`{}^2`) - for all types of core-Drude bond, a global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field. -#. Alternately :ref:`Schroeder and Steinhauser ` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K. -#. In both these force fields hydrogen atoms are treated as non-polarizable. +* :ref:`Lamoureux and Roux ` suggest adopting a global half-stiffness, :math:`K_D` = 500 kcal/(mol Ang :math:`{}^2`) - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol Ang :math:`{}^2`) - for all types of core-Drude bond, a global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field. +* Alternately :ref:`Schroeder and Steinhauser ` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K. +* In both these force fields hydrogen atoms are treated as non-polarizable. + The motion of of the Drude particles can be calculated by minimizing the energy of the induced dipoles at each timestep, by an interative, self-consistent procedure. The Drude particles can be massless and @@ -58,6 +74,7 @@ important features: #. The possibility to thermostat the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles. #. The Drude dipoles on covalently bonded atoms interact too strongly due to the short distances, so an atom may capture the Drude particle (shell) of a neighbor, or the induced dipoles within the same molecule may align too much. To avoid this, damping at short of the interactions between the point charges composing the induced dipole can be done by :ref:`Thole ` functions. + ---------- diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 1611a0bbab..ac2892623f 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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channel:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,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,237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,22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,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:[],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,444,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,231,236,238,241,242,244,247,252,265,303,304,313,315,331,343,348,352,353,354,356,372,383,385,389,403,417,421,448,454,472,483,487,488,490,491,495,498,499,507,508,517,518],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,331,333,335,338,342,343,362,373,376,397,409,410,411,424,438,452,453,457,459,461,485,487,488,489,490,498,499,500,504,507,517,518],integer:[3,490],integr:[],integral:[298,445],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,245,451,490],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,241,248,258,267,269,274,312,315,316,331,339,343,345,346,507,508,516],intensiv:[66,209,508],intepol:517,inter:[14,18,43,64,65,158,181,182,202,227,252,254,268,307,315,373,384,395,500,511,517,520,522],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,322,323,331,332,338,343,347,348,349,352,353,358,359,360,361,363,365,367,373,374,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,453,454,455,457,459,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,485,488,490,492,494,495,499,500,502,507,508,511,520],interatom:[3,4,7,9,10,178,202,268,340,341,390,395,412,414,422,438,441,460,474,517],intercept:130,interchang:6,interconnect:18,interconvert:414,intereract:40,interesect:352,interest:[1,5,7,8,9,11,13,76,177,298,338,341,374,413,436,452,453,488,517],interf:[389,512],interfac:[],interfer:[12,269,391],interg:[6,511],intergr:499,interi:436,interior:[3,6,42,352,493],interlac:438,interleav:[6,178,498],intermedi:[6,12,62,205,268,296,366,384,488,489,498,502],intermix:485,intermolecular:[154,391],intern:[],internal:[3,205,211,301,517],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:251,interpenetr:438,interpentr:[464,465,467],interpol:[6,15,38,57,111,198,205,206,215,240,255,296,373,374,384,395,443,445,453,466,472,473],interpret:[2,6,11,205,221,418,462,485,488,504,517],interrupt:305,intersect:[3,6,130,206,352,354,493],intersert:352,interspers:382,interstiti:[176,441],intertia:[3,104],interv:[3,6,100,204,219,252,269,305,310,311,323,460,466,485,504,517],intestieti:130,intial:[6,389,391],intiial:[42,495],intiti:[3,330],intra:315,intra_energi:244,intramolecular:[29,154,244],introduc:[6,9,101,118,205,237,269,305,310,315,366,373,390,405,414,426,430,434,471,504,517],introduct:[],intuit:376,inv:[130,177,316],invalid:[3,12,76,98,181,283,384,435,436,492],invari:[118,145,150,152],invent:318,invers:[],inverse:511,invert:[1,6,182,297],invis:352,invoc:[176,227,389,457,459,488],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,241,242,243,244,245,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,318,320,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,357,359,360,362,363,366,368,372,373,374,375,376,382,384,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,422,426,427,428,429,430,431,432,433,434,435,436,439,443,444,446,447,449,454,455,457,459,461,462,471,472,473,474,475,476,478,479,480,481,482,484,487,488,489,491,493,495,498,499,501,502,504,507,508,511,517,518],invokd:3,invoke:[3,12,17],involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,225,244,255,300,303,308,331,373,381,382,384,394,411,417,424,471,473,475,486,487,493,495,499,504,505],ioff:[383,490],ion:[6,7,9,160,295,328,343,374,395,406,415,416,438,441,460,470,475,482,490,511],ionic:[6,9,396,398,406,414,415,447,460,511],ioniz:[404,414],ionocoval:9,iparam:[3,226],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,42,61,224,228,230,269,315],irrelev:446,irrespect:[435,436],irrevers:234,is_act: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:[7,42,65,180,224,244,376,490,492,494],rectilinear:[130,177,203],rector:54,recurs:[42,224,395,477],recust:42,recv:487,red:[2,205,206,227,298],redefin:[3,492,498,517],redirect:12,redo:12,reduc:[],reduct:[18,19,129,130,177,267,305,373],redund:415,ree:465,reed:[267,305],rees:[7,9,13],ref:[340,341,381],refactor:6,refer:[],referenc:[3,6,12,66,72,76,126,131,202,203,209,219,244,304,345,374,405,420,446,454,488,508,517],reflect:[],refman:9,reformat:7,refresh:215,reg:493,regard:[6,62,266,318,319,324,449,453],regardless:[15,76,178,181,201,221,230,252,269,271,272,273,275,276,277,302,315,325,331,389,487,493,500],regim:[6,339,346,406,499],region:[],region_spher:8,region_styl:352,regist:[8,128,154,327],regoin:6,regress:517,regspher:178,regstrip:354,regul:6,regular:[1,3,42,65,97,176,180,202,205,216,224,244,304,343,374,406,424,487,490,492,494],reigon:517,reinhardt:[340,341],reject:[178,227,452,505],rel:[1,6,14,27,36,42,62,76,101,114,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,244,250,253,265,266,292,296,301,310,312,313,320,328,331,333,338,339,343,350,354,373,374,382,414,417,418,435,436,438,454,481,491,499,504,508,511,518],relat:[],relationship:[6,240,306,356,373,460,481,511,517],relax:[],releas:[0,5,7,8,13,225],relect:[3,443],reles:43,relev:[2,6,12,42,83,86,123,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,238,241,243,244,245,248,249,255,256,257,259,260,261,262,263,265,266,268,278,279,280,281,282,283,284,285,286,287,288,291,295,299,300,301,303,304,307,309,311,312,313,316,317,318,320,325,329,331,332,333,338,339,342,343,344,345,346,347,348,349,350,351,353,354,373,378,382,392,393,397,403,405,406,408,409,411,414,416,417,418,419,420,425,427,428,429,431,432,433,435,436,443,444,445,449,454,462,469,472,480,481,482,487,503,518],reli:[3,12,307,414,453,482,490,500],reloc:12,remain:[7,12,33,37,42,51,56,62,76,96,115,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,252,253,260,269,270,275,276,277,289,290,292,294,299,300,323,331,334,335,336,342,343,354,356,364,367,383,395,414,421,434,441,443,470,485,490,491,495,500,502,504,508,511,512,517,518],remaina:395,remaind:[9,178,202,231,301,331,344,475,490],remap:[3,6,12,62,64,76,161,178,201,230,250,266,292,373,490,491,492],remedi:[6,511],rememb:[2,512],remot:512,remov:[2,3,6,8,13,55,76,77,82,101,118,126,128,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,241,252,253,258,261,265,267,269,275,276,277,289,290,292,294,300,306,315,316,318,331,334,335,336,338,354,373,384,408,436,441,490,493,501,502,512,517,518],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,355,501,512],render:[12,13,202,205,206],rendon:[269,270],reneighbor:[3,8,12,40,60,76,224,244,331,344,354,409,507,508],renssela:300,renumb:76,reorder:[3,12,40,487],rep:505,repeat:[2,6,205,206,227,228,244,324,376,395,473,475,477,485,504],repeatedli:2,repel:250,repes:202,replac:[2,3,6,11,12,42,66,98,99,129,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,252,274,303,304,310,312,391,405,428,445,472,491,492,497,498,508,517,518,520,522],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:343,repres:[1,3,6,8,9,12,15,41,42,43,62,71,76,99,125,128,190,198,202,203,205,218,219,220,221,222,228,234,245,247,252,255,269,298,300,302,310,315,316,320,328,343,345,352,374,384,390,395,417,424,434,435,436,438,439,440,447,450,452,453,476,477,485,487,490,500,502,505,511,517,520],represent:[3,6,8,9,60,62,146,180,202,245,246,298,343,395,414,417,441,454,490,493,511],reprocess:495,reproduc:[3,269,349,405,412,418],repul:438,repuls:[6,7,36,41,46,47,120,250,306,348,349,352,391,395,403,405,409,414,418,420,434,438,442,460,469,475,478,481,482,500],reqir:[306,308],request:[3,6,8,12,42,114,181,198,202,249,255,313,319,331,333,371,373,443,452,453,485,495,500,504,512,517,518,520],requir:[],rerun:[],rescal:[],research:[5,7,89,90,239,255,259,319,441,485,504],resembl:[310,512],resepct:6,reserv:[12,249,511],reservoir:[100,237,244,248,252,343],reset:[],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[],resid:13,residu:249,residue1:385,resist:[6,249],resolut:[220,460,472],resolv:[228,298,331,436,512],resort:3,resourc:[7,390,412],respa:[3,16,235,249,269,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,498,499,510,517],respecifi:441,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,44,46,47,48,49,50,52,54,55,57,62,75,76,96,98,107,108,124,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,247,250,252,253,255,269,271,272,273,274,275,276,277,278,279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ater:[],watkin:195,wave:[7,9,41,214,267,309,350,392,414],wavefunct:[392,414],wavelength:[130,177],wavepacket:[41,392,414,490],wavevector:297,wbodi:92,weak:[10,101,306],web:[1,4,8,10,14,15,16,17,402],webb:215,weber:[3,5,7,9,15,97,154,413,440,450,470,471,478,502],websit:[8,452,453],weckner:449,weight:[],welcom:488,well:[1,3,6,7,8,9,11,12,13,15,16,17,18,27,41,52,71,76,101,118,124,153,156,164,178,187,205,206,212,216,218,222,224,225,226,228,231,236,244,248,252,255,259,261,266,269,274,285,291,301,302,315,317,325,338,341,349,382,384,389,394,416,417,420,421,422,435,436,438,441,454,462,473,474,475,488,490,492,494,499,504,509,511,512,516,521],wennberg:373,went:[3,11],were:[3,5,6,7,9,11,12,13,15,16,19,34,42,43,53,57,63,75,76,114,118,121,124,128,155,158,178,181,182,194,202,205,206,209,212,218,221,222,224,230,236,241,248,249,283,292,316,349,350,354,365,373,386,388,391,414,418,421,425,449,453,472,485,487,488,490,491,492,493,495,497,505,508,512,517,518,521,522],weren:495,western:9,westview:481,what:[],whatev:[8,12,14,15,120,125,128,129,131,205,206,210,211,228,269,302,304,349,376,381,382,384,389,401,403,441,452,453,504,511,517],wheat:206,whelan:177,when:[0,1,2,3,4,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,62,64,65,66,68,73,76,77,84,88,95,97,101,102,114,115,116,118,119,121,124,125,128,129,131,154,155,156,161,165,166,168,174,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,202,203,204,205,206,207,209,210,211,212,213,214,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,235,236,238,240,241,242,243,244,246,247,249,252,255,256,258,259,264,269,270,271,272,273,274,275,276,277,278,279,283,286,287,289,290,292,294,296,300,301,302,303,304,305,307,308,309,310,314,315,316,317,318,320,328,329,331,332,333,338,339,343,344,345,346,348,349,350,351,352,353,354,355,356,357,359,360,362,363,364,366,367,368,370,371,372,373,374,376,380,381,382,383,384,385,386,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,443,444,445,446,447,449,450,452,453,454,455,461,462,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,492,493,494,495,496,497,498,499,500,501,502,504,505,507,508,509,510,512,516,517,518,520,522],whenev:[0,8,12,14,76,206,217,315,376,420,488,499,503,517,522],whenth:3,where:[1,3,6,8,9,10,11,12,14,15,18,21,23,24,25,26,27,28,29,32,35,36,37,40,41,42,44,48,49,50,52,56,64,66,68,69,70,72,73,74,75,76,78,80,84,85,86,87,89,91,92,93,94,96,97,98,99,101,102,103,104,105,106,107,108,109,115,117,120,124,125,126,127,128,129,130,131,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,173,175,177,179,181,182,185,187,197,201,202,205,206,209,210,211,212,213,218,219,223,224,227,228,230,231,235,236,237,239,241,242,244,245,246,247,248,250,252,253,254,255,258,259,262,264,266,267,269,270,274,283,287,295,296,297,298,301,303,304,305,308,310,315,316,317,318,320,324,325,328,330,333,334,335,336,339,340,341,343,346,347,348,349,351,352,353,354,357,359,360,361,362,363,366,367,368,371,374,376,381,382,383,384,385,386,389,390,391,394,395,396,398,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,426,430,435,436,437,438,439,440,441,443,446,447,449,450,451,452,453,454,460,461,464,467,468,469,470,471,472,473,474,475,478,481,482,484,485,487,488,489,490,492,493,494,495,497,499,500,502,504,505,506,507,508,511,516,517,518,520,522],wherea:[6,11,101,216,245,269,306,338,343,511],wherebi:307,wherev:248,whether:[6,8,11,12,17,40,41,55,62,64,66,75,76,113,119,121,154,165,166,198,205,206,208,209,210,211,218,222,225,226,227,228,229,230,234,241,244,253,266,269,274,304,318,331,339,345,346,354,356,371,373,374,383,387,389,398,400,404,419,421,425,435,436,438,443,453,460,470,485,488,490,491,493,495,502,503,504,507,517,518],which:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,28,29,32,33,37,38,39,40,41,42,43,45,46,47,48,51,52,54,55,56,57,59,61,62,64,66,67,68,70,71,73,75,76,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,94,96,97,98,99,100,102,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,128,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,189,190,191,192,195,197,198,201,202,203,205,206,207,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,258,259,263,264,266,267,268,269,270,271,272,273,274,275,276,277,279,281,283,284,285,287,288,289,290,291,292,293,294,296,297,298,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,320,321,322,323,325,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,348,349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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,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202,channel:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,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,227,229,237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,21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25,226,231,236,238,241,242,244,247,252,265,303,304,313,315,331,343,348,352,353,354,356,372,383,385,389,403,417,421,448,454,472,483,487,488,490,491,495,498,499,507,508,517,518],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,331,333,335,338,342,343,362,373,376,397,409,410,411,424,438,452,453,457,459,461,485,487,488,489,490,498,499,500,504,507,517,518],integer:[3,490],integr:[],integral:[298,445],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,245,451,490],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,241,248,258,267,269,274,312,315,316,331,339,343,345,346,507,508,516],intensiv:[66,209,508],intepol:517,inter:[14,18,43,64,65,158,181,182,202,227,252,254,268,307,315,373,384,395,500,511,517,520,522],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,322,323,331,332,338,343,347,348,349,352,353,358,359,360,361,363,365,367,373,374,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,453,454,455,457,459,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,485,488,490,492,494,495,499,500,502,507,508,511,520],interatom:[3,4,7,9,10,178,202,268,340,341,390,395,412,414,422,438,441,460,474,517],intercept:130,interchang:6,interconnect:18,interconvert:414,intereract:40,interesect:352,interest:[1,5,7,8,9,11,13,76,177,298,338,341,374,413,436,452,453,488,517],interf:[389,512],interfac:[],interfer:[12,269,391],interg:[6,511],intergr:499,interi:436,interior:[3,6,42,352,493],interlac:438,interleav:[6,178,498],intermedi:[6,12,62,205,268,296,366,384,488,489,498,502],intermix:485,intermolecular:[154,391],intern:[],internal:[3,205,211,301,517],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:251,interpenetr:438,interpentr:[464,465,467],interpol:[6,15,38,57,111,198,205,206,215,240,255,296,373,374,384,395,443,445,453,466,472,473],interpret:[2,6,11,205,221,418,462,485,488,504,517],interrupt:305,intersect:[3,6,130,206,352,354,493],intersert:352,interspers:382,interstiti:[176,441],intertia:[3,104],interv:[3,6,100,204,219,252,269,305,310,311,323,460,466,485,504,517],intestieti:130,intial:[6,389,391],intiial:[42,495],intiti:[3,330],intra:315,intra_energi:244,intramolecular:[29,154,244],introduc:[6,9,101,118,205,237,269,305,310,315,366,373,390,405,414,426,430,434,471,504,517],introduct:[],intuit:376,inv:[130,177,316],invalid:[3,12,76,98,181,283,384,435,436,492],invari:[118,145,150,152],invent:318,invers:[],inverse:511,invert:[1,6,182,297],invis:352,invoc:[176,227,389,457,459,488],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,241,242,243,244,245,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,318,320,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,357,359,360,362,363,366,368,372,373,374,375,376,382,384,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,422,426,427,428,429,430,431,432,433,434,435,436,439,443,444,446,447,449,454,455,457,459,461,462,471,472,473,474,475,476,478,479,480,481,482,484,487,488,489,491,493,495,498,499,501,502,504,507,508,511,517,518],invokd:3,invoke:[3,12,17],involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,225,244,255,300,303,308,331,373,381,382,384,394,411,417,424,471,473,475,486,487,493,495,499,504,505],ioff:[383,490],ion:[6,7,9,160,295,328,343,374,395,406,415,416,438,441,460,470,475,482,490,511],ionic:[6,9,396,398,406,414,415,447,460,511],ioniz:[404,414],ionocoval:9,iparam:[3,226],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,42,61,224,228,230,269,315],irrelev:446,irrespect:[435,436],irre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:485,tdrude:[163,234,253,511],teal:206,tech:[7,13],technic:[6,7,9,255,308,331,453],techniqu:[6,7,9,96,209,228,267,305,315,347,350,374,443,472,511],technolgi:9,technolog:[9,14,19,249],tediou:304,tell:[2,6,11,12,37,56,197,209,297,367,385,452,453,470,488,490,492,511],telsa:17,temeperatur:11,temp:[],temp_drud:511,temp_eff:108,tempcom:[156,157,171],temper:[],temperar:298,temperatur:[],temperature_definit:215,tempfix:505,templ:[7,9,18],templat:[3,8,13,17,19,41,178,179,181,231,244,301,315,318,383,490],templeton2010:215,templeton2011:215,templeton:[9,215],tempor:245,temporari:[2,3,497],temporarili:[198,314,503,504],ten:14,tend:[29,269,296],tensil:[7,230],tensor:[3,6,8,66,91,92,98,99,100,104,117,124,139,142,143,144,145,148,149,150,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,228,255,258,269,270,274,300,302,315,346,373,374,383,414,435,436,441,457,459,508,517],tenth:[139,210,372],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,64,96,97,98,100,122,124,153,154,156,157,166,171,172,185,186,187,198,206,210,211,217,219,221,222,230,236,237,245,246,247,252,253,254,255,268,269,270,271,272,273,274,275,276,277,289,290,292,294,298,302,305,314,315,329,334,335,336,343,345,347,349,357,358,368,373,382,385,390,391,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,426,430,433,434,435,436,438,439,440,441,443,444,447,454,460,469,471,473,474,475,478,481,499,500,502,508,511],termin:[130,269,382,384,457,459,489,498],termostat:335,terrel:381,terri:7,tersoff:[],tersoff_1:[473,474,475],tersoff_2:[473,474,475],tersoff_mod:474,tertiari:190,tessel:[9,176],test:[],test_descriptor_str:3,testf:198,testu:198,tether:[6,313,320,328,330,341,416],tetot:[9,460],tex:8,texa:449,texas_holdem:314,text:[2,3,4,6,7,8,12,13,38,42,57,198,202,203,205,206,209,215,218,219,220,221,222,224,229,240,249,303,342,343,355,374,376,384,412,415,425,438,445,461,472,486,490,491,507,512,517,519,520],textur:17,tfac_insert:244,tfactor:[3,206],tfinal:517,tfix:314,tflag:205,tfmc:[],th4:177,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,60,61,62,64,66,72,76,81,95,97,101,116,118,120,124,127,128,131,153,176,179,180,181,187,198,201,202,204,206,209,214,216,218,221,222,224,225,226,227,228,230,231,232,235,240,241,244,245,246,247,250,251,252,255,267,296,297,301,302,303,305,306,308,310,313,314,315,316,319,320,321,327,328,329,331,335,336,338,339,343,346,347,348,349,350,351,352,353,354,356,373,374,380,381,382,383,384,385,386,389,391,394,395,396,398,399,400,412,414,417,418,424,435,436,438,443,445,452,453,454,460,462,469,470,471,472,475,477,479,481,482,485,486,487,488,490,491,492,493,494,495,498,499,502,504,505,507,517,518,520],thank:[249,473,475],thb:453,thb_cutoff:453,thb_cutoff_sq:[452,453],thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,60,62,64,66,67,70,72,75,76,79,80,87,88,91,93,96,97,98,99,100,104,114,115,117,119,120,124,126,127,128,129,131,152,155,156,158,160,161,164,165,171,173,175,176,178,180,181,182,184,185,187,188,189,190,192,193,195,196,197,198,202,203,205,206,209,210,211,212,214,217,218,219,221,222,223,224,225,226,227,228,230,231,236,238,243,244,245,247,248,249,252,253,255,258,266,269,271,272,273,274,275,276,277,278,279,280,281,287,289,290,292,294,300,301,302,303,304,306,307,314,315,316,317,318,331,332,335,338,342,343,345,346,349,351,352,354,355,356,357,359,360,361,362,363,366,367,368,371,373,374,376,378,379,381,382,383,384,385,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,444,446,447,449,450,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,486,488,490,491,492,493,494,495,499,500,502,503,508,511,512,517,520,521],them:[1,2,3,6,7,8,9,11,12,13,14,17,40,41,42,55,62,76,100,114,119,126,129,131,154,180,185,202,205,206,207,217,218,219,221,222,224,227,228,230,241,249,252,253,261,265,269,271,272,273,274,275,276,277,289,290,294,296,302,304,312,313,314,315,318,331,334,335,336,338,342,343,345,349,350,351,353,354,357,374,376,378,383,384,385,389,390,395,402,412,415,417,421,424,443,454,462,476,477,485,488,490,497,502,505,511,512,517,518],themselv:[6,9,11,181,210,211,224,253,373,374,384,386,390,395,405,412,434,438,439,440,461,517],theor:338,theorem:[245,252,319,395,410],theoret:[116,249,305,471],theori:[3,6,9,12,41,152,215,229,246,269,297,373,374,395,441,481,504],thereaft:[76,260,299,315,339,346,488],therebi:[344,435,436],therefor:[3,6,12,67,96,163,234,237,244,253,255,318,338,374,407,451,453,471,476,499,511],therein:[6,438],thereof:96,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,66,121,488,508],thermo_press:[66,124,228,234,269,271,272,273,274,275,276,277,302,507,508,511],thermo_styl:[],thermo_temp:[66,124,155,227,228,244,269,271,272,273,274,275,276,277,289,290,292,294,297,302,334,335,336,507,508,511],thermoberendsen:6,thermochem:516,thermochemistri:414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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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\ No newline at end of file diff --git a/doc/html/tutorial_drude.html b/doc/html/tutorial_drude.html index cea0dba9aa..e414d5d007 100644 --- a/doc/html/tutorial_drude.html +++ b/doc/html/tutorial_drude.html @@ -8,7 +8,7 @@ - <no title> — LAMMPS documentation + Tutorial for Thermalized Drude oscillators in LAMMPS — LAMMPS documentation @@ -109,7 +109,7 @@

    • Docs »
      • -
    • <no title>
      • +
    • Tutorial for Thermalized Drude oscillators in LAMMPS
    • @@ -124,7 +124,17 @@
      -

      Overview of Drude induced dipoles

      +
      +

      Tutorial for Thermalized Drude oscillators in LAMMPS

      +

      This tutorial explains how to use Drude oscillators in LAMMPS to +simulate polarizable systems using the USER-DRUDE package. As an +illustration, the input files for a simulation of 250 phenol molecules +are documented. First of all, LAMMPS has to be compiled with the +USER-DRUDE package activated. Then, the data file and input scripts +have to be modified to include the Drude dipoles and how to handle +them.

      +
      +

      Overview of Drude induced dipoles

      Polarizable atoms acquire an induced electric dipole moment under the action of an external electric field, for example the electric field created by the surrounding particles. Drude oscillators represent @@ -148,12 +158,12 @@ particle remains close ot the core. The values of Drude mass, Drude charge, and force constant can be chosen following different strategies, as in the following examples of polarizable force fields:

      -
        +
        • Lamoureux and Roux suggest adopting a global half-stiffness, \(K_D\) = 500 kcal/(mol Ang \({}^2\)) - which corresponds to a force constant \(k_D\) = 4184 kJ/(mol Ang \({}^2\)) - for all types of core-Drude bond, a global mass \(m_D\) = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field.
        • Alternately Schroeder and Steinhauser suggest adopting a global charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.
          • -
      -

      #. In both these force fields hydrogen atoms are treated as non-polarizable. -The motion of of the Drude particles can be calculated by minimizing +

    • In both these force fields hydrogen atoms are treated as non-polarizable.
      • +
    +

    The motion of of the Drude particles can be calculated by minimizing the energy of the induced dipoles at each timestep, by an interative, self-consistent procedure. The Drude particles can be massless and therefore do not contribute to the kinetic energy. However, the @@ -505,6 +515,7 @@ review the different thermostats and ensemble combinations.

    (Noskov) Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).

    (SWM4-NDP) Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys Let, 418, 245-249 (2006)

    + diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index 987f580aa2..3ab8afcae3 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -5,6 +5,14 @@ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } }); +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + Tutorial for Thermalized Drude oscillators in LAMMPS :h3 This tutorial explains how to use Drude oscillators in LAMMPS to @@ -52,14 +60,14 @@ constant \(k_D\) = 4184 kJ/(mol Ang \(\{\}^2\)) - for all types of \ core-Drude bond, a global mass \(m_D\) = 0.4 g/mol (or u) for all types \ of Drude particles, and to calculate the Drude charges for individual \ atom types from the atom polarizabilities using equation (1). This \ -choice is followed in the polarizable CHARMM force field. :olb,l +choice is followed in the polarizable CHARMM force field. :ulb,l Alternately "Schroeder and Steinhauser"_#Schroeder suggest adopting a global \ charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u) \ for all Drude particles, and to calculate the force constant for each \ type of core-Drude bond from equation (1). The timesteps used by these \ authors are between 0.5 and 2 fs, with the degrees of freedom of the \ Drude oscillators kept cold at 1 K. :l -In both these force fields hydrogen atoms are treated as non-polarizable. :ole,l +In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l The motion of of the Drude particles can be calculated by minimizing From 0f3e4182e8691e273df3d217ec54ef2a1c8dd280 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Jun 2016 23:21:39 +0000 Subject: [PATCH 064/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/ASPHERE/fix_npt_asphere.cpp | 4 +-- src/ASPHERE/fix_nvt_asphere.cpp | 2 +- src/BODY/fix_nph_body.cpp | 4 +-- src/BODY/fix_npt_body.cpp | 4 +-- src/BODY/fix_nvt_body.cpp | 2 +- src/KOKKOS/fix_nph_kokkos.cpp | 4 +-- src/KOKKOS/fix_npt_kokkos.cpp | 4 +-- src/KOKKOS/fix_nvt_kokkos.cpp | 2 +- src/MANYBODY/pair_vashishta.cpp | 12 ++++++--- src/MC/fix_tfmc.cpp | 9 ++++--- src/RIGID/fix_rigid_nh.cpp | 10 +++---- src/RIGID/fix_rigid_nh.h | 2 +- src/RIGID/fix_rigid_nh_small.cpp | 10 +++---- src/RIGID/fix_rigid_nh_small.h | 2 +- src/SHOCK/fix_nphug.cpp | 4 +-- src/USER-EFF/fix_nph_eff.cpp | 4 +-- src/USER-EFF/fix_npt_eff.cpp | 4 +-- src/USER-EFF/fix_nvt_eff.cpp | 2 +- src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +- src/USER-INTEL/fix_npt_intel.cpp | 4 +-- src/USER-INTEL/fix_nvt_intel.cpp | 2 +- src/USER-INTEL/fix_nvt_sllod_intel.cpp | 2 +- src/USER-OMP/fix_nph_asphere_omp.cpp | 4 +-- src/USER-OMP/fix_nph_omp.cpp | 4 +-- src/USER-OMP/fix_nph_sphere_omp.cpp | 4 +-- src/USER-OMP/fix_nphug_omp.cpp | 4 +-- src/USER-OMP/fix_npt_asphere_omp.cpp | 4 +-- src/USER-OMP/fix_npt_omp.cpp | 4 +-- src/USER-OMP/fix_npt_sphere_omp.cpp | 4 +-- src/USER-OMP/fix_nvt_asphere_omp.cpp | 2 +- src/USER-OMP/fix_nvt_omp.cpp | 2 +- src/USER-OMP/fix_nvt_sllod_omp.cpp | 2 +- src/USER-OMP/fix_nvt_sphere_omp.cpp | 2 +- src/USER-REAXC/pair_reax_c.cpp | 1 - src/USER-TALLY/compute_force_tally.cpp | 1 + src/USER-TALLY/compute_pe_tally.cpp | 1 + src/USER-TALLY/compute_stress_tally.cpp | 1 + src/comm.cpp | 4 +++ src/compute_angmom_chunk.cpp | 8 +++--- src/compute_dipole_chunk.cpp | 9 ++++--- src/compute_gyration.cpp | 5 ++-- src/compute_gyration_chunk.cpp | 20 +++++++++----- src/compute_inertia_chunk.cpp | 8 +++--- src/compute_msd_chunk.cpp | 8 +++--- src/compute_omega_chunk.cpp | 8 +++--- src/compute_temp_chunk.cpp | 30 ++++++++++++--------- src/compute_temp_region.cpp | 2 +- src/compute_torque_chunk.cpp | 8 +++--- src/compute_vcm_chunk.cpp | 8 +++--- src/fix_deprecated.cpp | 4 +-- src/fix_heat.cpp | 2 ++ src/fix_nh.cpp | 17 +++++++----- src/fix_nh.h | 2 +- src/fix_nph.cpp | 4 +-- src/fix_nph_sphere.cpp | 4 +-- src/fix_npt.cpp | 4 +-- src/fix_npt_sphere.cpp | 4 +-- src/fix_nvt.cpp | 2 +- src/fix_nvt_sllod.cpp | 2 +- src/fix_nvt_sphere.cpp | 2 +- src/fix_recenter.cpp | 4 +++ src/fix_spring.cpp | 36 ++++++++++++++++++------- src/fix_spring_rg.cpp | 17 +++++++++--- src/fix_tmd.cpp | 7 +++-- src/lattice.cpp | 11 +++++++- src/molecule.cpp | 8 +++--- src/replicate.cpp | 4 +-- 67 files changed, 236 insertions(+), 151 deletions(-) diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 2625bc6391..205630376a 100755 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -46,7 +46,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 5b8b943ab4..f43e731c23 100755 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -45,5 +45,5 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1808b9ade8..99e33a3d22 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -50,7 +50,7 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -68,5 +68,5 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 17014ba17c..077a7babd4 100755 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -50,7 +50,7 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -68,5 +68,5 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index d6601f4966..464f42eae9 100755 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -49,5 +49,5 @@ FixNVTBody::FixNVTBody(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 350832a3d7..f3f7c271d6 100755 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -47,7 +47,7 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -65,7 +65,7 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : newarg[3] = this->id_temp; this->modify->add_compute(4,newarg); delete [] newarg; - this->pflag = 1; + this->pcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 3832fb3e57..bbc26b8e88 100755 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -47,7 +47,7 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -65,7 +65,7 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : newarg[3] = this->id_temp; this->modify->add_compute(4,newarg); delete [] newarg; - this->pflag = 1; + this->pcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index bf6ce0de2b..c479251c33 100755 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -46,7 +46,7 @@ FixNVTKokkos::FixNVTKokkos(LAMMPS *lmp, int narg, char **arg) : this->modify->add_compute(3,newarg); delete [] newarg; - this->tflag = 1; + this->tcomputeflag = 1; } namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 7456c08791..aa030540f4 100755 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -488,13 +488,16 @@ void PairVashishta::setup_params() // set cutsq using shortcut to reduce neighbor list for accelerated // calculations. cut must remain unchanged as it is a potential parameter + double tmp_par; for (m = 0; m < nparams; m++) { params[m].cutsq = params[m].cut * params[m].cut; params[m].cutsq2 = params[m].r0 * params[m].r0; - params[m].lam1inv = 1.0/params[m].lambda1; - params[m].lam4inv = 1.0/params[m].lambda4; + tmp_par = params[m].lambda1; + params[m].lam1inv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; + tmp_par = params[m].lambda4; + params[m].lam4inv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; params[m].zizj = params[m].zi*params[m].zj * force->qqr2e; // note that bigd does not have 1/2 factor params[m].mbigd = params[m].bigd; @@ -502,8 +505,9 @@ void PairVashishta::setup_params() params[m].big2b = 2.0*params[m].bigb; params[m].big6w = 6.0*params[m].bigw; - params[m].rcinv = 1.0/params[m].cut; - params[m].rc2inv = 1.0/params[m].cutsq; + tmp_par = params[m].cut; + params[m].rcinv = (tmp_par == 0.0) ? 0.0 : 1.0/tmp_par; + params[m].rc2inv = params[m].rcinv*params[m].rcinv; params[m].rc4inv = params[m].rc2inv*params[m].rc2inv; params[m].rc6inv = params[m].rc2inv*params[m].rc4inv; params[m].rceta = pow(params[m].rcinv,params[m].eta); diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index eea0a0bf31..8ce1308694 100755 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -229,9 +229,12 @@ void FixTFMC::initial_integrate(int vflag) // zero com motion if (comflag == 1 && group->count(igroup) != 0) { MPI_Allreduce(xcm_d,xcm_dall,3,MPI_DOUBLE,MPI_SUM,world); - xcm_dall[0] /= masstotal; - xcm_dall[1] /= masstotal; - xcm_dall[2] /= masstotal; + if (masstotal > 0.0) { + xcm_dall[0] /= masstotal; + xcm_dall[1] /= masstotal; + xcm_dall[2] /= masstotal; + } else xcm_dall[0] = xcm_dall[1] = xcm_dall[2] = 0.0; + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { if (xflag) x[i][0] -= xcm_dall[0]; diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 5db799e9f0..a2c6c338b7 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -148,6 +148,9 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; + + id_temp = NULL; + id_press = NULL; } /* ---------------------------------------------------------------------- */ @@ -162,10 +165,8 @@ FixRigidNH::~FixRigidNH() if (rfix) delete [] rfix; - if (tcomputeflag) { - modify->delete_compute(id_temp); - delete [] id_temp; - } + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; // delete pressure if fix created it @@ -1265,7 +1266,6 @@ int FixRigidNH::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); if (tcomputeflag) { modify->delete_compute(id_temp); tcomputeflag = 0; diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index 684579b8af..08208e5aac 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -69,7 +69,7 @@ class FixRigidNH : public FixRigid { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tcomputeflag,pcomputeflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external void couple(); void remap(); diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5708bb6602..d8ec174f72 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -163,6 +163,9 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; + + id_temp = NULL; + id_press = NULL; } /* ---------------------------------------------------------------------- */ @@ -176,10 +179,8 @@ FixRigidNHSmall::~FixRigidNHSmall() if (rfix) delete [] rfix; - if (tcomputeflag) { - modify->delete_compute(id_temp); - delete [] id_temp; - } + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; // delete pressure if fix created it @@ -1374,7 +1375,6 @@ int FixRigidNHSmall::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); if (tcomputeflag) { modify->delete_compute(id_temp); tcomputeflag = 0; diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index f771b8c41b..07510a59e3 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -68,7 +68,7 @@ class FixRigidNHSmall : public FixRigidSmall { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tcomputeflag,pcomputeflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external void couple(); void remap(); diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 480b667254..7fc0f8a381 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -135,7 +135,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -153,7 +153,7 @@ FixNPHug::FixNPHug(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; // create a new compute potential energy compute diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp index dc6bfe20d5..0fe8c8e6db 100644 --- a/src/USER-EFF/fix_nph_eff.cpp +++ b/src/USER-EFF/fix_nph_eff.cpp @@ -46,7 +46,7 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHEff::FixNPHEff(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp index 36a6f87cba..02f09839b1 100644 --- a/src/USER-EFF/fix_npt_eff.cpp +++ b/src/USER-EFF/fix_npt_eff.cpp @@ -46,7 +46,7 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTEff::FixNPTEff(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 36a9ff3293..ab82f9e0f8 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -46,5 +46,5 @@ FixNVTEff::FixNVTEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 1f6dea658f..1b4ec1f3fb 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -58,7 +58,7 @@ FixNVTSllodEff::FixNVTSllodEff(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp index 150464413e..2bfbd5e735 100644 --- a/src/USER-INTEL/fix_npt_intel.cpp +++ b/src/USER-INTEL/fix_npt_intel.cpp @@ -46,7 +46,7 @@ FixNPTIntel::FixNPTIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTIntel::FixNPTIntel(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp index 65854b07a8..3fe712c9ab 100644 --- a/src/USER-INTEL/fix_nvt_intel.cpp +++ b/src/USER-INTEL/fix_nvt_intel.cpp @@ -45,6 +45,6 @@ FixNVTIntel::FixNVTIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index 5505abb9ce..bab748ad74 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -59,7 +59,7 @@ FixNVTSllodIntel::FixNVTSllodIntel(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp index 3e0a6c9df0..dfcbc87e6f 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.cpp +++ b/src/USER-OMP/fix_nph_asphere_omp.cpp @@ -46,7 +46,7 @@ FixNPHAsphereOMP::FixNPHAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHAsphereOMP::FixNPHAsphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index be21da2eed..f2a4e66f55 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -46,7 +46,7 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHOMP::FixNPHOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp index a5626f9d1c..670009de2f 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.cpp +++ b/src/USER-OMP/fix_nph_sphere_omp.cpp @@ -46,7 +46,7 @@ FixNPHSphereOMP::FixNPHSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHSphereOMP::FixNPHSphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp index 7721781769..b652cf563a 100644 --- a/src/USER-OMP/fix_nphug_omp.cpp +++ b/src/USER-OMP/fix_nphug_omp.cpp @@ -135,7 +135,7 @@ FixNPHugOMP::FixNPHugOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -153,7 +153,7 @@ FixNPHugOMP::FixNPHugOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; // create a new compute potential energy compute diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp index 00bafe661a..1db62d40c0 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.cpp +++ b/src/USER-OMP/fix_npt_asphere_omp.cpp @@ -46,7 +46,7 @@ FixNPTAsphereOMP::FixNPTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTAsphereOMP::FixNPTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index c4af48542a..5610f62f36 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -46,7 +46,7 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTOMP::FixNPTOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp index 6baee93cb4..d71d1380b9 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.cpp +++ b/src/USER-OMP/fix_npt_sphere_omp.cpp @@ -46,7 +46,7 @@ FixNPTSphereOMP::FixNPTSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTSphereOMP::FixNPTSphereOMP(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index 23cc2e9581..bb1e784a37 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -45,5 +45,5 @@ FixNVTAsphereOMP::FixNVTAsphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index 18d02bff4d..f8f3c15b76 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -45,5 +45,5 @@ FixNVTOMP::FixNVTOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index 8105e831f7..bd704148a5 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -65,7 +65,7 @@ FixNVTSllodOMP::FixNVTSllodOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp index 6db9ad849a..22eda99883 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp @@ -45,5 +45,5 @@ FixNVTSphereOMP::FixNVTSphereOMP(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp index 59b39d4534..b1a14f84e6 100644 --- a/src/USER-REAXC/pair_reax_c.cpp +++ b/src/USER-REAXC/pair_reax_c.cpp @@ -386,7 +386,6 @@ void PairReaxC::init_style( ) delete [] fixarg; fix_reax = (FixReaxC *) modify->fix[modify->nfix-1]; } - } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 90464d7949..e9ecedd5ab 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -56,6 +56,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : ComputeForceTally::~ComputeForceTally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(fatom); delete[] vector; } diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index f18a58e44e..68c00b6d2e 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -55,6 +55,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : ComputePETally::~ComputePETally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(eatom); delete[] vector; } diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 2a5f522636..2575bd372a 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -56,6 +56,7 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : ComputeStressTally::~ComputeStressTally() { if (force && force->pair) force->pair->del_tally_callback(this); + memory->destroy(stress); delete[] vector; } diff --git a/src/comm.cpp b/src/comm.cpp index 825460720d..f29d1bf7df 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -688,6 +688,10 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag, int maxbytes; MPI_Allreduce(&nbytes,&maxbytes,1,MPI_INT,MPI_MAX,world); + // no need to communicate without data + + if (maxbytes == 0) return; + char *buf,*bufcopy; memory->create(buf,maxbytes,"comm:buf"); memory->create(bufcopy,maxbytes,"comm:bufcopy"); diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 93a843ac31..5e88f5bc25 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -136,9 +136,11 @@ void ComputeAngmomChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute angmom for each chunk diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 449fb002b6..cb618055f6 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -159,10 +159,11 @@ void ComputeDipoleChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - if (masstotal[i] == 0.0) masstotal[i] = 1.0; - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute dipole for each chunk diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0c1c58a4fd..7f06df9103 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -109,6 +109,7 @@ void ComputeGyration::compute_vector() } MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world); - if (masstotal == 0.0) return; - for (int i = 0; i < 6; i++) vector[i] = vector[i]/masstotal; + if (masstotal > 0.0) + for (int i = 0; i < 6; i++) + vector[i] /= masstotal; } diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index e006a82299..58fe33bc3c 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -143,7 +143,8 @@ void ComputeGyrationChunk::compute_vector() MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) - rgall[i] = sqrt(rgall[i]/masstotal[i]); + if (masstotal[i] > 0.0) + rgall[i] = sqrt(rgall[i]/masstotal[i]); } /* ---------------------------------------------------------------------- */ @@ -191,9 +192,12 @@ void ComputeGyrationChunk::compute_array() if (nchunk) MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world); - for (i = 0; i < nchunk; i++) - for (j = 0; j < 6; j++) - rgtall[i][j] = rgtall[i][j]/masstotal[i]; + for (i = 0; i < nchunk; i++) { + if (masstotal[i] > 0.0) { + for (j = 0; j < 6; j++) + rgtall[i][j] = rgtall[i][j]/masstotal[i]; + } + } } @@ -253,9 +257,11 @@ void ComputeGyrationChunk::com_chunk() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } } diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 33660b839f..c4e83fa4a1 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -136,9 +136,11 @@ void ComputeInertiaChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute inertia tensor for each chunk diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 9d9ddcb3bd..30eee1d64a 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -201,9 +201,11 @@ void ComputeMSDChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // MSD is difference between current and initial COM diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index c437dd66b3..54e0b8f906 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -138,9 +138,11 @@ void ComputeOmegaChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute inertia tensor for each chunk diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 5a5853514f..87d6e11864 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -472,9 +472,13 @@ void ComputeTempChunk::vcm_compute() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); for (i = 0; i < nchunk; i++) { - vcmall[i][0] /= masstotal[i]; - vcmall[i][1] /= masstotal[i]; - vcmall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + vcmall[i][0] /= masstotal[i]; + vcmall[i][1] /= masstotal[i]; + vcmall[i][2] /= masstotal[i]; + } else { + vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0; + } } } @@ -689,7 +693,7 @@ void ComputeTempChunk::internal(int icol) void ComputeTempChunk::remove_bias(int i, double *v) { - int index = cchunk->ichunk[i]; + int index = cchunk->ichunk[i]-1; if (index < 0) return; v[0] -= vcmall[index][0]; v[1] -= vcmall[index][1]; @@ -711,11 +715,11 @@ void ComputeTempChunk::remove_bias_all() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - index = ichunk[i]; + index = ichunk[i]-1; if (index < 0) continue; - v[i][0] -= vbias[0]; - v[i][1] -= vbias[1]; - v[i][2] -= vbias[2]; + v[i][0] -= vcmall[index][0]; + v[i][1] -= vcmall[index][1]; + v[i][2] -= vcmall[index][2]; } } @@ -726,7 +730,7 @@ void ComputeTempChunk::remove_bias_all() void ComputeTempChunk::restore_bias(int i, double *v) { - int index = cchunk->ichunk[i]; + int index = cchunk->ichunk[i]-1; if (index < 0) return; v[0] += vcmall[index][0]; v[1] += vcmall[index][1]; @@ -749,11 +753,11 @@ void ComputeTempChunk::restore_bias_all() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - index = ichunk[i]; + index = ichunk[i]-1; if (index < 0) continue; - v[i][0] += vbias[0]; - v[i][1] += vbias[1]; - v[i][2] += vbias[2]; + v[i][0] += vcmall[index][0]; + v[i][1] += vcmall[index][1]; + v[i][2] += vcmall[index][2]; } } diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 158c93b2fb..33e07bfb1e 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -209,7 +209,7 @@ void ComputeTempRegion::remove_bias_all() int *mask = atom->mask; int nlocal = atom->nlocal; - if (nlocal > maxbias) { + if (atom->nmax > maxbias) { memory->destroy(vbiasall); maxbias = atom->nmax; memory->create(vbiasall,maxbias,3,"temp/region:vbiasall"); diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 41ae0c628c..5462debcfc 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -136,9 +136,11 @@ void ComputeTorqueChunk::compute_array() MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - comall[i][0] /= masstotal[i]; - comall[i][1] /= masstotal[i]; - comall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + comall[i][0] /= masstotal[i]; + comall[i][1] /= masstotal[i]; + comall[i][2] /= masstotal[i]; + } } // compute torque on each chunk diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index a3751fa13a..cd864b2aa8 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -146,9 +146,11 @@ void ComputeVCMChunk::compute_array() MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < nchunk; i++) { - vcmall[i][0] /= masstotal[i]; - vcmall[i][1] /= masstotal[i]; - vcmall[i][2] /= masstotal[i]; + if (masstotal[i] > 0.0) { + vcmall[i][0] /= masstotal[i]; + vcmall[i][1] /= masstotal[i]; + vcmall[i][2] /= masstotal[i]; + } else vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0; } } diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 8139a14d9d..9c0b6686d1 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -34,8 +34,8 @@ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : " dim, origin, delta, region, bound, discard, units\n\n"; if (comm->me == 0) { - if (screen) fprintf(screen,message); - if (logfile) fprintf(logfile,message); + if (screen) fputs(message,screen); + if (logfile) fputs(message,logfile); } } error->all(FLERR,"This fix command has been removed from LAMMPS"); diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 0609d45efb..5da405ae3f 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -133,6 +133,8 @@ void FixHeat::init() if (group->count(igroup) == 0) error->all(FLERR,"Fix heat group has no atoms"); masstotal = group->mass(igroup); + if (masstotal <= 0.0) + error->all(FLERR,"Fix heat group has invalid mass"); } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index b300fd2d46..2f1081216b 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -80,6 +80,11 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) flipflag = 1; dipole_flag = 0; + tcomputeflag = 0; + pcomputeflag = 0; + id_temp = NULL; + id_press = NULL; + // turn on tilt factor scaling, whenever applicable dimension = domain->dimension; @@ -558,7 +563,7 @@ FixNH::~FixNH() // delete temperature and pressure if fix created them - if (tflag) modify->delete_compute(id_temp); + if (tcomputeflag) modify->delete_compute(id_temp); delete [] id_temp; if (tstat_flag) { @@ -569,7 +574,7 @@ FixNH::~FixNH() } if (pstat_flag) { - if (pflag) modify->delete_compute(id_press); + if (pcomputeflag) modify->delete_compute(id_press); delete [] id_press; if (mpchain) { delete [] etap; @@ -1347,9 +1352,9 @@ int FixNH::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (tflag) { + if (tcomputeflag) { modify->delete_compute(id_temp); - tflag = 0; + tcomputeflag = 0; } delete [] id_temp; int n = strlen(arg[1]) + 1; @@ -1381,9 +1386,9 @@ int FixNH::modify_param(int narg, char **arg) } else if (strcmp(arg[0],"press") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); - if (pflag) { + if (pcomputeflag) { modify->delete_compute(id_press); - pflag = 0; + pcomputeflag = 0; } delete [] id_press; int n = strlen(arg[1]) + 1; diff --git a/src/fix_nh.h b/src/fix_nh.h index 7227a22968..e468d49817 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -76,7 +76,7 @@ class FixNH : public Fix { char *id_temp,*id_press; class Compute *temperature,*pressure; - int tflag,pflag; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix. 0 = external double *eta,*eta_dot; // chain thermostat for particles double *eta_dotdot; diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 6f3678ed3a..a331a07d24 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -46,7 +46,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 93d9bf8af2..852234074f 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -46,7 +46,7 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 0326c06c77..e14200f6a2 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -46,7 +46,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 6e7c074d5e..d3773e0d17 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -46,7 +46,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; // create a new compute pressure style // id = fix-ID + press, compute group = all @@ -64,5 +64,5 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : newarg[3] = id_temp; modify->add_compute(4,newarg); delete [] newarg; - pflag = 1; + pcomputeflag = 1; } diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index a86f46c3b5..35ee085da1 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -45,5 +45,5 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 8257afae05..87e86f2351 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -63,7 +63,7 @@ FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index c886935f12..b65b3adfae 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -45,5 +45,5 @@ FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) : modify->add_compute(3,newarg); delete [] newarg; - tflag = 1; + tcomputeflag = 1; } diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 7d30c2f865..e10edcb2d9 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -52,6 +52,7 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 1; global_freq = 1; + dynamic_group_allow = 1; /* ---------------------------------------------------------------------- */ @@ -186,6 +187,9 @@ void FixRecenter::initial_integrate(int vflag) // current COM double xcm[3]; + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + group->xcm(igroup,masstotal,xcm); // shift coords by difference between actual COM and requested COM diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index ddc161e50d..fb2b21b71d 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -47,6 +47,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; extscalar = 1; extvector = 1; + dynamic_group_allow = 1; group2 = NULL; @@ -166,6 +167,10 @@ void FixSpring::post_force(int vflag) void FixSpring::spring_tether() { double xcm[3]; + + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + group->xcm(igroup,masstotal,xcm); // fx,fy,fz = components of k * (r-r0) / masstotal @@ -192,9 +197,11 @@ void FixSpring::spring_tether() if (dr < 0.0) ftotal[3] = -ftotal[3]; espring = 0.5*k_spring * dr*dr; - fx /= masstotal; - fy /= masstotal; - fz /= masstotal; + if (masstotal > 0.0) { + fx /= masstotal; + fy /= masstotal; + fz /= masstotal; + } // apply restoring force to atoms in group @@ -231,6 +238,13 @@ void FixSpring::spring_tether() void FixSpring::spring_couple() { double xcm[3],xcm2[3]; + + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); + + if (group->dynamic[igroup2]) + masstotal2 = group->mass(igroup2); + group->xcm(igroup,masstotal,xcm); group->xcm(igroup2,masstotal2,xcm2); @@ -259,12 +273,16 @@ void FixSpring::spring_couple() if (dr < 0.0) ftotal[3] = -ftotal[3]; espring = 0.5*k_spring * dr*dr; - fx2 = fx/masstotal2; - fy2 = fy/masstotal2; - fz2 = fz/masstotal2; - fx /= masstotal; - fy /= masstotal; - fz /= masstotal; + if (masstotal2 > 0.0) { + fx2 = fx/masstotal2; + fy2 = fy/masstotal2; + fz2 = fz/masstotal2; + } + if (masstotal > 0.0) { + fx /= masstotal; + fy /= masstotal; + fz /= masstotal; + } // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 5e267340c1..4145e01047 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -42,6 +42,8 @@ FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) : rg0_flag = 0; if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1; else rg0 = force->numeric(FLERR,arg[4]); + + dynamic_group_allow = 1; } /* ---------------------------------------------------------------------- */ @@ -94,6 +96,8 @@ void FixSpringRG::post_force(int vflag) // compute current Rg and center-of-mass double xcm[3]; + if (group->dynamic[igroup]) + masstotal = group->mass(igroup); group->xcm(igroup,masstotal,xcm); double rg = group->gyration(igroup,masstotal,xcm); @@ -108,6 +112,7 @@ void FixSpringRG::post_force(int vflag) int *type = atom->type; imageint *image = atom->image; double *mass = atom->mass; + double *rmass = atom->rmass; int nlocal = atom->nlocal; double massfrac; @@ -120,10 +125,14 @@ void FixSpringRG::post_force(int vflag) dy = unwrap[1] - xcm[1]; dz = unwrap[2] - xcm[2]; term1 = 2.0 * k * (1.0 - rg0/rg); - massfrac = mass[type[i]]/masstotal; - f[i][0] -= term1*dx*massfrac; - f[i][1] -= term1*dy*massfrac; - f[i][2] -= term1*dz*massfrac; + if (masstotal > 0.0) { + if (rmass) massfrac = rmass[i]/masstotal; + else massfrac = mass[type[i]]/masstotal; + + f[i][0] -= term1*dx*massfrac; + f[i][1] -= term1*dy*massfrac; + f[i][2] -= term1*dz*massfrac; + } } } diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 4be97a816e..d326685368 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -85,6 +85,8 @@ FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) } masstotal = group->mass(igroup); + if (masstotal == 0.0) + error->all(FLERR,"Cannot use fix TMD on massless group"); // rho_start = initial rho // xold = initial x or 0.0 if not in group @@ -155,10 +157,7 @@ void FixTMD::init() int flag = 0; for (int i = 0; i < modify->nfix; i++) { if (strcmp(modify->fix[i]->style,"tmd") == 0) flag = 1; - if (flag && strcmp(modify->fix[i]->style,"nve") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"nvt") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"npt") == 0) flag = 2; - if (flag && strcmp(modify->fix[i]->style,"nph") == 0) flag = 2; + if (flag && modify->fix[i]->time_integrate) flag = 2; } if (flag == 2) error->all(FLERR,"Fix tmd must come after integration fixes"); diff --git a/src/lattice.cpp b/src/lattice.cpp index e851760792..484ce27972 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -53,7 +53,16 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (style == NONE) { if (narg != 2) error->all(FLERR,"Illegal lattice command"); - xlattice = ylattice = zlattice = force->numeric(FLERR,arg[1]); + + // Domain defines a default lattice of style "none" with + // spacing 1.0 before the force class is initialized, so + // we have to fall back to using atof() in that case. + + if (force) + xlattice = ylattice = zlattice = force->numeric(FLERR,arg[1]); + else + xlattice = ylattice = zlattice = atof(arg[1]); + if (xlattice <= 0.0) error->all(FLERR,"Illegal lattice command"); return; } diff --git a/src/molecule.cpp b/src/molecule.cpp index 99b5718133..91557b32ba 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -245,9 +245,11 @@ void Molecule::compute_com() com[1] += x[i][1]*onemass; com[2] += x[i][2]*onemass; } - com[0] /= masstotal; - com[1] /= masstotal; - com[2] /= masstotal; + if (masstotal > 0.0) { + com[0] /= masstotal; + com[1] /= masstotal; + com[2] /= masstotal; + } } memory->destroy(dxcom); diff --git a/src/replicate.cpp b/src/replicate.cpp index 941ec32492..e2ed718f65 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -116,9 +116,9 @@ void Replicate::command(int narg, char **arg) // also set atomKK for Kokkos version of Atom class Atom *old = atom; - if (lmp->kokkos) atom = new AtomKokkos(lmp); + atomKK = NULL; + if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp); else atom = new Atom(lmp); - atomKK = (AtomKokkos*) atom; atom->settings(old); atom->create_avec(old->atom_style,old->avec->nargcopy,old->avec->argcopy,0); From 921133d65d0bed19a733ccd386e69dbc28c8c03f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Jun 2016 23:22:33 +0000 Subject: [PATCH 065/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15110 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_spring.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index fb2b21b71d..88be8a3145 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -277,12 +277,13 @@ void FixSpring::spring_couple() fx2 = fx/masstotal2; fy2 = fy/masstotal2; fz2 = fz/masstotal2; - } + } else fx2 = fy2 = fz2 = 0.0 + if (masstotal > 0.0) { fx /= masstotal; fy /= masstotal; fz /= masstotal; - } + } else fx = fy = fz = 0.0 // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal From c2cca5dd622faf6d5d122b8faaa3504c5d342e55 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Jun 2016 23:40:32 +0000 Subject: [PATCH 066/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15112 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/version.h b/src/version.h index 6c57fcff1a..ecf6b405ff 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "31 May 2016" +#define LAMMPS_VERSION "6 Jun 2016" From 34111922f0751fd985754a79eef6e1f5944859e1 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Jun 2016 23:41:23 +0000 Subject: [PATCH 067/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15113 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Manual.html | 4 ++-- doc/html/_sources/Manual.txt | 5 +++-- doc/html/fix_lb_rigid_pc_sphere.html | 2 +- doc/html/searchindex.js | 2 +- doc/src/Manual.txt | 4 ++-- 5 files changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 5daf6fc5e7..3c516d3e61 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -134,8 +134,8 @@

    LAMMPS Documentation

    -
    -

    31 May 2016 version

    +
    +

    6 Jun 2016 version

    Version info:

    diff --git a/doc/html/_sources/Manual.txt b/doc/html/_sources/Manual.txt index 64ba9ec68c..bc0efc421a 100644 --- a/doc/html/_sources/Manual.txt +++ b/doc/html/_sources/Manual.txt @@ -5,8 +5,8 @@ LAMMPS Documentation ==================== -31 May 2016 version -------------------- +6 Jun 2016 version +------------------ Version info: ------------- @@ -30,6 +30,7 @@ the first page of the manual (this page). * There is also a `Developer.pdf `_ file in the doc directory, which describes the internal structure and algorithms of LAMMPS. + LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html index 984513a2c2..ca3adc0748 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -176,7 +176,7 @@ created to be used in place of that fix, to integrate the equations of motion of spherical rigid bodies when a lattice-Boltzmann fluid is present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of +The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of a set of spherical rigid bodies experiencing velocity dependent hydrodynamic forces. 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202,channel:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,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,227,229,237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,21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25,226,231,236,238,241,242,244,247,252,265,303,304,313,315,331,343,348,352,353,354,356,372,383,385,389,403,417,421,448,454,472,483,487,488,490,491,495,498,499,507,508,517,518],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,331,333,335,338,342,343,362,373,376,397,409,410,411,424,438,452,453,457,459,461,485,487,488,489,490,498,499,500,504,507,517,518],integer:[3,490],integr:[],integral:[298,445],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,245,451,490],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,241,248,258,267,269,274,312,315,316,331,339,343,345,346,507,508,516],intensiv:[66,209,508],intepol:517,inter:[14,18,43,64,65,158,181,182,202,227,252,254,268,307,315,373,384,395,500,511,517,520,522],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,322,323,331,332,338,343,347,348,349,352,353,358,359,360,361,363,365,367,373,374,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,453,454,455,457,459,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,485,488,490,492,494,495,499,500,502,507,508,511,520],interatom:[3,4,7,9,10,178,202,268,340,341,390,395,412,414,422,438,441,460,474,517],intercept:130,interchang:6,interconnect:18,interconvert:414,intereract:40,interesect:352,interest:[1,5,7,8,9,11,13,76,177,298,338,341,374,413,436,452,453,488,517],interf:[389,512],interfac:[],interfer:[12,269,391],interg:[6,511],intergr:499,interi:436,interior:[3,6,42,352,493],interlac:438,interleav:[6,178,498],intermedi:[6,12,62,205,268,296,366,384,488,489,498,502],intermix:485,intermolecular:[154,391],intern:[],internal:[3,205,211,301,517],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:251,interpenetr:438,interpentr:[464,465,467],interpol:[6,15,38,57,111,198,205,206,215,240,255,296,373,374,384,395,443,445,453,466,472,473],interpret:[2,6,11,205,221,418,462,485,488,504,517],interrupt:305,intersect:[3,6,130,206,352,354,493],intersert:352,interspers:382,interstiti:[176,441],intertia:[3,104],interv:[3,6,100,204,219,252,269,305,310,311,323,460,466,485,504,517],intestieti:130,intial:[6,389,391],intiial:[42,495],intiti:[3,330],intra:315,intra_energi:244,intramolecular:[29,154,244],introduc:[6,9,101,118,205,237,269,305,310,315,366,373,390,405,414,426,430,434,471,504,517],introduct:[],intuit:376,inv:[130,177,316],invalid:[3,12,76,98,181,283,384,435,436,492],invari:[118,145,150,152],invent:318,invers:[],inverse:511,invert:[1,6,182,297],invis:352,invoc:[176,227,389,457,459,488],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,241,242,243,244,245,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,318,320,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,357,359,360,362,363,366,368,372,373,374,375,376,382,384,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,422,426,427,428,429,430,431,432,433,434,435,436,439,443,444,446,447,449,454,455,457,459,461,462,471,472,473,474,475,476,478,479,480,481,482,484,487,488,489,491,493,495,498,499,501,502,504,507,508,511,517,518],invokd:3,invoke:[3,12,17],involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,225,244,255,300,303,308,331,373,381,382,384,394,411,417,424,471,473,475,486,487,493,495,499,504,505],ioff:[383,490],ion:[6,7,9,160,295,328,343,374,395,406,415,416,438,441,460,470,475,482,490,511],ionic:[6,9,396,398,406,414,415,447,460,511],ioniz:[404,414],ionocoval:9,iparam:[3,226],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,42,61,224,228,230,269,315],irrelev:446,irrespect:[435,436],irre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:485,tdrude:[163,234,253,511],teal:206,tech:[7,13],technic:[6,7,9,255,308,331,453],techniqu:[6,7,9,96,209,228,267,305,315,347,350,374,443,472,511],technolgi:9,technolog:[9,14,19,249],tediou:304,tell:[2,6,11,12,37,56,197,209,297,367,385,452,453,470,488,490,492,511],telsa:17,temeperatur:11,temp:[],temp_drud:511,temp_eff:108,tempcom:[156,157,171],temper:[],temperar:298,temperatur:[],temperature_definit:215,tempfix:505,templ:[7,9,18],templat:[3,8,13,17,19,41,178,179,181,231,244,301,315,318,383,490],templeton2010:215,templeton2011:215,templeton:[9,215],tempor:245,temporari:[2,3,497],temporarili:[198,314,503,504],ten:14,tend:[29,269,296],tensil:[7,230],tensor:[3,6,8,66,91,92,98,99,100,104,117,124,139,142,143,144,145,148,149,150,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,228,255,258,269,270,274,300,302,315,346,373,374,383,414,435,436,441,457,459,508,517],tenth:[139,210,372],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,64,96,97,98,100,122,124,153,154,156,157,166,171,172,185,186,187,198,206,210,211,217,219,221,222,230,236,237,245,246,247,252,253,254,255,268,269,270,271,272,273,274,275,276,277,289,290,292,294,298,302,305,314,315,329,334,335,336,343,345,347,349,357,358,368,373,382,385,390,391,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,426,430,433,434,435,436,438,439,440,441,443,444,447,454,460,469,471,473,474,475,478,481,499,500,502,508,511],termin:[130,269,382,384,457,459,489,498],termostat:335,terrel:381,terri:7,tersoff:[],tersoff_1:[473,474,475],tersoff_2:[473,474,475],tersoff_mod:474,tertiari:190,tessel:[9,176],test:[],test_descriptor_str:3,testf:198,testu:198,tether:[6,313,320,328,330,341,416],tetot:[9,460],tex:8,texa:449,texas_holdem:314,text:[2,3,4,6,7,8,12,13,38,42,57,198,202,203,205,206,209,215,218,219,220,221,222,224,229,240,249,303,342,343,355,374,376,384,412,415,425,438,445,461,472,486,490,491,507,512,517,519,520],textur:17,tfac_insert:244,tfactor:[3,206],tfinal:517,tfix:314,tflag:205,tfmc:[],th4:177,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,60,61,62,64,66,72,76,81,95,97,101,116,118,120,124,127,128,131,153,176,179,180,181,187,198,201,202,204,206,209,214,216,218,221,222,224,225,226,227,228,230,231,232,235,240,241,244,245,246,247,250,251,252,255,267,296,297,301,302,303,305,306,308,310,313,314,315,316,319,320,321,327,328,329,331,335,336,338,339,343,346,347,348,349,350,351,352,353,354,356,373,374,380,381,382,383,384,385,386,389,391,394,395,396,398,399,400,412,414,417,418,424,435,436,438,443,445,452,453,454,460,462,469,470,471,472,475,477,479,481,482,485,486,487,488,490,491,492,493,494,495,498,499,502,504,505,507,517,518,520],thank:[249,473,475],thb:453,thb_cutoff:453,thb_cutoff_sq:[452,453],thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,60,62,64,66,67,70,72,75,76,79,80,87,88,91,93,96,97,98,99,100,104,114,115,117,119,120,124,126,127,128,129,131,152,155,156,158,160,161,164,165,171,173,175,176,178,180,181,182,184,185,187,188,189,190,192,193,195,196,197,198,202,203,205,206,209,210,211,212,214,217,218,219,221,222,223,224,225,226,227,228,230,231,236,238,243,244,245,247,248,249,252,253,255,258,266,269,271,272,273,274,275,276,277,278,279,280,281,287,289,290,292,294,300,301,302,303,304,306,307,314,315,316,317,318,331,332,335,338,342,343,345,346,349,351,352,354,355,356,357,359,360,361,362,363,366,367,368,371,373,374,376,378,379,381,382,383,384,385,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,444,446,447,449,450,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,486,488,490,491,492,493,494,495,499,500,502,503,508,511,512,517,520,521],them:[1,2,3,6,7,8,9,11,12,13,14,17,40,41,42,55,62,76,100,114,119,126,129,131,154,180,185,202,205,206,207,217,218,219,221,222,224,227,228,230,241,249,252,253,261,265,269,271,272,273,274,275,276,277,289,290,294,296,302,304,312,313,314,315,318,331,334,335,336,338,342,343,345,349,350,351,353,354,357,374,376,378,383,384,385,389,390,395,402,412,415,417,421,424,443,454,462,476,477,485,488,490,497,502,505,511,512,517,518],themselv:[6,9,11,181,210,211,224,253,373,374,384,386,390,395,405,412,434,438,439,440,461,517],theor:338,theorem:[245,252,319,395,410],theoret:[116,249,305,471],theori:[3,6,9,12,41,152,215,229,246,269,297,373,374,395,441,481,504],thereaft:[76,260,299,315,339,346,488],therebi:[344,435,436],therefor:[3,6,12,67,96,163,234,237,244,253,255,318,338,374,407,451,453,471,476,499,511],therein:[6,438],thereof:96,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,66,121,488,508],thermo_press:[66,124,228,234,269,271,272,273,274,275,276,277,302,507,508,511],thermo_styl:[],thermo_temp:[66,124,155,227,228,244,269,271,272,273,274,275,276,277,289,290,292,294,297,302,334,335,336,507,508,511],thermoberendsen:6,thermochem:516,thermochemistri:414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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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el:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,1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237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222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452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:[],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,444,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,23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s:[42,224,395,477],recust:42,recv:487,red:[2,205,206,227,298],redefin:[3,492,498,517],redirect:12,redo:12,reduc:[],reduct:[18,19,129,130,177,267,305,373],redund:415,ree:465,reed:[267,305],rees:[7,9,13],ref:[340,341,381],refactor:6,refer:[],referenc:[3,6,12,66,72,76,126,131,202,203,209,219,244,304,345,374,405,420,446,454,488,508,517],reflect:[],refman:9,reformat:7,refresh:215,reg:493,regard:[6,62,266,318,319,324,449,453],regardless:[15,76,178,181,201,221,230,252,269,271,272,273,275,276,277,302,315,325,331,389,487,493,500],regim:[6,339,346,406,499],region:[],region_spher:8,region_styl:352,regist:[8,128,154,327],regoin:6,regress:517,regspher:178,regstrip:354,regul:6,regular:[1,3,42,65,97,176,180,202,205,216,224,244,304,343,374,406,424,487,490,492,494],reigon:517,reinhardt:[340,341],reject:[178,227,452,505],rel:[1,6,14,27,36,42,62,76,101,114,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,244,250,253,265,266,292,296,301,310,312,313,320,328,331,333,338,339,343,350,354,373,374,382,414,417,418,435,436,438,454,481,491,499,504,508,511,518],relat:[],relationship:[6,240,306,356,373,460,481,511,517],relax:[],releas:[0,5,7,8,13,225],relect:[3,443],reles:43,relev:[2,6,12,42,83,86,123,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,238,241,243,244,245,248,249,255,256,257,259,260,261,262,263,265,266,268,278,279,280,281,282,283,284,285,286,287,288,291,295,299,300,301,303,304,307,309,311,312,313,316,317,318,320,325,329,331,332,333,338,339,342,343,344,345,346,347,348,349,350,351,353,354,373,378,382,392,393,397,403,405,406,408,409,411,414,416,417,418,419,420,425,427,428,429,431,432,433,435,436,443,444,445,449,454,462,469,472,480,481,482,487,503,518],reli:[3,12,307,414,453,482,490,500],reloc:12,remain:[7,12,33,37,42,51,56,62,76,96,115,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,252,253,260,269,270,275,276,277,289,290,292,294,299,300,323,331,334,335,336,342,343,354,356,364,367,383,395,414,421,434,441,443,470,485,490,491,495,500,502,504,508,511,512,517,518],remaina:395,remaind:[9,178,202,231,301,331,344,475,490],remap:[3,6,12,62,64,76,161,178,201,230,250,266,292,373,490,491,492],remedi:[6,511],rememb:[2,512],remot:512,remov:[2,3,6,8,13,55,76,77,82,101,118,126,128,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,241,252,253,258,261,265,267,269,275,276,277,289,290,292,294,300,306,315,316,318,331,334,335,336,338,354,373,384,408,436,441,490,493,501,502,512,517,518],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,355,501,512],render:[12,13,202,205,206],rendon:[269,270],reneighbor:[3,8,12,40,60,76,224,244,331,344,354,409,507,508],renssela:300,renumb:76,reorder:[3,12,40,487],rep:505,repeat:[2,6,205,206,227,228,244,324,376,395,473,475,477,485,504],repeatedli:2,repel:250,repes:202,replac:[2,3,6,11,12,42,66,98,99,129,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,252,274,303,304,310,312,391,405,428,445,472,491,492,497,498,508,517,518,520,522],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:343,repres:[1,3,6,8,9,12,15,41,42,43,62,71,76,99,125,128,190,198,202,203,205,218,219,220,221,222,228,234,245,247,252,255,269,298,300,302,310,315,316,320,328,343,345,352,374,384,390,395,417,424,434,435,436,438,439,440,447,450,452,453,476,477,485,487,490,500,502,505,511,517,520],represent:[3,6,8,9,60,62,146,180,202,245,246,298,343,395,414,417,441,454,490,493,511],reprocess:495,reproduc:[3,269,349,405,412,418],repul:438,repuls:[6,7,36,41,46,47,120,250,306,348,349,352,391,395,403,405,409,414,418,420,434,438,442,460,469,475,478,481,482,500],reqir:[306,308],request:[3,6,8,12,42,114,181,198,202,249,255,313,319,331,333,371,373,443,452,453,485,495,500,504,512,517,518,520],requir:[],rerun:[],rescal:[],research:[5,7,89,90,239,255,259,319,441,485,504],resembl:[310,512],resepct:6,reserv:[12,249,511],reservoir:[100,237,244,248,252,343],reset:[],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[],resid:13,residu:249,residue1:385,resist:[6,249],resolut:[220,460,472],resolv:[228,298,331,436,512],resort:3,resourc:[7,390,412],respa:[3,16,235,249,269,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,498,499,510,517],respecifi:441,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,44,46,47,48,49,50,52,54,55,57,62,75,76,96,98,107,108,124,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,247,250,252,253,255,269,271,272,273,274,275,276,277,278,279,285,287,289,290,292,294,306,307,315,316,320,328,330,343,348,351,357,359,360,362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ivers:[3,6,9,12,13,18,96,249,373,374,384,388,435,440,449,451,475,484,487,517],universit:[9,13],unix:[12,17,251,501],unknown:[3,12,67,78,490],unless:[2,3,9,11,12,15,16,56,60,71,114,130,163,177,178,202,203,206,207,214,228,231,244,252,269,271,272,273,275,276,277,301,302,315,331,342,375,382,403,443,472,488,493,497,502,517],unlik:[12,98,178,220,252,308,373,390,395,412,415,421,438,439,440,461,470],unlike:[33,51,62,168,191,202,252,269,274,302,310,334,335,336,364,372,412,420,425,439,440,453,487,492,497,502,517,522],unlimit:450,unlucki:3,unmark:7,unmodifi:332,unnecessari:16,unoccupi:343,unoptim:205,unpack:[0,8,11,389],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:206,unperturb:96,unphys:[3,6,253,269,315,490],unpredict:[313,500],unpublish:441,unrecogn:3,unrel:[8,9,13,184,512],unreli:443,unrestrain:314,unrestrict:392,unscal:[3,125,172,202,203,333,491],unset:[3,373,414],unshift:408,unsmooth:432,unsolv:[386,400],unsort:206,unspecifi:[230,490],unsplit:511,unstabl:[3,255],unstag:512,unstrain:230,unsuccess:[3,301],unsupport:[3,505],untar:12,until:[2,3,6,12,14,38,40,42,57,76,131,198,205,224,228,231,240,244,249,285,301,324,331,333,340,356,372,373,385,388,389,395,418,445,472,485,490,491,495,496,498,504,516,517],untilt:493,unus:395,unusu:[3,8,385],unwant:[3,178,373],unwrap:[3,70,79,80,87,88,98,99,104,114,115,117,125,153,173,202,203,206,207,217,227,229,249,266,315,328,333,490,491,494,500],unwrapexpand:202,unzip:12,up_intern:205,updat:[0,3,6,8,12,13,135,136,137,147,148,149,150,201,202,203,209,216,225,226,234,242,245,252,253,255,258,262,263,266,267,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,300,302,304,305,310,315,323,324,333,334,335,336,338,343,354,355,389,395,408,441,443,452,453,459,485,490,492,500,501,504,511],update:257,upenn:[11,13],upgrad:12,upon:[6,216,249,395,476,504],upper:[2,3,42,60,62,76,97,114,116,154,167,174,201,206,219,220,224,228,234,253,255,269,305,310,348,349,354,355,382,418,460,493,518],uppercas:[],upsid:6,upsilon:417,upstream:512,upto:[3,492,498],upward:231,urbana:[249,373,374,435],urey_bradlei:20,url:512,usa:9,usabl:[12,244,412],usag:[3,6,8,296,310,331,421,434,490],usage:253,use:[],use_ldg:17,usec:510,used:[206,252,254],useful:441,user:[],user_manifold:512,user_misc:[30,31,35,188,193,196,362],userguid:9,usernam:512,using:[],usr:[11,12,14,491],usual:[2,3,6,12,14,17,18,24,28,32,35,36,48,64,76,96,129,156,157,158,163,171,176,195,202,203,205,210,211,216,218,227,228,229,230,244,247,252,254,267,274,297,305,306,312,314,315,331,339,343,346,348,352,356,363,371,384,385,389,400,403,406,408,417,421,422,425,434,435,436,443,446,457,459,461,469,471,476,485,489,491,495,499,501,504,507,508,517,522],usualli:[3,456,458],util:[8,12,17,18,389,417,509],utilizi:12,utilz:[12,509],utsa:449,uttormark:13,uwo:9,v11:6,v22:6,v33:6,v_0:[3,343],v_2:441,v_3:441,v_4:441,v_a:[8,230],v_abc:[488,508,517],v_area:[2,517],v_atomfil:500,v_c:172,v_cluster:304,v_dc:172,v_delta:96,v_dhug:[267,305],v_diff:[174,345],v_displac:230,v_dk:172,v_dlj:172,v_drai:[267,305],v_dx:[266,493],v_dy:[266,493],v_dz:266,v_e_hbond:420,v_ea:[452,453],v_eb:[452,453],v_eqeq:[452,453],v_espac:212,v_f:488,v_fac:488,v_flux:248,v_foo:[488,517],v_ij:450,v_increas:247,v_integr:345,v_jx:100,v_jy:100,v_jz:100,v_k11:100,v_k22:100,v_k33:100,v_k:172,v_ke:[202,203,521],v_left:493,v_lgr_po:[267,305],v_lgr_vel:[267,305],v_linear:[348,351,353],v_lj:[172,391],v_mol:206,v_mu:435,v_myi:266,v_myindex:517,v_myke:129,v_mystep:497,v_myvar:[8,206],v_myvec:[131,517],v_myx:266,v_n:[255,441],v_name1:[172,230],v_name2:[172,230],v_name:[3,6,76,96,129,131,201,202,203,205,206,210,211,212,213,217,218,219,220,221,222,223,236,247,248,250,252,253,266,317,325,333,334,335,336,345,348,351,353,488,493,497,500,506,508,517,518],v_nstep:354,v_occ:416,v_omega:266,v_oscil:[212,213,223,236,317],v_phi:247,v_prefactor:[210,211,462],v_press:153,v_pressdown:[351,353],v_push:212,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:250,v_r1:176,v_r2:176,v_r:[176,250,285],v_rad:354,v_radiu:250,v_ramp:[348,351,353],v_rate:[230,250],v_rebo:391,v_scale1:[210,211],v_scale2:[210,211],v_size:[210,211],v_t_qm:305,v_temp:339,v_theta:[247,493],v_torsion:391,v_tp:230,v_up:493,v_v0:517,v_v11:6,v_v22:6,v_v33:6,v_v:[266,517],v_valu:[205,488],v_vx:266,v_vy:266,v_vz:[266,518],v_wiggl:[348,351,353],v_x:[2,178,250,266,348,351,353,488,493,517],v_xave:6,v_xmax:6,v_xx:178,v_y:[178,250,493],v_yi:178,v_z:493,vacanc:[4,176,340,441],vacf:[],vacuum:[343,374,406,475,482],valanc:395,vale:3,valenc:[308,395,414,452,453],valent:395,valeriu:9,valid:[2,3,6,9,11,12,76,130,164,177,206,228,244,252,296,315,331,354,356,371,376,412,414,417,441,450,490,491,498,500,517],valon:438,valu:[],valuabl:509,value0:517,value1:[12,158,217,218,219,220,221,222,274,345,354,501],value2:[12,158,217,218,219,220,221,222,274,345,354,501],valuei:219,valu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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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\ No newline at end of file diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 992ad7b6a8..649903a4ee 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

    LAMMPS Documentation :c,h3 -31 May 2016 version :c,h4 +6 Jun 2016 version :c,h4 Version info: :h4 From c3cc03e12ffc621a467702fc74d267b507e6fce0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Jun 2016 06:42:02 -0400 Subject: [PATCH 068/111] fix issue in balance command where file output has to come over subbox update --- src/balance.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/balance.cpp b/src/balance.cpp index c615db6112..db7361703c 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -325,10 +325,6 @@ void Balance::command(int narg, char **arg) bisection(1); } - // output of final result - - if (outflag) dumpout(update->ntimestep,fp); - // reset proc sub-domains // for either brick or tiled comm style @@ -344,6 +340,10 @@ void Balance::command(int narg, char **arg) delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); + // output of final result + + if (outflag) dumpout(update->ntimestep,fp); + // check if any atoms were lost bigint natoms; From 8a90e44c0965559f72a4df26bb33ea63904b206e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Jun 2016 06:42:13 -0400 Subject: [PATCH 069/111] fix typo (missing ;). --- src/fix_spring.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 88be8a3145..560ca291ae 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -277,13 +277,13 @@ void FixSpring::spring_couple() fx2 = fx/masstotal2; fy2 = fy/masstotal2; fz2 = fz/masstotal2; - } else fx2 = fy2 = fz2 = 0.0 + } else fx2 = fy2 = fz2 = 0.0; if (masstotal > 0.0) { fx /= masstotal; fy /= masstotal; fz /= masstotal; - } else fx = fy = fz = 0.0 + } else fx = fy = fz = 0.0; // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal From 34bf28cce05cdbd810dbe544d8f8c53c042a8c9b Mon Sep 17 00:00:00 2001 From: Martin Bauer Date: Tue, 7 Jun 2016 12:48:56 +0200 Subject: [PATCH 070/111] Another Python3 compatibility fix --- python/lammps.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/python/lammps.py b/python/lammps.py index 114468e36e..c2fd1a536b 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -79,6 +79,9 @@ class lammps: if cmdargs: cmdargs.insert(0,"lammps.py") narg = len(cmdargs) + for i in range(narg): + if type(cmdargs[i]) is str: + cmdargs[i] = cmdargs[i].encode() cargs = (c_char_p*narg)(*cmdargs) self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \ MPI_Comm, c_void_p()] @@ -98,6 +101,9 @@ class lammps: if cmdargs: cmdargs.insert(0,"lammps.py") narg = len(cmdargs) + for i in range(narg): + if type(cmdargs[i]) is str: + cmdargs[i] = cmdargs[i].encode() cargs = (c_char_p*narg)(*cmdargs) self.lmp = c_void_p() self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp)) From 930e2aa033ee0857c8b55d06d2dab1fab3126211 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 13:44:22 +0000 Subject: [PATCH 071/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15115 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_spring.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 88be8a3145..560ca291ae 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -277,13 +277,13 @@ void FixSpring::spring_couple() fx2 = fx/masstotal2; fy2 = fy/masstotal2; fz2 = fz/masstotal2; - } else fx2 = fy2 = fz2 = 0.0 + } else fx2 = fy2 = fz2 = 0.0; if (masstotal > 0.0) { fx /= masstotal; fy /= masstotal; fz /= masstotal; - } else fx = fy = fz = 0.0 + } else fx = fy = fz = 0.0; // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal From 78c5aafccf4fbc51063fbe724c3e241117f64695 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 14:48:10 +0000 Subject: [PATCH 072/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15116 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/set.cpp | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/src/set.cpp b/src/set.cpp index 37a0e815c4..56fbf42e54 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -430,8 +430,12 @@ void Set::command(int narg, char **arg) } else if (strcmp(arg[iarg],"dpd/theta") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); - if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); - else dvalue = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0; + else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else { + dvalue = force->numeric(FLERR,arg[iarg+1]); + if (dvalue < 0.0) error->all(FLERR,"Illegal set command"); + } if (!atom->dpd_flag) error->all(FLERR,"Cannot set dpd/theta for this atom style"); set(DPDTHETA); @@ -632,7 +636,20 @@ void Set::set(int keyword) atom->rmass[i] = atom->vfrac[i] * dvalue; } else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue; - else if (keyword == DPDTHETA) atom->dpdTheta[i] = dvalue; + + else if (keyword == DPDTHETA) { + if (dvalue >= 0.0) atom->dpdTheta[i] = dvalue; + else { + double onemass; + if (atom->rmass) onemass = atom->rmass[i]; + else onemass = atom->mass[atom->type[i]]; + double vx = atom->v[i][0]; + double vy = atom->v[i][1]; + double vz = atom->v[i][2]; + double tfactor = force->mvv2e / (domain->dimension * force->boltz); + atom->dpdTheta[i] = tfactor * onemass * (vx*vx + vy*vy + vz*vz); + } + } // set shape of ellipsoidal particle From 97ae23af75e5e4e24b735517d7718872501c08d9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 14:49:54 +0000 Subject: [PATCH 073/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15117 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/set.txt | 14 ++++++++++++-- doc/html/searchindex.js | 2 +- doc/html/set.html | 14 ++++++++++++-- doc/src/set.txt | 14 ++++++++++++-- 4 files changed, 37 insertions(+), 7 deletions(-) diff --git a/doc/html/_sources/set.txt b/doc/html/_sources/set.txt index 0e524366fe..92dffc024d 100644 --- a/doc/html/_sources/set.txt +++ b/doc/html/_sources/set.txt @@ -84,6 +84,8 @@ Syntax *smd/mass/density* = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) *dpd/theta* value = internal temperature of DPD particles (temperature units) + value can be an atom-style variable (see below) + value can be NULL which sets internal temp of each particle to KE temp *i_name* value = value for custom integer vector with name *d_name* value = value for custom floating-point vector with name @@ -383,8 +385,16 @@ other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the *diameter* keyword. -Keyword *dpd/theta* sets the internal temperature of a DPD particle -as defined by the USER-DPD package. +Keyword *dpd/theta* sets the internal temperature of a DPD particle as +defined by the USER-DPD package. If the specified value is a number +it must be >= 0.0. If the specified value is NULL, then the kinetic +temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 +m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle's internal +temperature is set to Tkin. If the specified value is an atom-style +variable, then the variable is evaluated for each particle. If a +value >= 0.0, the internal temperature is set to that value. If it is +< 0.0, the computation of Tkin is performed and the internal +temperature is set to that value. Keywords *i_name* and *d_name* refer to custom integer and floating-point properties that have been added to each atom via the diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index adad7193b0..51f163a57c 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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el:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,1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237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222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452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:[],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,444,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,23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s:[42,224,395,477],recust:42,recv:487,red:[2,205,206,227,298],redefin:[3,492,498,517],redirect:12,redo:12,reduc:[],reduct:[18,19,129,130,177,267,305,373],redund:415,ree:465,reed:[267,305],rees:[7,9,13],ref:[340,341,381],refactor:6,refer:[],referenc:[3,6,12,66,72,76,126,131,202,203,209,219,244,304,345,374,405,420,446,454,488,508,517],reflect:[],refman:9,reformat:7,refresh:215,reg:493,regard:[6,62,266,318,319,324,449,453],regardless:[15,76,178,181,201,221,230,252,269,271,272,273,275,276,277,302,315,325,331,389,487,493,500],regim:[6,339,346,406,499],region:[],region_spher:8,region_styl:352,regist:[8,128,154,327],regoin:6,regress:517,regspher:178,regstrip:354,regul:6,regular:[1,3,42,65,97,176,180,202,205,216,224,244,304,343,374,406,424,487,490,492,494],reigon:517,reinhardt:[340,341],reject:[178,227,452,505],rel:[1,6,14,27,36,42,62,76,101,114,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,244,250,253,265,266,292,296,301,310,312,313,320,328,331,333,338,339,343,350,354,373,374,382,414,417,418,435,436,438,454,481,491,499,504,508,511,518],relat:[],relationship:[6,240,306,356,373,460,481,511,517],relax:[],releas:[0,5,7,8,13,225],relect:[3,443],reles:43,relev:[2,6,12,42,83,86,123,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,238,241,243,244,245,248,249,255,256,257,259,260,261,262,263,265,266,268,278,279,280,281,282,283,284,285,286,287,288,291,295,299,300,301,303,304,307,309,311,312,313,316,317,318,320,325,329,331,332,333,338,339,342,343,344,345,346,347,348,349,350,351,353,354,373,378,382,392,393,397,403,405,406,408,409,411,414,416,417,418,419,420,425,427,428,429,431,432,433,435,436,443,444,445,449,454,462,469,472,480,481,482,487,503,518],reli:[3,12,307,414,453,482,490,500],reloc:12,remain:[7,12,33,37,42,51,56,62,76,96,115,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,252,253,260,269,270,275,276,277,289,290,292,294,299,300,323,331,334,335,336,342,343,354,356,364,367,383,395,414,421,434,441,443,470,485,490,491,495,500,502,504,508,511,512,517,518],remaina:395,remaind:[9,178,202,231,301,331,344,475,490],remap:[3,6,12,62,64,76,161,178,201,230,250,266,292,373,490,491,492],remedi:[6,511],rememb:[2,512],remot:512,remov:[2,3,6,8,13,55,76,77,82,101,118,126,128,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,241,252,253,258,261,265,267,269,275,276,277,289,290,292,294,300,306,315,316,318,331,334,335,336,338,354,373,384,408,436,441,490,493,501,502,512,517,518],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,355,501,512],render:[12,13,202,205,206],rendon:[269,270],reneighbor:[3,8,12,40,60,76,224,244,331,344,354,409,507,508],renssela:300,renumb:76,reorder:[3,12,40,487],rep:505,repeat:[2,6,205,206,227,228,244,324,376,395,473,475,477,485,504],repeatedli:2,repel:250,repes:202,replac:[2,3,6,11,12,42,66,98,99,129,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,252,274,303,304,310,312,391,405,428,445,472,491,492,497,498,508,517,518,520,522],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:343,repres:[1,3,6,8,9,12,15,41,42,43,62,71,76,99,125,128,190,198,202,203,205,218,219,220,221,222,228,234,245,247,252,255,269,298,300,302,310,315,316,320,328,343,345,352,374,384,390,395,417,424,434,435,436,438,439,440,447,450,452,453,476,477,485,487,490,500,502,505,511,517,520],represent:[3,6,8,9,60,62,146,180,202,245,246,298,343,395,414,417,441,454,490,493,511],reprocess:495,reproduc:[3,269,349,405,412,418],repul:438,repuls:[6,7,36,41,46,47,120,250,306,348,349,352,391,395,403,405,409,414,418,420,434,438,442,460,469,475,478,481,482,500],reqir:[306,308],request:[3,6,8,12,42,114,181,198,202,249,255,313,319,331,333,371,373,443,452,453,485,495,500,504,512,517,518,520],requir:[],rerun:[],rescal:[],research:[5,7,89,90,239,255,259,319,441,485,504],resembl:[310,512],resepct:6,reserv:[12,249,511],reservoir:[100,237,244,248,252,343],reset:[],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[],resid:13,residu:249,residue1:385,resist:[6,249],resolut:[220,460,472],resolv:[228,298,331,436,512],resort:3,resourc:[7,390,412],respa:[3,16,235,249,269,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,498,499,510,517],respecifi:441,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,44,46,47,48,49,50,52,54,55,57,62,75,76,96,98,107,108,124,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,247,250,252,253,255,269,271,272,273,274,275,276,277,278,279,285,287,289,290,292,294,306,307,315,316,320,328,330,343,348,351,357,359,360,362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ivers:[3,6,9,12,13,18,96,249,373,374,384,388,435,440,449,451,475,484,487,517],universit:[9,13],unix:[12,17,251,501],unknown:[3,12,67,78,490],unless:[2,3,9,11,12,15,16,56,60,71,114,130,163,177,178,202,203,206,207,214,228,231,244,252,269,271,272,273,275,276,277,301,302,315,331,342,375,382,403,443,472,488,493,497,502,517],unlik:[12,98,178,220,252,308,373,390,395,412,415,421,438,439,440,461,470],unlike:[33,51,62,168,191,202,252,269,274,302,310,334,335,336,364,372,412,420,425,439,440,453,487,492,497,502,517,522],unlimit:450,unlucki:3,unmark:7,unmodifi:332,unnecessari:16,unoccupi:343,unoptim:205,unpack:[0,8,11,389],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:206,unperturb:96,unphys:[3,6,253,269,315,490],unpredict:[313,500],unpublish:441,unrecogn:3,unrel:[8,9,13,184,512],unreli:443,unrestrain:314,unrestrict:392,unscal:[3,125,172,202,203,333,491],unset:[3,373,414],unshift:408,unsmooth:432,unsolv:[386,400],unsort:206,unspecifi:[230,490],unsplit:511,unstabl:[3,255],unstag:512,unstrain:230,unsuccess:[3,301],unsupport:[3,505],untar:12,until:[2,3,6,12,14,38,40,42,57,76,131,198,205,224,228,231,240,244,249,285,301,324,331,333,340,356,372,373,385,388,389,395,418,445,472,485,490,491,495,496,498,504,516,517],untilt:493,unus:395,unusu:[3,8,385],unwant:[3,178,373],unwrap:[3,70,79,80,87,88,98,99,104,114,115,117,125,153,173,202,203,206,207,217,227,229,249,266,315,328,333,490,491,494,500],unwrapexpand:202,unzip:12,up_intern:205,updat:[0,3,6,8,12,13,135,136,137,147,148,149,150,201,202,203,209,216,225,226,234,242,245,252,253,255,258,262,263,266,267,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,300,302,304,305,310,315,323,324,333,334,335,336,338,343,354,355,389,395,408,441,443,452,453,459,485,490,492,500,501,504,511],update:257,upenn:[11,13],upgrad:12,upon:[6,216,249,395,476,504],upper:[2,3,42,60,62,76,97,114,116,154,167,174,201,206,219,220,224,228,234,253,255,269,305,310,348,349,354,355,382,418,460,493,518],uppercas:[],upsid:6,upsilon:417,upstream:512,upto:[3,492,498],upward:231,urbana:[249,373,374,435],urey_bradlei:20,url:512,usa:9,usabl:[12,244,412],usag:[3,6,8,296,310,331,421,434,490],usage:253,use:[],use_ldg:17,usec:510,used:[206,252,254],useful:441,user:[],user_manifold:512,user_misc:[30,31,35,188,193,196,362],userguid:9,usernam:512,using:[],usr:[11,12,14,491],usual:[2,3,6,12,14,17,18,24,28,32,35,36,48,64,76,96,129,156,157,158,163,171,176,195,202,203,205,210,211,216,218,227,228,229,230,244,247,252,254,267,274,297,305,306,312,314,315,331,339,343,346,348,352,356,363,371,384,385,389,400,403,406,408,417,421,422,425,434,435,436,443,446,457,459,461,469,471,476,485,489,491,495,499,501,504,507,508,517,522],usualli:[3,456,458],util:[8,12,17,18,389,417,509],utilizi:12,utilz:[12,509],utsa:449,uttormark:13,uwo:9,v11:6,v22:6,v33:6,v_0:[3,343],v_2:441,v_3:441,v_4:441,v_a:[8,230],v_abc:[488,508,517],v_area:[2,517],v_atomfil:500,v_c:172,v_cluster:304,v_dc:172,v_delta:96,v_dhug:[267,305],v_diff:[174,345],v_displac:230,v_dk:172,v_dlj:172,v_drai:[267,305],v_dx:[266,493],v_dy:[266,493],v_dz:266,v_e_hbond:420,v_ea:[452,453],v_eb:[452,453],v_eqeq:[452,453],v_espac:212,v_f:488,v_fac:488,v_flux:248,v_foo:[488,517],v_ij:450,v_increas:247,v_integr:345,v_jx:100,v_jy:100,v_jz:100,v_k11:100,v_k22:100,v_k33:100,v_k:172,v_ke:[202,203,521],v_left:493,v_lgr_po:[267,305],v_lgr_vel:[267,305],v_linear:[348,351,353],v_lj:[172,391],v_mol:206,v_mu:435,v_myi:266,v_myindex:517,v_myke:129,v_mystep:497,v_myvar:[8,206],v_myvec:[131,517],v_myx:266,v_n:[255,441],v_name1:[172,230],v_name2:[172,230],v_name:[3,6,76,96,129,131,201,202,203,205,206,210,211,212,213,217,218,219,220,221,222,223,236,247,248,250,252,253,266,317,325,333,334,335,336,345,348,351,353,488,493,497,500,506,508,517,518],v_nstep:354,v_occ:416,v_omega:266,v_oscil:[212,213,223,236,317],v_phi:247,v_prefactor:[210,211,462],v_press:153,v_pressdown:[351,353],v_push:212,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:250,v_r1:176,v_r2:176,v_r:[176,250,285],v_rad:354,v_radiu:250,v_ramp:[348,351,353],v_rate:[230,250],v_rebo:391,v_scale1:[210,211],v_scale2:[210,211],v_size:[210,211],v_t_qm:305,v_temp:339,v_theta:[247,493],v_torsion:391,v_tp:230,v_up:493,v_v0:517,v_v11:6,v_v22:6,v_v33:6,v_v:[266,517],v_valu:[205,488],v_vx:266,v_vy:266,v_vz:[266,518],v_wiggl:[348,351,353],v_x:[2,178,250,266,348,351,353,488,493,517],v_xave:6,v_xmax:6,v_xx:178,v_y:[178,250,493],v_yi:178,v_z:493,vacanc:[4,176,340,441],vacf:[],vacuum:[343,374,406,475,482],valanc:395,vale:3,valenc:[308,395,414,452,453],valent:395,valeriu:9,valid:[2,3,6,9,11,12,76,130,164,177,206,228,244,252,296,315,331,354,356,371,376,412,414,417,441,450,490,491,498,500,517],valon:438,valu:[],valuabl:509,value0:517,value1:[12,158,217,218,219,220,221,222,274,345,354,501],value2:[12,158,217,218,219,220,221,222,274,345,354,501],valuei:219,valu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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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el:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,1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237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222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452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:[],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,444,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,23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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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\ No newline at end of file diff --git a/doc/html/set.html b/doc/html/set.html index 5ce9389c80..89ea2eb1ff 100644 --- a/doc/html/set.html +++ b/doc/html/set.html @@ -206,6 +206,8 @@ smd/mass/density = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) dpd/theta value = internal temperature of DPD particles (temperature units) + value can be an atom-style variable (see below) + value can be NULL which sets internal temp of each particle to KE temp i_name value = value for custom integer vector with name d_name value = value for custom floating-point vector with name @@ -463,8 +465,16 @@ prevent different individual physical bodies from penetrating each other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the diameter keyword.

    -

    Keyword dpd/theta sets the internal temperature of a DPD particle -as defined by the USER-DPD package.

    +

    Keyword dpd/theta sets the internal temperature of a DPD particle as +defined by the USER-DPD package. If the specified value is a number +it must be >= 0.0. If the specified value is NULL, then the kinetic +temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 +m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle’s internal +temperature is set to Tkin. If the specified value is an atom-style +variable, then the variable is evaluated for each particle. If a +value >= 0.0, the internal temperature is set to that value. If it is +< 0.0, the computation of Tkin is performed and the internal +temperature is set to that value.

    Keywords i_name and d_name refer to custom integer and floating-point properties that have been added to each atom via the fix property/atom command. When that command diff --git a/doc/src/set.txt b/doc/src/set.txt index 184e147d11..83bab5c06c 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -93,6 +93,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {smd/mass/density} = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) {dpd/theta} value = internal temperature of DPD particles (temperature units) + value can be an atom-style variable (see below) + value can be NULL which sets internal temp of each particle to KE temp {i_name} value = value for custom integer vector with name {d_name} value = value for custom floating-point vector with name :pre :ule @@ -390,8 +392,16 @@ other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the {diameter} keyword. -Keyword {dpd/theta} sets the internal temperature of a DPD particle -as defined by the USER-DPD package. +Keyword {dpd/theta} sets the internal temperature of a DPD particle as +defined by the USER-DPD package. If the specified value is a number +it must be >= 0.0. If the specified value is NULL, then the kinetic +temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 +m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle's internal +temperature is set to Tkin. If the specified value is an atom-style +variable, then the variable is evaluated for each particle. If a +value >= 0.0, the internal temperature is set to that value. If it is +< 0.0, the computation of Tkin is performed and the internal +temperature is set to that value. Keywords {i_name} and {d_name} refer to custom integer and floating-point properties that have been added to each atom via the From 2927a9aee1f3056e15e9c0960c4136275c44ac0d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:20:19 +0000 Subject: [PATCH 074/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15118 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-DPD/atom_vec_dpd.cpp | 74 +++++++++++++++++++++++++++++-- src/USER-DPD/atom_vec_dpd.h | 4 +- src/USER-DPD/compute_dpd.cpp | 3 +- src/USER-DPD/compute_dpd_atom.cpp | 10 +++-- 4 files changed, 81 insertions(+), 10 deletions(-) diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 0b1866e65c..92028b60e6 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -35,9 +35,9 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp) mass_type = 1; comm_x_only = comm_f_only = 0; // we communicate not only x forward but also dpdTheta - size_forward = 6; // 3 + dpdTheta + uCond + uMech + size_forward = 7; // 3 + dpdTheta + uCond + uMech + uChem size_reverse = 3; // 3 - size_border = 9; // 6 + dpdTheta + uCond + uMech + size_border = 12; // 6 + dpdTheta + uCond + uMech + uChem + uCG + uCGnew size_velocity = 3; size_data_atom = 6; // we read id + type + dpdTheta + x + y + z size_data_vel = 4; @@ -73,8 +73,12 @@ void AtomVecDPD::grow(int n) dpdTheta = memory->grow(atom->dpdTheta, nmax, "atom:dpdTheta"); uCond = memory->grow(atom->uCond,nmax,"atom:uCond"); uMech = memory->grow(atom->uMech,nmax,"atom:uMech"); + uChem = memory->grow(atom->uChem,nmax,"atom:uChem"); + uCG = memory->grow(atom->uCG,nmax,"atom:uCG"); + uCGnew = memory->grow(atom->uCGnew,nmax,"atom:uCGnew"); duCond = memory->grow(atom->duCond,nmax,"atom:duCond"); duMech = memory->grow(atom->duMech,nmax,"atom:duMech"); + duChem = memory->grow(atom->duChem,nmax,"atom:duChem"); if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) @@ -94,8 +98,12 @@ void AtomVecDPD::grow_reset() dpdTheta = atom->dpdTheta; uCond = atom->uCond; uMech = atom->uMech; + uChem = atom->uChem; + uCG = atom->uCG; + uCGnew = atom->uCGnew; duCond = atom->duCond; duMech = atom->duMech; + duChem = atom->duChem; } /* ---------------------------------------------------------------------- @@ -117,6 +125,9 @@ void AtomVecDPD::copy(int i, int j, int delflag) dpdTheta[j] = dpdTheta[i]; uCond[j] = uCond[i]; uMech[j] = uMech[i]; + uChem[j] = uChem[i]; + uCG[j] = uCG[i]; + uCGnew[j] = uCGnew[i]; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) @@ -141,6 +152,7 @@ int AtomVecDPD::pack_comm(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; } } else { if (domain->triclinic == 0) { @@ -160,6 +172,7 @@ int AtomVecDPD::pack_comm(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; } } return m; @@ -186,6 +199,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; } } else { if (domain->triclinic == 0) { @@ -209,6 +223,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; } } else { dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; @@ -231,6 +246,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; } } } @@ -252,6 +268,7 @@ void AtomVecDPD::unpack_comm(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; } } @@ -273,6 +290,7 @@ void AtomVecDPD::unpack_comm_vel(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; } } @@ -328,6 +346,9 @@ int AtomVecDPD::pack_border(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } } else { if (domain->triclinic == 0) { @@ -350,6 +371,9 @@ int AtomVecDPD::pack_border(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } } @@ -384,6 +408,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } } else { if (domain->triclinic == 0) { @@ -410,6 +437,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } } else { dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; @@ -435,6 +465,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf, buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } } } @@ -458,6 +491,9 @@ int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf) buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } return m; } @@ -474,6 +510,9 @@ int AtomVecDPD::pack_border_hybrid(int n, int *list, double *buf) buf[m++] = dpdTheta[j]; buf[m++] = uCond[j]; buf[m++] = uMech[j]; + buf[m++] = uChem[j]; + buf[m++] = uCG[j]; + buf[m++] = uCGnew[j]; } return m; } @@ -497,6 +536,9 @@ void AtomVecDPD::unpack_border(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; + uCG[i] = buf[m++]; + uCGnew[i] = buf[m++]; } if (atom->nextra_border) @@ -527,6 +569,9 @@ void AtomVecDPD::unpack_border_vel(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; + uCG[i] = buf[m++]; + uCGnew[i] = buf[m++]; } if (atom->nextra_border) @@ -547,6 +592,7 @@ int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; } return m; } @@ -563,6 +609,9 @@ int AtomVecDPD::unpack_border_hybrid(int n, int first, double *buf) dpdTheta[i] = buf[m++]; uCond[i] = buf[m++]; uMech[i] = buf[m++]; + uChem[i] = buf[m++]; + uCG[i] = buf[m++]; + uCGnew[i] = buf[m++]; } return m; } @@ -588,6 +637,9 @@ int AtomVecDPD::pack_exchange(int i, double *buf) buf[m++] = dpdTheta[i]; buf[m++] = uCond[i]; buf[m++] = uMech[i]; + buf[m++] = uChem[i]; + buf[m++] = uCG[i]; + buf[m++] = uCGnew[i]; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) @@ -618,6 +670,9 @@ int AtomVecDPD::unpack_exchange(double *buf) dpdTheta[nlocal] = buf[m++]; uCond[nlocal] = buf[m++]; uMech[nlocal] = buf[m++]; + uChem[nlocal] = buf[m++]; + uCG[nlocal] = buf[m++]; + uCGnew[nlocal] = buf[m++]; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) @@ -638,7 +693,7 @@ int AtomVecDPD::size_restart() int i; int nlocal = atom->nlocal; - int n = 14 * nlocal; // 11 + dpdTheta + uCond + uMech + int n = 15 * nlocal; // 11 + dpdTheta + uCond + uMech + uChem if (atom->nextra_restart) for (int iextra = 0; iextra < atom->nextra_restart; iextra++) @@ -670,6 +725,7 @@ int AtomVecDPD::pack_restart(int i, double *buf) buf[m++] = dpdTheta[i]; buf[m++] = uCond[i]; buf[m++] = uMech[i]; + buf[m++] = uChem[i]; if (atom->nextra_restart) for (int iextra = 0; iextra < atom->nextra_restart; iextra++) @@ -706,6 +762,7 @@ int AtomVecDPD::unpack_restart(double *buf) dpdTheta[nlocal] = buf[m++]; uCond[nlocal] = buf[m++]; uMech[nlocal] = buf[m++]; + uChem[nlocal] = buf[m++]; double **extra = atom->extra; if (atom->nextra_store) { @@ -742,8 +799,12 @@ void AtomVecDPD::create_atom(int itype, double *coord) dpdTheta[nlocal] = 0.0; uCond[nlocal] = 0.0; uMech[nlocal] = 0.0; + uChem[nlocal] = 0.0; + uCG[nlocal] = 0.0; + uCGnew[nlocal] = 0.0; duCond[nlocal] = 0.0; duMech[nlocal] = 0.0; + duChem[nlocal] = 0.0; atom->nlocal++; } @@ -781,6 +842,9 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) rho[nlocal] = 0.0; uCond[nlocal] = 0.0; uMech[nlocal] = 0.0; + uChem[nlocal] = 0.0; + uCG[nlocal] = 0.0; + uCGnew[nlocal] = 0.0; atom->nlocal++; } @@ -870,8 +934,12 @@ bigint AtomVecDPD::memory_usage() if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax); if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax); if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax); + if (atom->memcheck("uChem")) bytes += memory->usage(uChem,nmax); + if (atom->memcheck("uCG")) bytes += memory->usage(uCG,nmax); + if (atom->memcheck("uCGnew")) bytes += memory->usage(uCGnew,nmax); if (atom->memcheck("duCond")) bytes += memory->usage(duCond,nmax); if (atom->memcheck("duMech")) bytes += memory->usage(duMech,nmax); + if (atom->memcheck("duChem")) bytes += memory->usage(duChem,nmax); return bytes; } diff --git a/src/USER-DPD/atom_vec_dpd.h b/src/USER-DPD/atom_vec_dpd.h index 753705e763..71ef48d053 100644 --- a/src/USER-DPD/atom_vec_dpd.h +++ b/src/USER-DPD/atom_vec_dpd.h @@ -58,8 +58,8 @@ class AtomVecDPD : public AtomVec { void write_data(FILE *, int, double **); int write_data_hybrid(FILE *, double *); bigint memory_usage(); - double *uCond,*uMech,*dpdTheta,*rho; - double *duCond,*duMech; + double *uCond,*uMech,*uChem,*uCG,*uCGnew,*rho,*dpdTheta; + double *duCond,*duMech,*duChem; protected: tagint *tag; diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 87eab0baac..59716362c7 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -59,6 +59,7 @@ void ComputeDpd::compute_vector() double *uCond = atom->uCond; double *uMech = atom->uMech; + double *uChem = atom->uChem; double *dpdTheta = atom->dpdTheta; int nlocal = atom->nlocal; int *mask = atom->mask; @@ -72,7 +73,7 @@ void ComputeDpd::compute_vector() if (mask[i] & groupbit){ dpdU[0] += uCond[i]; dpdU[1] += uMech[i]; - dpdU[2] += uCond[i] + uMech[i]; + dpdU[2] += uChem[i]; dpdU[3] += 1.0 / dpdTheta[i]; dpdU[4]++; } diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index 8d944a292f..10f5d8203f 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -40,7 +40,7 @@ ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) : if (narg != 3) error->all(FLERR,"Illegal compute dpd/atom command"); peratom_flag = 1; - size_peratom_cols = 3; + size_peratom_cols = 4; nmax = 0; dpdAtom = NULL; @@ -77,21 +77,23 @@ void ComputeDpdAtom::compute_peratom() double *uCond = atom->uCond; double *uMech = atom->uMech; + double *uChem = atom->uChem; double *dpdTheta = atom->dpdTheta; + int nlocal = atom->nlocal; int *mask = atom->mask; - if (atom->nmax > nmax) { + if (nlocal > nmax) { memory->destroy(dpdAtom); nmax = atom->nmax; memory->create(dpdAtom,nmax,size_peratom_cols,"dpd/atom:dpdAtom"); array_atom = dpdAtom; } - const int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit){ dpdAtom[i][0] = uCond[i]; dpdAtom[i][1] = uMech[i]; - dpdAtom[i][2] = dpdTheta[i]; + dpdAtom[i][2] = uChem[i]; + dpdAtom[i][3] = dpdTheta[i]; } } } From 9fbe6666772346700cff5e8c249902d38d026828 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:20:33 +0000 Subject: [PATCH 075/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15119 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/USER-DPD/fix_eos_table_rx.cpp | 791 +++++++++++++++++++ src/USER-DPD/fix_eos_table_rx.h | 153 ++++ src/USER-DPD/fix_rx.cpp | 804 +++++++++++++++++++ src/USER-DPD/fix_rx.h | 134 ++++ src/USER-DPD/pair_exp6_rx.cpp | 968 +++++++++++++++++++++++ src/USER-DPD/pair_exp6_rx.h | 137 ++++ src/USER-DPD/pair_multi_lucy_rx.cpp | 960 +++++++++++++++++++++++ src/USER-DPD/pair_multi_lucy_rx.h | 161 ++++ src/USER-DPD/pair_table_rx.cpp | 1126 +++++++++++++++++++++++++++ src/USER-DPD/pair_table_rx.h | 172 ++++ 10 files changed, 5406 insertions(+) create mode 100644 src/USER-DPD/fix_eos_table_rx.cpp create mode 100644 src/USER-DPD/fix_eos_table_rx.h create mode 100644 src/USER-DPD/fix_rx.cpp create mode 100644 src/USER-DPD/fix_rx.h create mode 100644 src/USER-DPD/pair_exp6_rx.cpp create mode 100644 src/USER-DPD/pair_exp6_rx.h create mode 100644 src/USER-DPD/pair_multi_lucy_rx.cpp create mode 100644 src/USER-DPD/pair_multi_lucy_rx.h create mode 100644 src/USER-DPD/pair_table_rx.cpp create mode 100644 src/USER-DPD/pair_table_rx.h diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp new file mode 100644 index 0000000000..f7acada9d5 --- /dev/null +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -0,0 +1,791 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (U.S. Army Research Laboratory) +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_eos_table_rx.h" +#include "atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "comm.h" +#include +#include "modify.h" + +#define MAXLINE 1024 + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixEOStableRX::FixEOStableRX(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg != 8) error->all(FLERR,"Illegal fix eos/table/rx command"); + restart_peratom = 1; + nevery = 1; + + bool rx_flag = false; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style,"rx",2) == 0) rx_flag = true; + if (!rx_flag) error->all(FLERR,"FixEOStableRX requires a fix rx command."); + + nspecies = atom->nspecies_dpd; + if(nspecies==0) error->all(FLERR,"There are no rx species specified."); + + if (strcmp(arg[3],"linear") == 0) tabstyle = LINEAR; + else error->all(FLERR,"Unknown table style in fix eos/table/rx"); + + tablength = force->inumeric(FLERR,arg[5]); + if (tablength < 2) error->all(FLERR,"Illegal number of eos/table/rx entries"); + + ntables = 0; + tables = NULL; + tables2 = NULL; + int me; + MPI_Comm_rank(world,&me); + for (int ii=0;iisrealloc(tables,(ntables+1)*sizeof(Table),"eos:table/rx"); + tables2 = (Table *) + memory->srealloc(tables2,(ntables+1)*sizeof(Table),"eos:table/rx"); + + Table *tb = &tables[ntables]; + Table *tb2 = &tables2[ntables]; + + null_table(tb); + null_table(tb2); + + ntables++; + } + + ntables = 0; + Table *tb = &tables[ntables]; + Table *tb2 = &tables2[ntables]; + + if (me == 0) read_table(tb,tb2,arg[4],arg[6]); + + for (int ii=0;iininput <= 1) error->one(FLERR,"Invalid eos/table/rx length"); + + tb->lo = tb->rfile[0]; + tb->hi = tb->rfile[tb->ninput-1]; + if (tb->lo >= tb->hi) error->all(FLERR,"eos/table/rx values are not increasing"); + + if (tb2->ninput <= 1) error->one(FLERR,"Invalid eos/table/rx length"); + + tb2->lo = tb2->rfile[0]; + tb2->hi = tb2->rfile[tb2->ninput-1]; + if (tb2->lo >= tb2->hi) error->all(FLERR,"eos/table/rx values are not increasing"); + + // spline read-in and compute r,e,f vectors within table + + spline_table(tb); + compute_table(tb); + spline_table(tb2); + compute_table(tb2); + ntables++; + } + + // Read the Formation Enthalpies + read_file(arg[7]); + + comm_forward = 3; + comm_reverse = 2; +} + +/* ---------------------------------------------------------------------- */ + +FixEOStableRX::~FixEOStableRX() +{ + for (int m = 0; m < ntables; m++) { + free_table(&tables[m]); + free_table(&tables2[m]); + } + memory->sfree(tables); + memory->sfree(tables2); + + delete [] dHf; +} + +/* ---------------------------------------------------------------------- */ + +int FixEOStableRX::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::setup(int vflag) +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *uChem = atom->uChem; + double *dpdTheta = atom->dpdTheta; + double duChem; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + duChem = uCG[i] - uCGnew[i]; + uChem[i] += duChem; + uCG[i] = double(0.0); + uCGnew[i] = double(0.0); + } + + // Communicate the updated momenta and velocities to all nodes + comm->forward_comm_fix(this); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + temperature_lookup(i,uCond[i]+uMech[i]+uChem[i],dpdTheta[i]); +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::init() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *uChem = atom->uChem; + double *dpdTheta = atom->dpdTheta; + double tmp; + + if(this->restart_reset){ + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + temperature_lookup(i,uCond[i]+uMech[i]+uChem[i],dpdTheta[i]); + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature <= zero"); + energy_lookup(i,dpdTheta[i],tmp); + uCond[i] = tmp / double(2.0); + uMech[i] = tmp / double(2.0); + uChem[i] = double(0.0); + } + } +} + + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::post_integrate() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *uChem = atom->uChem; + double *dpdTheta = atom->dpdTheta; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + temperature_lookup(i,uCond[i]+uMech[i]+uChem[i],dpdTheta[i]); + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature <= zero"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::end_of_step() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *uChem = atom->uChem; + double *dpdTheta = atom->dpdTheta; + double duChem; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + // Communicate the ghost uCGnew + comm->reverse_comm_fix(this); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + duChem = uCG[i] - uCGnew[i]; + uChem[i] += duChem; + uCG[i] = double(0.0); + uCGnew[i] = double(0.0); + } + + // Communicate the updated momenta and velocities to all nodes + comm->forward_comm_fix(this); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + temperature_lookup(i,uCond[i]+uMech[i]+uChem[i],dpdTheta[i]); + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature <= zero"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::read_file(char *file) +{ + int params_per_line = 2; + char **words = new char*[params_per_line+1]; + + dHf = new double[nspecies]; + + // open file on proc 0 + + FILE *fp; + fp = NULL; + if (comm->me == 0) { + fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open eos table/rx potential file %s",file); + error->one(FLERR,str); + } + } + + // one set of params can span multiple lines + int n,nwords,ispecies; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Incorrect format in eos table/rx potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; + + for (ispecies = 0; ispecies < nspecies; ispecies++) + if (strcmp(words[0],&atom->dname[ispecies][0]) == 0) break; + if (ispecies == nspecies) continue; + + dHf[ispecies] = atof(words[1]); + } + + delete [] words; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::null_table(Table *tb) +{ + tb->rfile = tb->efile = NULL; + tb->e2file = NULL; + tb->r = tb->e = tb->de = NULL; + tb->e2 = NULL; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::free_table(Table *tb) +{ + memory->destroy(tb->rfile); + memory->destroy(tb->efile); + memory->destroy(tb->e2file); + + memory->destroy(tb->r); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->e2); +} + +/* ---------------------------------------------------------------------- + read table file, only called by proc 0 +------------------------------------------------------------------------- */ + +void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword) +{ + char line[MAXLINE]; + + // open file + + FILE *fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open file %s",file); + error->one(FLERR,str); + } + + // loop until section found with matching keyword + + while (1) { + if (fgets(line,MAXLINE,fp) == NULL) + error->one(FLERR,"Did not find keyword in table file"); + if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line + if (line[0] == '#') continue; // comment + char *word = strtok(line," \t\n\r"); + if (strcmp(word,keyword) == 0) break; // matching keyword + fgets(line,MAXLINE,fp); // no match, skip section + param_extract(tb,line); + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + } + + // read args on 2nd line of section + // allocate table arrays for file values + + fgets(line,MAXLINE,fp); + param_extract(tb,line); + tb2->ninput = tb->ninput; + memory->create(tb->rfile,tb->ninput,"eos:rfile"); + memory->create(tb->efile,tb->ninput,"eos:efile"); + memory->create(tb2->rfile,tb2->ninput,"eos:rfile"); + memory->create(tb2->efile,tb2->ninput,"eos:efile"); + + for (int ispecies=1;ispeciesninput = tb->ninput; + tbl2->ninput = tb2->ninput; + + memory->create(tbl->rfile,tbl->ninput,"eos:rfile"); + memory->create(tbl->efile,tbl->ninput,"eos:efile"); + memory->create(tbl2->rfile,tbl2->ninput,"eos:rfile"); + memory->create(tbl2->efile,tbl2->ninput,"eos:efile"); + } + + // read r,e table values from file + + int itmp; + double rtmp, tmpE; + int nwords; + char * word; + int ispecies; + int ninputs = tb->ninput; + + fgets(line,MAXLINE,fp); + for (int i = 0; i < ninputs; i++) { + fgets(line,MAXLINE,fp); + + nwords = atom->count_words(line); + if(nwords != nspecies+2){ + printf("nwords=%d nspecies=%d\n",nwords,nspecies); + error->all(FLERR,"Illegal fix eos/table/rx command"); + } + nwords = 0; + word = strtok(line," \t\n\r\f"); + itmp = atoi(word); + word = strtok(NULL," \t\n\r\f"); + rtmp = atof(word); + + for (int icolumn=0;icolumnrfile[i] = rtmp; + tbl->efile[i] = tmpE; + + tbl2->rfile[i] = tmpE; + tbl2->efile[i] = rtmp; + } + } + fclose(fp); +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in e2file +------------------------------------------------------------------------- */ + +void FixEOStableRX::spline_table(Table *tb) +{ + memory->create(tb->e2file,tb->ninput,"eos:e2file"); + + double ep0 = 0.0; + double epn = 0.0; + spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file); + +} + +/* ---------------------------------------------------------------------- + compute r,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void FixEOStableRX::compute_table(Table *tb) +{ + // delta = table spacing for N-1 bins + int tlm1 = tablength-1; + + tb->delta = (tb->hi - tb->lo)/ tlm1; + tb->invdelta = 1.0/tb->delta; + tb->deltasq6 = tb->delta*tb->delta / 6.0; + + // N-1 evenly spaced bins in r from min to max + // r,e = value at lower edge of bin + // de values = delta values of e,f + // r,e are N in length so de arrays can compute difference + + memory->create(tb->r,tablength,"eos:r"); + memory->create(tb->e,tablength,"eos:e"); + memory->create(tb->de,tlm1,"eos:de"); + memory->create(tb->e2,tablength,"eos:e2"); + + double a; + for (int i = 0; i < tablength; i++) { + a = tb->lo + i*tb->delta; + tb->r[i] = a; + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a); + } + + for (int i = 0; i < tlm1; i++) { + tb->de[i] = tb->e[i+1] - tb->e[i]; + } +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value + N is required, other params are optional +------------------------------------------------------------------------- */ + +void FixEOStableRX::param_extract(Table *tb, char *line) +{ + int ispecies; + ncolumn = 0; + + eosSpecies = new int[nspecies]; + for (ispecies = 0; ispecies < nspecies; ispecies++) + eosSpecies[ispecies] = -1; + + tb->ninput = 0; + + char *word = strtok(line," \t\n\r\f"); + if (strcmp(word,"N") == 0) { + word = strtok(NULL," \t\n\r\f"); + tb->ninput = atoi(word); + } else + error->one(FLERR,"Invalid keyword in fix eos/table/rx parameters"); + word = strtok(NULL," \t\n\r\f"); + + while (word) { + for (ispecies = 0; ispecies < nspecies; ispecies++) + if (strcmp(word,&atom->dname[ispecies][0]) == 0){ + eosSpecies[ncolumn] = ispecies; + ncolumn++; + break; + } + if (ispecies == nspecies){ + printf("name=%s not found in species list\n",word); + error->one(FLERR,"Invalid keyword in fix eos/table/rx parameters"); + } + word = strtok(NULL," \t\n\r\f"); + } + + for (int icolumn = 0; icolumn < ncolumn; icolumn++) + if(eosSpecies[icolumn]==-1) + error->one(FLERR,"EOS data is missing from fix eos/table/rx tabe"); + if(ncolumn != nspecies){ + printf("ncolumns=%d nspecies=%d\n",ncolumn,nspecies); + error->one(FLERR,"The number of columns in fix eos/table/rx does not match the number of species"); + } + if (tb->ninput == 0) error->one(FLERR,"fix eos/table/rx parameters did not set N"); + +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,rfile,efile +------------------------------------------------------------------------- */ + +void FixEOStableRX::bcast_table(Table *tb) +{ + MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); + + int me; + MPI_Comm_rank(world,&me); + if (me > 0) { + memory->create(tb->rfile,tb->ninput,"eos:rfile"); + memory->create(tb->efile,tb->ninput,"eos:efile"); + } + + MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void FixEOStableRX::spline(double *x, double *y, int n, + double yp1, double ypn, double *y2) +{ + int i,k; + double p,qn,sig,un; + double *u = new double[n]; + + if (yp1 > 0.99e30) y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1); + } + for (i = 1; i < n-1; i++) { + sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]); + p = sig*y2[i-1] + 2.0; + y2[i] = (sig-1.0) / p; + u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]); + u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p; + } + if (ypn > 0.99e30) qn = un = 0.0; + else { + qn = 0.5; + un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2])); + } + y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0); + for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k]; + + delete [] u; +} + +/* ---------------------------------------------------------------------- */ + +double FixEOStableRX::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo,khi,k; + double h,b,a,y; + + klo = 0; + khi = n-1; + while (khi-klo > 1) { + k = (khi+klo) >> 1; + if (xa[k] > x) khi = k; + else klo = k; + } + h = xa[khi]-xa[klo]; + a = (xa[khi]-x) / h; + b = (x-xa[klo]) / h; + y = a*ya[klo] + b*ya[khi] + + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; + return y; +} + +/* ---------------------------------------------------------------------- + calculate potential ui at temperature thetai +------------------------------------------------------------------------- */ + +void FixEOStableRX::energy_lookup(int id, double thetai, double &ui) +{ + int itable; + double fraction, uTmp, nTotal; + + ui = double(0.0); + nTotal = double(0.0); + for(int ispecies=0;ispecieslo); + thetai = MIN(thetai,tb->hi); + + if (tabstyle == LINEAR) { + itable = static_cast ((thetai - tb->lo) * tb->invdelta); + fraction = (thetai - tb->r[itable]) * tb->invdelta; + uTmp = tb->e[itable] + fraction*tb->de[itable]; + + uTmp += dHf[ispecies]; + // mol fraction form: + ui += atom->dvector[ispecies][id]*uTmp; + nTotal += atom->dvector[ispecies][id]; + } + } + ui = ui - double(nTotal+1.5)*force->boltz*thetai; +} + +/* ---------------------------------------------------------------------- + calculate temperature thetai at energy ui +------------------------------------------------------------------------- */ + +void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) +{ + int it; + double t1,t2,u1,u2,f1,f2; + double maxit = 100; + double temp; + + + // Store the current thetai in t1 + t1 = thetai; + + // Compute u1 at thetai + energy_lookup(id,t1,u1); + + // Compute f1 + f1 = u1 - ui; + + // Compute guess of t2 + t2 = (double(1.0) + double(0.001))*t1; + + // Compute u2 at t2 + energy_lookup(id,t2,u2); + + // Compute f1 + f2 = u2 - ui; + + // Apply the Secant Method + for(it=0; itone(FLERR,"Divide by zero in secant solver."); + + temp = t2 - f2*(t2-t1)/(f2-f1); + if(fabs(temp-t2) < 1e-6) break; + f1 = f2; + t1 = t2; + t2 = temp; + energy_lookup(id,t2,u2); + f2 = u2 - ui; + } + if(it==maxit){ + printf("id=%d ui=%lf t1=%lf t2=%lf f1=%lf f2=%lf\n",id,ui,t1,t2,f1,f2); + error->one(FLERR,"Maxit exceeded in secant solver"); + } + thetai = temp; +} + +/* ---------------------------------------------------------------------- */ + +int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +{ + int ii,jj,m; + double *uChem = atom->uChem; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + m = 0; + for (ii = 0; ii < n; ii++) { + jj = list[ii]; + buf[m++] = uChem[jj]; + buf[m++] = uCG[jj]; + buf[m++] = uCGnew[jj]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::unpack_forward_comm(int n, int first, double *buf) +{ + int ii,m,last; + double *uChem = atom->uChem; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + m = 0; + last = first + n ; + for (ii = first; ii < last; ii++){ + uChem[ii] = buf[m++]; + uCG[ii] = buf[m++]; + uCGnew[ii] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int FixEOStableRX::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = uCG[i]; + buf[m++] = uCGnew[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStableRX::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + + uCG[j] += buf[m++]; + uCGnew[j] += buf[m++]; + } +} diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/USER-DPD/fix_eos_table_rx.h new file mode 100644 index 0000000000..bb2e507c44 --- /dev/null +++ b/src/USER-DPD/fix_eos_table_rx.h @@ -0,0 +1,153 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(eos/table/rx,FixEOStableRX) + +#else + +#ifndef LMP_FIX_EOS_TABLE_RX_H +#define LMP_FIX_EOS_TABLE_RX_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixEOStableRX : public Fix { + public: + FixEOStableRX(class LAMMPS *, int, char **); + virtual ~FixEOStableRX(); + int setmask(); + void setup(int); + virtual void init(); + virtual void post_integrate(); + virtual void end_of_step(); + void energy_lookup(int, double, double &); + void temperature_lookup(int, double, double &); + + protected: + enum{LINEAR}; + + int tabstyle,tablength; + struct Table { + int ninput; + double lo,hi; + double *rfile,*efile; + double *e2file; + double delta,invdelta,deltasq6; + double *r,*e,*de,*e2; + }; + int ntables; + Table *tables, *tables2; + + void allocate(); + void null_table(Table *); + void free_table(Table *); + void read_table(Table *, Table *, char *, char *); + void bcast_table(Table *); + void spline_table(Table *); + void compute_table(Table *); + + void param_extract(Table *, char *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + + int nspecies; + + void read_file(char *); + + double *dHf; + + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + int pack_forward_comm(int , int *, double *, int, int *); + void unpack_forward_comm(int , int , double *); + + int *eosSpecies; + int ncolumn; + }; +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: FixEOStableRX requires a fix rx command. + +The fix rx command must come before the pair style command in the input file + +E: There are no rx species specified + +There must be at least one species specified through the fix rx command + +E: Invalid eos/table/rx length + +The eos/table/rx table must have more than one entry. + +E: eos/table/rx values are not increasing + +The equation-of-state must an increasing function + +E: Internal temperature <= zero. + +Self-explanatory. + +E: Cannot open eos table/rx potential file %s + +Self-explanatory. + +E: Incorrect format in eos table/rx file + +Self-explanatory. + +E: Cannot open file %s + +Self-explanatory. + +E: Did not find keyword in table file + +Self-explanatory. + +E: Illegal fix eos/table/rx command + +Incorrect number of arguments specified for the fix eos/table/rx command. + +E: Invalid keyword in fix eos/table/rx parameters + +Self-explanatory. + +E: The number of columns in fix eos/table/rx does not match the number of species. + +Self-explanatory. Check format for fix eos/table/rx file. + +E: fix eos/table/rx parameters did not set N + +The number of table entries was not set in the eos/table/rx file + +E: Divide by zero in secant solver. + +The secant solver failed to find a solution. + +E: Maxit exceeded in secant solver + +The maximum number of interations was exceeded in the secant solver + +*/ diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp new file mode 100644 index 0000000000..10b297753e --- /dev/null +++ b/src/USER-DPD/fix_rx.cpp @@ -0,0 +1,804 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_rx.h" +#include "atom.h" +#include "error.h" +#include "group.h" +#include "modify.h" +#include "force.h" +#include "memory.h" +#include "comm.h" +#include "update.h" +#include "domain.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "pair_dpd_fdt_energy.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum{NONE,HARMONIC}; +enum{LUCY}; + +#define MAXLINE 1024 +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +FixRX::FixRX(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg < 6 || narg > 7) error->all(FLERR,"Illegal fix rx command"); + nevery = 1; + + nreactions = maxparam = 0; + params = NULL; + mol2param = NULL; + pairDPDE = NULL; + + // Keep track of the argument list. + int iarg = 3; + + // Read the kinetic file in arg[3]. + kineticsFile = arg[iarg++]; + + // Determine the local temperature averaging method in arg[4]. + wtFlag = 0; + localTempFlag = NONE; + + { + char *word = arg[iarg++]; + if (strcmp(word,"none") == 0) + { + wtFlag = 0; + localTempFlag = NONE; + } + else if (strcmp(word,"lucy") == 0) + { + wtFlag = LUCY; + localTempFlag = HARMONIC; + } + else + error->all(FLERR,"Illegal fix rx local temperature weighting technique"); + } + + // Determine the ODE solver/stepper strategy in arg[5]. + odeIntegrationFlag = ODE_LAMMPS_RK4; + + { + char *word = arg[iarg++]; + if (strcmp(word,"lammps_rk4") == 0 || strcmp(word,"rk4") == 0) + odeIntegrationFlag = ODE_LAMMPS_RK4; + else + error->all(FLERR,"Illegal ODE integration type"); + } + + /// Set the default ODE parameters here. Modify with arg[6]. + /// RK4: This is the # of steps that will be taken with h = dt_dpd / minSteps; + minSteps = 1; + + if (odeIntegrationFlag == ODE_LAMMPS_RK4 && narg==7) + { + // Only one option: the # of steps to take. + char *word = arg[iarg++]; + minSteps = atoi( word ); + } +} + +/* ---------------------------------------------------------------------- */ + +FixRX::~FixRX() +{ + // De-Allocate memory to prevent memory leak + for (int ii = 0; ii < nreactions; ii++){ + delete [] stoich[ii]; + delete [] stoichReactants[ii]; + delete [] stoichProducts[ii]; + } + delete [] stoich; + delete [] stoichReactants; + delete [] stoichProducts; + delete [] kR; +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::post_constructor() +{ + int maxspecies = 1000; + int nUniqueSpecies = 0; + bool match; + + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style,"property/atom",13) == 0) + error->all(FLERR,"fix rx cannot be combined with fix property/atom"); + + char **tmpspecies = new char*[maxspecies]; + for(int jj=0; jj < maxspecies; jj++) + tmpspecies[jj] = NULL; + + // open file on proc 0 + + FILE *fp; + fp = NULL; + if (comm->me == 0) { + fp = fopen(kineticsFile,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open rx file %s",kineticsFile); + error->one(FLERR,str); + } + } + + // Assign species names to tmpspecies array and determine the number of unique species + + int n,nwords,ispecies; + char line[MAXLINE],*ptr; + int eof = 0; + char * word; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // words = ptrs to all words in line + + nwords = 0; + word = strtok(line," \t\n\r\f"); + while (word != NULL){ + word = strtok(NULL, " \t\n\r\f"); + match=false; + for(int jj=0;jj=maxspecies) + error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx."); + tmpspecies[nUniqueSpecies] = new char[strlen(word)]; + strcpy(tmpspecies[nUniqueSpecies],word); + nUniqueSpecies++; + } + word = strtok(NULL, " \t\n\r\f"); + if(strcmp(word,"+") != 0 && strcmp(word,"=") != 0) break; + word = strtok(NULL, " \t\n\r\f"); + } + } + atom->nspecies_dpd = nUniqueSpecies; + nspecies = atom->nspecies_dpd; + + // new id = fix-ID + FIX_STORE_ATTRIBUTE + // new fix group = group for this fix + + id_fix_species = NULL; + id_fix_species_old = NULL; + + n = strlen(id) + strlen("_SPECIES") + 1; + id_fix_species = new char[n]; + n = strlen(id) + strlen("_SPECIES_OLD") + 1; + id_fix_species_old = new char[n]; + + strcpy(id_fix_species,id); + strcat(id_fix_species,"_SPECIES"); + strcpy(id_fix_species_old,id); + strcat(id_fix_species_old,"_SPECIES_OLD"); + + char **newarg = new char*[nspecies+5]; + char **newarg2 = new char*[nspecies+5]; + newarg[0] = id_fix_species; + newarg[1] = group->names[igroup]; + newarg[2] = (char *) "property/atom"; + newarg2[0] = id_fix_species_old; + newarg2[1] = group->names[igroup]; + newarg2[2] = (char *) "property/atom"; + for(int ii=0; iiadd_fix(nspecies+5,newarg); + fix_species = (FixPropertyAtom *) modify->fix[modify->nfix-1]; + + modify->add_fix(nspecies+5,newarg2); + fix_species_old = (FixPropertyAtom *) modify->fix[modify->nfix-1]; + + if(nspecies==0) error->all(FLERR,"There are no rx species specified."); + + for(int jj=0;jjpair_match("dpd/fdt/energy",1); + if (pairDPDE == NULL) + error->all(FLERR,"Must use pair_style dpd/fdt/energy with fix rx"); + + bool eos_flag = false; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"eos/table/rx") == 0) eos_flag = true; + if(!eos_flag) error->all(FLERR,"fix rx requires fix eos/table/rx to be specified"); +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::setup_pre_force(int vflag) +{ + int nlocal = atom->nlocal; + int nghost = atom->nghost; + int *mask = atom->mask; + double *dpdTheta = atom->dpdTheta; + int newton_pair = force->newton_pair; + double tmp, theta; + int ii; + + if(localTempFlag){ + if (newton_pair) { + dpdThetaLocal = new double[nlocal+nghost]; + for (ii = 0; ii < nlocal+nghost; ii++) + dpdThetaLocal[ii] = double(0.0); + } else { + dpdThetaLocal = new double[nlocal]; + for (ii = 0; ii < nlocal; ii++) + dpdThetaLocal[ii] = double(0.0); + } + computeLocalTemperature(); + } + + for (int id = 0; id < nlocal; id++) + for (int ispecies=0; ispeciesdvector[ispecies][id]; + atom->dvector[ispecies+nspecies][id] = tmp; + } + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + if(localTempFlag) theta = dpdThetaLocal[i]; + else theta=dpdTheta[i]; + + // Set the reaction rate constants to zero: no reactions occur at step 0 + for(int irxn=0;irxnforward_comm_fix(this); + if(localTempFlag) delete [] dpdThetaLocal; +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::pre_force(int vflag) +{ + int nlocal = atom->nlocal; + int nghost = atom->nghost; + int *mask = atom->mask; + double *dpdTheta = atom->dpdTheta; + int newton_pair = force->newton_pair; + int ii; + double theta; + + if(localTempFlag){ + if (newton_pair) { + dpdThetaLocal = new double[nlocal+nghost]; + for (ii = 0; ii < nlocal+nghost; ii++) + dpdThetaLocal[ii] = double(0.0); + } else { + dpdThetaLocal = new double[nlocal]; + for (ii = 0; ii < nlocal; ii++) + dpdThetaLocal[ii] = double(0.0); + } + computeLocalTemperature(); + double *dpdTheta = this->dpdThetaLocal; + } + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + if(localTempFlag) theta = dpdThetaLocal[i]; + else theta=dpdTheta[i]; + + //Compute the reaction rate constants + for(int irxn=0;irxnboltz/theta); + if(odeIntegrationFlag==ODE_LAMMPS_RK4) rk4(i); + } + + // Communicate the updated momenta and velocities to all nodes + comm->forward_comm_fix(this); + if(localTempFlag) delete [] dpdThetaLocal; +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::read_file(char *file) +{ + nreactions = 0; + + // open file on proc 0 + + FILE *fp; + fp = NULL; + if (comm->me == 0) { + fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open rx file %s",file); + error->one(FLERR,str); + } + } + + // Count the number of reactions from kinetics file + + int n,nwords,ispecies; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + nreactions++; + } + + // open file on proc 0 + if (comm->me == 0) fp = fopen(file,"r"); + + // read each reaction from kinetics file + eof=0; + char * word; + double tmpStoich; + double sign; + + Arr = new double[nreactions]; + nArr = new double[nreactions]; + Ea = new double[nreactions]; + tempExp = new double[nreactions]; + stoich = new double*[nreactions]; + stoichReactants = new double*[nreactions]; + stoichProducts = new double*[nreactions]; + for (int ii=0;iime == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // words = ptrs to all words in line + + nwords = 0; + word = strtok(line," \t\n\r\f"); + while (word != NULL){ + tmpStoich = atof(word); + word = strtok(NULL, " \t\n\r\f"); + for (ispecies = 0; ispecies < nspecies; ispecies++){ + if (strcmp(word,&atom->dname[ispecies][0]) == 0){ + stoich[nreactions][ispecies] += sign*tmpStoich; + if(signall(FLERR,"Illegal fix rx command"); + } + word = strtok(NULL, " \t\n\r\f"); + if(strcmp(word,"=") == 0) sign = double(1.0); + if(strcmp(word,"+") != 0 && strcmp(word,"=") != 0){ + if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation"); + Arr[nreactions] = atof(word); + word = strtok(NULL, " \t\n\r\f"); + if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation"); + nArr[nreactions] = atof(word); + word = strtok(NULL, " \t\n\r\f"); + if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation"); + Ea[nreactions] = atof(word); + sign = double(-1.0); + break; + } + word = strtok(NULL, " \t\n\r\f"); + } + nreactions++; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::setupParams() +{ + int i,j,n; + + // set mol2param for all combinations + // must be a single exact match to lines read from file + + memory->destroy(mol2param); + memory->create(mol2param,nspecies,"pair:mol2param"); + + for (i = 0; i < nspecies; i++) { + n = -1; + for (j = 0; j < nreactions; j++) { + if (i == params[j].ispecies) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = j; + } + } + mol2param[i] = n; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::rk4(int id) +{ + double *k1 = new double[6*nspecies + nreactions]; + double *k2 = k1 + nspecies; + double *k3 = k2 + nspecies; + double *k4 = k3 + nspecies; + double *y = k4 + nspecies; + double *yp = y + nspecies; + + double *dummyArray = yp + nspecies; // Passed to the rhs function. + + const int numSteps = minSteps; + + const double h = update->dt / double(numSteps); + + // Update ConcOld + for (int ispecies = 0; ispecies < nspecies; ispecies++) + { + const double tmp = atom->dvector[ispecies][id]; + atom->dvector[ispecies+nspecies][id] = tmp; + y[ispecies] = tmp; + } + + // Run the requested steps with h. + for (int step = 0; step < numSteps; step++) + { + // k1 + rhs(0.0,y,k1,dummyArray); + + // k2 + for (int ispecies = 0; ispecies < nspecies; ispecies++) + yp[ispecies] = y[ispecies] + double(0.5)*h*k1[ispecies]; + + rhs(0.0,yp,k2,dummyArray); + + // k3 + for (int ispecies = 0; ispecies < nspecies; ispecies++) + yp[ispecies] = y[ispecies] + double(0.5)*h*k2[ispecies]; + + rhs(0.0,yp,k3,dummyArray); + + // k4 + for (int ispecies = 0; ispecies < nspecies; ispecies++) + yp[ispecies] = y[ispecies] + h*k3[ispecies]; + + rhs(0.0,yp,k4,dummyArray); + + for (int ispecies = 0; ispecies < nspecies; ispecies++) + y[ispecies] += h*(k1[ispecies]/6.0 + k2[ispecies]/3.0 + + k3[ispecies]/3.0 + k4[ispecies]/6.0); + + } // end for (int step... + + // Store the solution back in atom->dvector. + for (int ispecies = 0; ispecies < nspecies; ispecies++){ + if(y[ispecies] < double(-1.0e-10)) + error->one(FLERR,"Computed concentration in RK4 solver is < -1.0e-10"); + else if(y[ispecies] < double(0.0)) + y[ispecies] = double(0.0); + atom->dvector[ispecies][id] = y[ispecies]; + } + delete [] k1; +} + +/* ---------------------------------------------------------------------- */ + +int FixRX::rhs(double t, const double *y, double *dydt, void *params) +{ + double rxnRateLawForward; + double *rxnRateLaw = (double *) params; + double VDPD = domain->xprd * domain->yprd * domain->zprd / atom->natoms; + double concentration; + int nspecies = atom->nspecies_dpd; + + for(int ispecies=0; ispeciesx; + int *type = atom->type; + int nlocal = atom->nlocal; + int nghost = atom->nghost; + int newton_pair = force->newton_pair; + + // local temperature variables + double wij, fr, fr4; + double *dpdTheta = atom->dpdTheta; + + // Initialize the local density and local temperature arrays + if (newton_pair) { + sumWeights = new double[nlocal+nghost]; + for (ii = 0; ii < nlocal+nghost; ii++) + sumWeights[ii] = double(0.0); + } else { + sumWeights = new double[nlocal]; + for (ii = 0; ii < nlocal; ii++) + dpdThetaLocal[ii] = double(0.0); + } + + inum = pairDPDE->list->inum; + ilist = pairDPDE->list->ilist; + numneigh = pairDPDE->list->numneigh; + firstneigh = pairDPDE->list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < pairDPDE->cutsq[itype][jtype]) { + double rcut = sqrt(pairDPDE->cutsq[itype][jtype]); + double rij = sqrt(rsq); + double tmpFactor = double(1.0)-rij/rcut; + double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor; + double ratio = rij/rcut; + + // Lucy's Weight Function + if(wtFlag==LUCY){ + wij = (double(1.0)+double(3.0)*ratio) * (double(1.0)-ratio)*(double(1.0)-ratio)*(double(1.0)-ratio); + dpdThetaLocal[i] += wij/dpdTheta[j]; + if (newton_pair || j < nlocal) + dpdThetaLocal[j] += wij/dpdTheta[i]; + } + + sumWeights[i] += wij; + if (newton_pair || j < nlocal) { + sumWeights[j] += wij; + } + + } + } + } + if (newton_pair) comm->reverse_comm_fix(this); + + // self-interaction for local temperature + for (i = 0; i < nlocal; i++){ + + // Lucy Weight Function + if(wtFlag==LUCY){ + wij = double(1.0); + dpdThetaLocal[i] += wij / dpdTheta[i]; + } + sumWeights[i] += wij; + + // Normalized local temperature + dpdThetaLocal[i] = dpdThetaLocal[i] / sumWeights[i]; + + if(localTempFlag == HARMONIC) + dpdThetaLocal[i] = double(1.0) / dpdThetaLocal[i]; + + } + + delete [] sumWeights; +} + +/* ---------------------------------------------------------------------- */ + +int FixRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +{ + int ii,jj,m; + double tmp; + + m = 0; + for (ii = 0; ii < n; ii++) { + jj = list[ii]; + for(int ispecies=0;ispeciesdvector[ispecies][jj]; + buf[m++] = tmp; + tmp = atom->dvector[ispecies+nspecies][jj]; + buf[m++] = tmp; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::unpack_forward_comm(int n, int first, double *buf) +{ + int ii,m,last; + double tmp; + + m = 0; + last = first + n ; + for (ii = first; ii < last; ii++){ + for(int ispecies=0;ispeciesdvector[ispecies][ii] = tmp; + tmp = buf[m++]; + atom->dvector[ispecies+nspecies][ii] = tmp; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixRX::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = dpdThetaLocal[i]; + buf[m++] = sumWeights[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixRX::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + + dpdThetaLocal[j] += buf[m++]; + sumWeights[j] += buf[m++]; + } +} diff --git a/src/USER-DPD/fix_rx.h b/src/USER-DPD/fix_rx.h new file mode 100644 index 0000000000..912b75ed5f --- /dev/null +++ b/src/USER-DPD/fix_rx.h @@ -0,0 +1,134 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(rx,FixRX) + +#else + +#ifndef LMP_FIX_RX_H +#define LMP_FIX_RX_H + +#include "fix.h" + +typedef int (*fnptr)(double, const double *, double *, void *); +namespace LAMMPS_NS { + +enum { ODE_LAMMPS_RK4 }; + +class FixRX : public Fix { + public: + FixRX(class LAMMPS *, int, char **); + ~FixRX(); + int setmask(); + void post_constructor(); + virtual void init(); + virtual void setup_pre_force(int); + virtual void pre_force(int); + + protected: + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + int pack_forward_comm(int , int *, double *, int, int *); + void unpack_forward_comm(int , int , double *); + + double tmpArg; + + int *mol2param; // mapping from molecule to parameters + int nreactions; // # of stored parameter sets + int maxparam; // max # of parameter sets + struct Param { + double cp; + int ispecies; + char *name; // names of unique molecules and interaction type + }; + Param *params; // parameter set for an I-J-K interaction + + int nspecies; + void read_file(char *); + void setupParams(); + double *Arr, *nArr, *Ea, *tempExp; + double **stoich, **stoichReactants, **stoichProducts; + double *kR; + void rk4(int); + + class PairDPDfdtEnergy *pairDPDE; + double *dpdThetaLocal; + double *sumWeights; + void computeLocalTemperature(); + int localTempFlag,wtFlag,odeIntegrationFlag; + double sigFactor; + + int rhs(double, const double *, double *, void *); + + private: + char *kineticsFile; + char *id_fix_species,*id_fix_species_old; + class FixPropertyAtom *fix_species,*fix_species_old; + + // ODE Parameters + int minSteps; //!< Minimum # of steps for the ODE solver(s). + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: fix rx cannot be combined with fix property/atom + +Self-explanatory + +E: Cannot open rx file %s + +Self-explanatory + +E: Exceeded the maximum number of species permitted in fix rx + +Reduce the number of species in the fix rx reaction kinetics file + +E: There are no rx species specified. + +Self-explanatory + +E: Must use pair_style dpd/fdt/energy with fix rx. + +Self-explanatory + +E: fix rx requires fix eos/table/rx to be specified. + +Self-explanatory + +E: Missing parameters in reaction kinetic equation. + +Self-explanatory + +E: Potential file has duplicate entry. + +Self-explanatory + +E: Computed concentration in RK4 solver is < -1.0e-10. + +Self-explanatory: Adjust settings for the RK4 solver. + +*/ diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp new file mode 100644 index 0000000000..e6aeb9ac7d --- /dev/null +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -0,0 +1,968 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_exp6_rx.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "modify.h" +#include "fix.h" +#include "float.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define MAXLINE 1024 +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +PairExp6rx::PairExp6rx(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; + + nspecies = 0; + nparams = maxparam = 0; + params = NULL; + mol2param = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairExp6rx::~PairExp6rx() +{ + memory->destroy(params); + memory->destroy(mol2param); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairExp6rx::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair; + double rsq,rinv,r2inv,r6inv,forceExp6,factor_lj; + double rCut,rCutInv,rCut2inv,rCut6inv,rCutExp,urc,durc; + double rm2ij,rm6ij; + double r,rexp; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwlOld = 0.0; + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + double alphaOld12_ij, rmOld12_ij, epsilonOld12_ij; + double alphaOld21_ij, rmOld21_ij, epsilonOld21_ij; + double alpha12_ij, rm12_ij, epsilon12_ij; + double alpha21_ij, rm21_ij, epsilon21_ij; + double rminv, buck1, buck2; + double epsilonOld1_i,alphaOld1_i,rmOld1_i; + double epsilonOld1_j,alphaOld1_j,rmOld1_j; + double epsilonOld2_i,alphaOld2_i,rmOld2_i; + double epsilonOld2_j,alphaOld2_j,rmOld2_j; + double epsilon1_i,alpha1_i,rm1_i; + double epsilon1_j,alpha1_j,rm1_j; + double epsilon2_i,alpha2_i,rm2_i; + double epsilon2_j,alpha2_j,rm2_j; + double evdwlOldEXP6_12, evdwlOldEXP6_21; + double evdwlEXP6_12, evdwlEXP6_21, fpairEXP6_12, fpairEXP6_21; + double fractionOld1_i, fractionOld1_j; + double fractionOld2_i, fractionOld2_j; + double fraction1_i, fraction1_j; + double fraction2_i, fraction2_j; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + const double nRep = double(12.0); + const double shift = double(1.05); + double rin1, aRep, uin1, win1, uin1rep, rin1exp, rin6, rin6inv; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + getParamsEXP6(i,epsilon1_i,alpha1_i,rm1_i,fraction1_i,epsilon2_i,alpha2_i,rm2_i,fraction2_i,epsilonOld1_i,alphaOld1_i,rmOld1_i,fractionOld1_i,epsilonOld2_i,alphaOld2_i,rmOld2_i,fractionOld2_i); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = double(1.0)/rsq; + r6inv = r2inv*r2inv*r2inv; + + r = sqrt(rsq); + rinv = double(1.0)/r; + + rCut2inv = double(1.0)/cutsq[itype][jtype]; + rCut6inv = rCut2inv*rCut2inv*rCut2inv; + rCut = sqrt(cutsq[itype][jtype]); + rCutInv = double(1.0)/rCut; + + // + // A. Compute the exp-6 potential + // + + // A1. Get alpha, epsilon and rm for particle j + getParamsEXP6(j,epsilon1_j,alpha1_j,rm1_j,fraction1_j,epsilon2_j,alpha2_j,rm2_j,fraction2_j,epsilonOld1_j,alphaOld1_j,rmOld1_j,fractionOld1_j,epsilonOld2_j,alphaOld2_j,rmOld2_j,fractionOld2_j); + + // A2. Apply Lorentz-Berthelot mixing rules for the i-j pair + alphaOld12_ij = sqrt(alphaOld1_i*alphaOld2_j); + rmOld12_ij = 0.5*(rmOld1_i + rmOld2_j); + epsilonOld12_ij = sqrt(epsilonOld1_i*epsilonOld2_j); + alphaOld21_ij = sqrt(alphaOld2_i*alphaOld1_j); + rmOld21_ij = 0.5*(rmOld2_i + rmOld1_j); + epsilonOld21_ij = sqrt(epsilonOld2_i*epsilonOld1_j); + + alpha12_ij = sqrt(alpha1_i*alpha2_j); + rm12_ij = 0.5*(rm1_i + rm2_j); + epsilon12_ij = sqrt(epsilon1_i*epsilon2_j); + alpha21_ij = sqrt(alpha2_i*alpha1_j); + rm21_ij = 0.5*(rm2_i + rm1_j); + epsilon21_ij = sqrt(epsilon2_i*epsilon1_j); + + if(rmOld12_ij!=double(0.0) && rmOld21_ij!=double(0.0)){ + if(alphaOld21_ij == double(6.0) || alphaOld12_ij == double(6.0)) + error->all(FLERR,"alpha_ij is 6.0 in pair exp6"); + + // A3. Compute some convenient quantities for evaluating the force + rminv = 1.0/rmOld12_ij; + buck1 = epsilonOld12_ij / (alphaOld12_ij - 6.0); + rexp = expValue(alphaOld12_ij*(1.0-r*rminv)); + rm2ij = rmOld12_ij*rmOld12_ij; + rm6ij = rm2ij*rm2ij*rm2ij; + + // Compute the shifted potential + rCutExp = expValue(alphaOld12_ij*(1.0-rCut*rminv)); + buck2 = 6.0*alphaOld12_ij; + urc = buck1*(6.0*rCutExp - alphaOld12_ij*rm6ij*rCut6inv); + durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv); + rin1 = shift*rmOld12_ij*func_rin(alphaOld12_ij); + if(r < rin1){ + rin6 = rin1*rin1*rin1*rin1*rin1*rin1; + rin6inv = double(1.0)/rin6; + + rin1exp = expValue(alphaOld12_ij*(1.0-rin1*rminv)); + + uin1 = buck1*(6.0*rin1exp - alphaOld12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut); + + win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc; + + aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep; + + uin1rep = aRep/pow(rin1,nRep); + + evdwlOldEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep); + + } else { + evdwlOldEXP6_12 = buck1*(6.0*rexp - alphaOld12_ij*rm6ij*r6inv) - urc - durc*(r-rCut); + } + + // A3. Compute some convenient quantities for evaluating the force + rminv = 1.0/rmOld21_ij; + buck1 = epsilonOld21_ij / (alphaOld21_ij - 6.0); + buck2 = 6.0*alphaOld21_ij; + rexp = expValue(alphaOld21_ij*(1.0-r*rminv)); + rm2ij = rmOld21_ij*rmOld21_ij; + rm6ij = rm2ij*rm2ij*rm2ij; + + // Compute the shifted potential + rCutExp = expValue(alphaOld21_ij*(1.0-rCut*rminv)); + buck2 = 6.0*alphaOld21_ij; + urc = buck1*(6.0*rCutExp - alphaOld21_ij*rm6ij*rCut6inv); + durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv); + rin1 = shift*rmOld21_ij*func_rin(alphaOld21_ij); + + if(r < rin1){ + rin6 = rin1*rin1*rin1*rin1*rin1*rin1; + rin6inv = double(1.0)/rin6; + + rin1exp = expValue(alphaOld21_ij*(1.0-rin1*rminv)); + + uin1 = buck1*(6.0*rin1exp - alphaOld21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut); + + win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc; + + aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep; + + uin1rep = aRep/pow(rin1,nRep); + + evdwlOldEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep); + + } else { + evdwlOldEXP6_21 = buck1*(6.0*rexp - alphaOld21_ij*rm6ij*r6inv) - urc - durc*(r-rCut); + } + + if (strcmp(site1,site2) == 0) + evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12; + else + evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*evdwlOldEXP6_21; + + evdwlOld *= factor_lj; + + uCG[i] += double(0.5)*evdwlOld; + uCG[j] += double(0.5)*evdwlOld; + } + + if(rm12_ij!=double(0.0) && rm21_ij!=double(0.0)){ + if(alpha21_ij == double(6.0) || alpha12_ij == double(6.0)) + error->all(FLERR,"alpha_ij is 6.0 in pair exp6"); + + // A3. Compute some convenient quantities for evaluating the force + rminv = 1.0/rm12_ij; + buck1 = epsilon12_ij / (alpha12_ij - 6.0); + buck2 = 6.0*alpha12_ij; + rexp = expValue(alpha12_ij*(1.0-r*rminv)); + rm2ij = rm12_ij*rm12_ij; + rm6ij = rm2ij*rm2ij*rm2ij; + + // Compute the shifted potential + rCutExp = expValue(alpha12_ij*(1.0-rCut*rminv)); + urc = buck1*(6.0*rCutExp - alpha12_ij*rm6ij*rCut6inv); + durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv); + rin1 = shift*rm12_ij*func_rin(alpha12_ij); + + if(r < rin1){ + rin6 = rin1*rin1*rin1*rin1*rin1*rin1; + rin6inv = double(1.0)/rin6; + + rin1exp = expValue(alpha12_ij*(1.0-rin1*rminv)); + + uin1 = buck1*(6.0*rin1exp - alpha12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut); + + win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc; + + aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep; + + uin1rep = aRep/pow(rin1,nRep); + + evdwlEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep); + + forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep); + fpairEXP6_12 = factor_lj*forceExp6*r2inv; + + } else { + + // A4. Compute the exp-6 force and energy + forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc; + fpairEXP6_12 = factor_lj*forceExp6*r2inv; + + evdwlEXP6_12 = buck1*(6.0*rexp - alpha12_ij*rm6ij*r6inv) - urc - durc*(r-rCut); + } + + rminv = 1.0/rm21_ij; + buck1 = epsilon21_ij / (alpha21_ij - 6.0); + buck2 = 6.0*alpha21_ij; + rexp = expValue(alpha21_ij*(1.0-r*rminv)); + rm2ij = rm21_ij*rm21_ij; + rm6ij = rm2ij*rm2ij*rm2ij; + + // Compute the shifted potential + rCutExp = expValue(alpha21_ij*(1.0-rCut*rminv)); + urc = buck1*(6.0*rCutExp - alpha21_ij*rm6ij*rCut6inv); + durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv); + rin1 = shift*rm21_ij*func_rin(alpha21_ij); + + if(r < rin1){ + rin6 = rin1*rin1*rin1*rin1*rin1*rin1; + rin6inv = double(1.0)/rin6; + + rin1exp = expValue(alpha21_ij*(1.0-rin1*rminv)); + + uin1 = buck1*(6.0*rin1exp - alpha21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut); + + win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc; + + aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep; + + uin1rep = aRep/pow(rin1,nRep); + + evdwlEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep); + + forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep); + fpairEXP6_21 = factor_lj*forceExp6*r2inv; + + } else { + + // A4. Compute the exp-6 force and energy + forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc; + fpairEXP6_21 = factor_lj*forceExp6*r2inv; + + evdwlEXP6_21 = buck1*(6.0*rexp - alpha21_ij*rm6ij*r6inv) - urc - durc*(r-rCut); + } + + // + // Apply Mixing Rule to get the overall force for the CG pair + // + if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12; + else fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*fpairEXP6_21; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (strcmp(site1,site2) == 0) + evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12; + else + evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12 + sqrt(fraction2_i*fraction1_j)*evdwlEXP6_21; + evdwl *= factor_lj; + + uCGnew[i] += double(0.5)*evdwl; + uCGnew[j] += double(0.5)*evdwl; + evdwl = evdwlOld; + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairExp6rx::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut_lj"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairExp6rx::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = force->numeric(FLERR,arg[0]); + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } + + allocated = 0; + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairExp6rx::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); + + bool rx_flag = false; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style,"rx",2) == 0) rx_flag = true; + if (!rx_flag) error->all(FLERR,"PairExp6rx requires a fix rx command."); + + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + int n; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + nspecies = atom->nspecies_dpd; + if(nspecies==0) error->all(FLERR,"There are no rx species specified."); + read_file(arg[2]); + + n = strlen(arg[3]) + 1; + site1 = new char[n]; + strcpy(site1,arg[3]); + + int ispecies; + for (ispecies = 0; ispecies < nspecies; ispecies++){ + if (strcmp(site1,&atom->dname[ispecies][0]) == 0) break; + } + if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) + error->all(FLERR,"Site1 name not recognized in pair coefficients"); + + n = strlen(arg[4]) + 1; + site2 = new char[n]; + strcpy(site2,arg[4]); + + for (ispecies = 0; ispecies < nspecies; ispecies++){ + if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break; + } + if (ispecies == nspecies && strcmp(site2,"1fluid") != 0) + error->all(FLERR,"Site2 name not recognized in pair coefficients"); + + fuchslinR = force->numeric(FLERR,arg[5]); + fuchslinEpsilon = force->numeric(FLERR,arg[6]); + + setup(); + + double cut_one = cut_global; + if (narg == 8) cut_one = force->numeric(FLERR,arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairExp6rx::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- */ + +void PairExp6rx::read_file(char *file) +{ + int params_per_line = 5; + char **words = new char*[params_per_line+1]; + + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; + + // open file on proc 0 + + FILE *fp; + fp = NULL; + if (comm->me == 0) { + fp = force->open_potential(file); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open exp6/rx potential file %s",file); + error->one(FLERR,str); + } + } + + // read each set of params from potential file + // one set of params can span multiple lines + + int n,nwords,ispecies; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Incorrect format in exp6/rx potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; + + for (ispecies = 0; ispecies < nspecies; ispecies++) + if (strcmp(words[0],&atom->dname[ispecies][0]) == 0) break; + if (ispecies == nspecies) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ispecies = ispecies; + + n = strlen(&atom->dname[ispecies][0]) + 1; + params[nparams].name = new char[n]; + strcpy(params[nparams].name,&atom->dname[ispecies][0]); + + n = strlen(words[1]) + 1; + params[nparams].potential = new char[n]; + strcpy(params[nparams].potential,words[1]); + if (strcmp(params[nparams].potential,"exp6") == 0){ + params[nparams].alpha = atof(words[2]); + params[nparams].epsilon = atof(words[3]); + params[nparams].rm = atof(words[4]); + if (params[nparams].epsilon <= 0.0 || params[nparams].rm <= 0.0 || + params[nparams].alpha < 0.0) + error->all(FLERR,"Illegal exp6/rx parameters. Rm and Epsilon must be greater than zero. Alpha cannot be negative."); + } else { + error->all(FLERR,"Illegal exp6/rx parameters. Interaction potential does not exist."); + } + nparams++; + } + + delete [] words; +} + +/* ---------------------------------------------------------------------- */ + +void PairExp6rx::setup() +{ + int i,j,n; + + // set mol2param for all combinations + // must be a single exact match to lines read from file + + memory->destroy(mol2param); + memory->create(mol2param,nspecies,"pair:mol2param"); + + for (i = 0; i < nspecies; i++) { + n = -1; + for (j = 0; j < nparams; j++) { + if (i == params[j].ispecies) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = j; + } + } + mol2param[i] = n; + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairExp6rx::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairExp6rx::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairExp6rx::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairExp6rx::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +void PairExp6rx::getParamsEXP6(int id,double &epsilon1,double &alpha1,double &rm1, double &fraction1,double &epsilon2,double &alpha2,double &rm2,double &fraction2,double &epsilon1_old,double &alpha1_old,double &rm1_old, double &fraction1_old,double &epsilon2_old,double &alpha2_old,double &rm2_old,double &fraction2_old) +{ + int iparam, jparam; + double rmi, rmj, rmij, rm3ij; + double epsiloni, epsilonj, epsilonij; + double alphai, alphaj, alphaij; + double epsilon_old, rm3_old, alpha_old, fraction_old; + double epsilon, rm3, alpha, fraction; + double fractionOFA, fractionOFA_old; + double nTotalOFA, nTotalOFA_old; + double nTotal, nTotal_old; + double xMolei, xMolej, xMolei_old, xMolej_old; + + rm3 = double(0.0); + epsilon = double(0.0); + alpha = double(0.0); + epsilon_old = double(0.0); + rm3_old = double(0.0); + alpha_old = double(0.0); + fraction_old = double(0.0); + fraction = double(0.0); + fractionOFA = double(0.0); + fractionOFA_old = double(0.0); + nTotalOFA = double(0.0); + nTotalOFA_old = double(0.0); + nTotal = double(0.0); + nTotal_old = double(0.0); + + // Compute the total number of molecules in the old and new CG particle as well as the total number of molecules in the fluid portion of the old and new CG particle + for (int ispecies = 0; ispecies < nspecies; ispecies++){ + nTotal += atom->dvector[ispecies][id]; + nTotal_old += atom->dvector[ispecies+nspecies][id]; + + iparam = mol2param[ispecies]; + if (iparam < 0 || strcmp(params[iparam].potential,"exp6") != 0) continue; + if (strcmp(site1,"1fluid") == 0 || strcmp(site2,"1fluid") == 0) { + if (strcmp(site1,params[iparam].name) == 0 || strcmp(site2,params[iparam].name) == 0) continue; + nTotalOFA_old += atom->dvector[ispecies+nspecies][id]; + nTotalOFA += atom->dvector[ispecies][id]; + } + } + if(nTotal < 1e-8 || nTotal_old < 1e-8) + error->all(FLERR,"The number of molecules in CG particle is less than 1e-8."); + + // Compute the mole fraction of molecules within the fluid portion of the particle (One Fluid Approximation) + fractionOFA_old = nTotalOFA_old / nTotal_old; + fractionOFA = nTotalOFA / nTotal; + + for (int ispecies = 0; ispecies < nspecies; ispecies++) { + iparam = mol2param[ispecies]; + if (iparam < 0 || strcmp(params[iparam].potential,"exp6") != 0) continue; + + // If Site1 matches a pure species, then grab the parameters + if (strcmp(site1,params[iparam].name) == 0){ + rm1_old = params[iparam].rm; + rm1 = params[iparam].rm; + epsilon1_old = params[iparam].epsilon; + epsilon1 = params[iparam].epsilon; + alpha1_old = params[iparam].alpha; + alpha1 = params[iparam].alpha; + + // Compute the mole fraction of Site1 + fraction1_old = atom->dvector[ispecies+nspecies][id]/nTotal_old; + fraction1 = atom->dvector[ispecies][id]/nTotal; + } + + // If Site2 matches a pure species, then grab the parameters + if (strcmp(site2,params[iparam].name) == 0){ + rm2_old = params[iparam].rm; + rm2 = params[iparam].rm; + epsilon2_old = params[iparam].epsilon; + epsilon2 = params[iparam].epsilon; + alpha2_old = params[iparam].alpha; + alpha2 = params[iparam].alpha; + + // Compute the mole fraction of Site2 + fraction2_old = atom->dvector[ispecies+nspecies][id]/nTotal_old; + fraction2 = atom->dvector[ispecies][id]/nTotal; + } + + // If Site1 or Site2 matches is a fluid, then compute the paramters + if (strcmp(site1,"1fluid") == 0 || strcmp(site2,"1fluid") == 0) { + if (strcmp(site1,params[iparam].name) == 0 || strcmp(site2,params[iparam].name) == 0) continue; + rmi = params[iparam].rm; + epsiloni = params[iparam].epsilon; + alphai = params[iparam].alpha; + xMolei = atom->dvector[ispecies][id]/nTotalOFA; + xMolei_old = atom->dvector[ispecies+nspecies][id]/nTotalOFA_old; + + for (int jspecies = 0; jspecies < nspecies; jspecies++) { + jparam = mol2param[jspecies]; + if (jparam < 0 || strcmp(params[jparam].potential,"exp6") != 0) continue; + if (strcmp(site1,params[jparam].name) == 0 || strcmp(site2,params[jparam].name) == 0) continue; + rmj = params[jparam].rm; + epsilonj = params[jparam].epsilon; + alphaj = params[jparam].alpha; + xMolej = atom->dvector[jspecies][id]/nTotalOFA; + xMolej_old = atom->dvector[jspecies+nspecies][id]/nTotalOFA_old; + + rmij = (rmi+rmj)/2.0; + rm3ij = rmij*rmij*rmij; + epsilonij = sqrt(epsiloni*epsilonj); + alphaij = sqrt(alphai*alphaj); + + if(fractionOFA_old > double(0.0)){ + rm3_old += xMolei_old*xMolej_old*rm3ij; + epsilon_old += xMolei_old*xMolej_old*rm3ij*epsilonij; + alpha_old += xMolei_old*xMolej_old*rm3ij*epsilonij*alphaij; + } + if(fractionOFA > double(0.0)){ + rm3 += xMolei*xMolej*rm3ij; + epsilon += xMolei*xMolej*rm3ij*epsilonij; + alpha += xMolei*xMolej*rm3ij*epsilonij*alphaij; + } + } + } + } + + if(strcmp(site1,"1fluid") == 0){ + rm1 = cbrt(rm3); + if(rm1 < 1e-16) { + rm1 = double(0.0); + epsilon1 = double(0.0); + alpha1 = double(0.0); + } else { + epsilon1 = epsilon / rm3; + alpha1 = alpha / epsilon1 / rm3; + } + + fraction1 = fractionOFA; + + rm1_old = cbrt(rm3_old); + if(rm1_old < 1e-16) { + rm1_old = double(0.0); + epsilon1_old = double(0.0); + alpha1_old = double(0.0); + } else { + epsilon1_old = epsilon_old / rm3_old; + alpha1_old = alpha_old / epsilon1_old / rm3_old; + } + fraction1_old = fractionOFA_old; + + // Fuchslin-Like Exp-6 Scaling + double powfuch = 0.0; + if(fuchslinEpsilon < 0.0){ + fuchslinEpsilon = -1.0*fuchslinEpsilon; + powfuch = pow(nTotalOFA,fuchslinEpsilon); + if(powfuch<1e-15) epsilon1 = 0.0; + else epsilon1 *= 1.0/powfuch; + + powfuch = pow(nTotalOFA_old,fuchslinEpsilon); + if(powfuch<1e-15) epsilon1_old = 0.0; + else epsilon1_old *= 1.0/powfuch; + + } else { + epsilon1 *= pow(nTotalOFA,fuchslinEpsilon); + epsilon1_old *= pow(nTotalOFA_old,fuchslinEpsilon); + } + + if(fuchslinR < 0.0){ + fuchslinR = -1.0*fuchslinR; + powfuch = pow(nTotalOFA,fuchslinR); + if(powfuch<1e-15) rm1 = 0.0; + else rm1 *= 1.0/powfuch; + + powfuch = pow(nTotalOFA_old,fuchslinR); + if(powfuch<1e-15) rm1_old = 0.0; + else rm1_old *= 1.0/powfuch; + + } else { + rm1 *= pow(nTotalOFA,fuchslinR); + rm1_old *= pow(nTotalOFA_old,fuchslinR); + } + } + + if(strcmp(site2,"1fluid") == 0){ + rm2 = cbrt(rm3); + if(rm2 < 1e-16) { + rm2 = double(0.0); + epsilon2 = double(0.0); + alpha2 = double(0.0); + } else { + epsilon2 = epsilon / rm3; + alpha2 = alpha / epsilon2 / rm3; + } + fraction2 = fractionOFA; + + rm2_old = cbrt(rm3_old); + if(rm2_old < 1e-16) { + rm2_old = double(0.0); + epsilon2_old = double(0.0); + alpha2_old = double(0.0); + } else { + epsilon2_old = epsilon_old / rm3_old; + alpha2_old = alpha_old / epsilon2_old / rm3_old; + } + fraction2_old = fractionOFA_old; + + // Fuchslin-Like Exp-6 Scaling + double powfuch = 0.0; + if(fuchslinEpsilon < 0.0){ + fuchslinEpsilon = -1.0*fuchslinEpsilon; + powfuch = pow(nTotalOFA,fuchslinEpsilon); + if(powfuch<1e-15) epsilon2 = 0.0; + else epsilon2 *= 1.0/powfuch; + + powfuch = pow(nTotalOFA_old,fuchslinEpsilon); + if(powfuch<1e-15) epsilon2_old = 0.0; + else epsilon2_old *= 1.0/powfuch; + + } else { + epsilon2 *= pow(nTotalOFA,fuchslinEpsilon); + epsilon2_old *= pow(nTotalOFA_old,fuchslinEpsilon); + } + + if(fuchslinR < 0.0){ + fuchslinR = -1.0*fuchslinR; + powfuch = pow(nTotalOFA,fuchslinR); + if(powfuch<1e-15) rm2 = 0.0; + else rm2 *= 1.0/powfuch; + + powfuch = pow(nTotalOFA_old,fuchslinR); + if(powfuch<1e-15) rm2_old = 0.0; + else rm2_old *= 1.0/powfuch; + + } else { + rm2 *= pow(nTotalOFA,fuchslinR); + rm2_old *= pow(nTotalOFA_old,fuchslinR); + } + } +} + +/* ---------------------------------------------------------------------- */ + +double PairExp6rx::func_rin(double &alpha) +{ + double function; + + const double alpha_min = double(11.0); + const double alpha_max = double(16.0); + const double a = double(3.7682065); + const double b = double(-1.4308614); + + function = a+b*pow(alpha,0.5); + function = expValue(function); + + return function; +} + +/* ---------------------------------------------------------------------- */ + +double PairExp6rx::expValue(double value) +{ + double returnValue; + if(value < DBL_MIN_EXP) returnValue = double(0.0); + else returnValue = exp(value); + + return returnValue; +} diff --git a/src/USER-DPD/pair_exp6_rx.h b/src/USER-DPD/pair_exp6_rx.h new file mode 100644 index 0000000000..ece29dcda7 --- /dev/null +++ b/src/USER-DPD/pair_exp6_rx.h @@ -0,0 +1,137 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(exp6/rx,PairExp6rx) + +#else + +#ifndef LMP_PAIR_EXP6_RX_H +#define LMP_PAIR_EXP6_RX_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairExp6rx : public Pair { + public: + PairExp6rx(class LAMMPS *); + virtual ~PairExp6rx(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + protected: + enum{LINEAR}; + double cut_global; + double **cut; + double **epsilon,**rm,**alpha; + double **rminv,**buck1,**buck2,**offset; + + void allocate(); + int *mol2param; // mapping from molecule to parameters + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + struct Param { + double epsilon,rm,alpha; + int ispecies; + char *name, *potential; // names of unique molecules and interaction type + char *tablename; // name of interaction table + }; + Param *params; // parameter set for an I-J-K interaction + + int nspecies; + void read_file(char *); + void setup(); + + char *site1, *site2; + double fuchslinR, fuchslinEpsilon; + void getParamsEXP6(int, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &); + double func_rin(double &); + double expValue(double); + +/* class FixRX *fixRX; */ +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: alpha_ij is 6.0 in pair exp6 + +Self-explanator + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: PairExp6rx requires a fix rx command + +The fix rx command must come before the pair style command in the input file + +E: There are no rx species specified + +There must be at least one species specified through the fix rx command + +E: Site1 name not recognized in pair coefficients + +The site1 keyword does not match the species keywords specified throug the fix rx command + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open exp6/rx potential file %s + +Self-explanatory + +E: Incorrect format in exp6/rx potential file + +Self-explanatory + +E: Illegal exp6/rx parameters. Rm and Epsilon must be greater than zero. Alpha cannot be negative. + +Self-explanatory + +E: Illegal exp6/rx parameters. Interaction potential does not exist. + +Self-explanatory + +E: Potential file has duplicate entry. + +Self-explanatory + +E: The number of molecules in CG particle is less than 1e-8. + +Self-explanatory. Check the species concentrations have been properly set +and check the reaction kinetic solver parameters in fix rx to more for +sufficient accuracy. + + +*/ diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp new file mode 100644 index 0000000000..6a349101d5 --- /dev/null +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -0,0 +1,960 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------------------------- + Contributing authors: + James Larentzos and Joshua Moore (U.S. Army Research Laboratory) + + Please cite the related publications: + J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor & J.K. Brennan + "A coarse-grain force field for RDX: Density dependent and energy conserving" + The Journal of Chemical Physics, 2016, 144, 104501. +------------------------------------------------------------------------------------------- */ + +#include "mpi.h" +#include +#include "math_const.h" +#include +#include +#include "pair_multi_lucy_rx.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" +#include "citeme.h" +#include "modify.h" +#include "fix.h" + +using namespace LAMMPS_NS; + +enum{NONE,RLINEAR,RSQ}; + +#define MAXLINE 1024 + +static const char cite_pair_multi_lucy_rx[] = + "pair_style multi/lucy/rx command:\n\n" + "@Article{Moore16,\n" + " author = {J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor and J. K. Brennan},\n" + " title = {A coarse-grain force field for RDX: Density dependent and energy conserving},\n" + " journal = {J. Chem. Phys.},\n" + " year = 2016,\n" + " volume = 144\n" + " pages = {104501}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairMultiLucyRX::PairMultiLucyRX(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_multi_lucy_rx); + + if (atom->rho_flag != 1) error->all(FLERR,"Pair multi/lucy/rx command requires atom_style with density (e.g. dpd, meso)"); + + ntables = 0; + tables = NULL; + + comm_forward = 1; + comm_reverse = 1; + +} + +/* ---------------------------------------------------------------------- */ + +PairMultiLucyRX::~PairMultiLucyRX() +{ + for (int m = 0; m < ntables; m++) free_table(&tables[m]); + memory->sfree(tables); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(tabindex); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairMultiLucyRX::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype,itable; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair; + double rsq,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + Table *tb; + + int tlm1 = tablength - 1; + + evdwlOld = 0.0; + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + double fractionOld1_i,fractionOld1_j; + double fractionOld2_i,fractionOld2_j; + double fraction1_i,fraction1_j; + double fraction2_i,fraction2_j; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + double pi = MathConst::MY_PI; + double A_i, A_j; + double fraction_i,fraction_j; + int jtable; + double *rho = atom->rho; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + computeLocalDensity(); + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + getParams(i,fractionOld1_i,fractionOld2_i,fraction1_i,fraction2_i); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + fpair = double(0.0); + getParams(j,fractionOld1_j,fractionOld2_j,fraction1_j,fraction2_j); + + tb = &tables[tabindex[itype][jtype]]; + if (rho[i]*rho[i] < tb->innersq || rho[j]*rho[j] < tb->innersq){ + printf("Table inner cutoff = %lf\n",sqrt(tb->innersq)); + printf("rho[%d]=%lf\n",i,rho[i]); + printf("rho[%d]=%lf\n",j,rho[j]); + error->one(FLERR,"Density < table inner cutoff"); + } + if (tabstyle == LOOKUP) { + itable = static_cast (((rho[i]*rho[i]) - tb->innersq) * tb->invdelta); + jtable = static_cast (((rho[j]*rho[j]) - tb->innersq) * tb->invdelta); + if (itable >= tlm1 || jtable >= tlm1){ + printf("Table outer index = %d\n",tlm1); + printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]); + printf("jtableIndex=%d rho[%d]=%lf\n",jtable,j,rho[j]); + error->one(FLERR,"Density > table outer cutoff"); + } + A_i = tb->f[itable]; + A_j = tb->f[jtable]; + fpair = double(0.5)*(A_i + A_j)*(double(1.0)+double(3.0)*sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype])); + fpair = fpair/sqrt(rsq); + + } else if (tabstyle == LINEAR) { + itable = static_cast ((rho[i]*rho[i] - tb->innersq) * tb->invdelta); + jtable = static_cast (((rho[j]*rho[j]) - tb->innersq) * tb->invdelta); + if (itable >= tlm1 || jtable >= tlm1){ + printf("Table outer index = %d\n",tlm1); + printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]); + printf("jtableIndex=%d rho[%d]=%lf\n",jtable,j,rho[j]); + error->one(FLERR,"Density > table outer cutoff"); + } + if(itable<0) itable=0; + if(itable>=tlm1) itable=tlm1; + if(jtable<0) jtable=0; + if(jtable>=tlm1)jtable=tlm1; + + fraction_i = (((rho[i]*rho[i]) - tb->rsq[itable]) * tb->invdelta); + fraction_j = (((rho[j]*rho[j]) - tb->rsq[jtable]) * tb->invdelta); + if(itable==0) fraction_i=double(0.0); + if(itable==tlm1) fraction_i=double(0.0); + if(jtable==0) fraction_j=double(0.0); + if(jtable==tlm1) fraction_j=double(0.0); + + A_i = tb->f[itable] + fraction_i*tb->df[itable]; + A_j = tb->f[jtable] + fraction_j*tb->df[jtable]; + + fpair = double(0.5)*(A_i + A_j)*(double(1.0)+double(3.0)*sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype]))*(double(1.0) - sqrt(rsq)/sqrt(cutsq[itype][jtype])); + + fpair = fpair / sqrt(rsq); + + } else error->one(FLERR,"Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx"); + + + if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpair; + else fpair = (sqrt(fractionOld1_i*fractionOld2_j) + sqrt(fractionOld2_i*fractionOld1_j))*fpair; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + if (evflag) ev_tally(i,j,nlocal,newton_pair, + 0.0,0.0,fpair,delx,dely,delz); + } + } + + tb = &tables[tabindex[itype][itype]]; + itable = static_cast (((rho[i]*rho[i]) - tb->innersq) * tb->invdelta); + if (tabstyle == LOOKUP) evdwl = tb->e[itable]; + else if (tabstyle == LINEAR){ + if (itable >= tlm1){ + printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]); + error->one(FLERR,"Density > table outer cutoff"); + } + if(itable==0) fraction_i=double(0.0); + else fraction_i = (((rho[i]*rho[i]) - tb->rsq[itable]) * tb->invdelta); + evdwl = tb->e[itable] + fraction_i*tb->de[itable]; + } else error->one(FLERR,"Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx"); + + evdwl *=(pi*cutsq[itype][itype]*cutsq[itype][itype])/double(84.0); + evdwlOld = fractionOld1_i*evdwl; + evdwl = fraction1_i*evdwl; + + uCG[i] += evdwlOld; + uCGnew[i] += evdwl; + + evdwl = evdwlOld; + + if (evflag) ev_tally(0,0,nlocal,newton_pair, + evdwl,0.0,0.0,0.0,0.0,0.0); + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::allocate() +{ + allocated = 1; + const int nt = atom->ntypes + 1; + + memory->create(setflag,nt,nt,"pair:setflag"); + memory->create(cutsq,nt,nt,"pair:cutsq"); + memory->create(tabindex,nt,nt,"pair:tabindex"); + + memset(&setflag[0][0],0,nt*nt*sizeof(int)); + memset(&cutsq[0][0],0,nt*nt*sizeof(double)); + memset(&tabindex[0][0],0,nt*nt*sizeof(int)); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::settings(int narg, char **arg) +{ + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + // new settings + + if (strcmp(arg[0],"lookup") == 0) tabstyle = LOOKUP; + else if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR; + else error->all(FLERR,"Unknown table style in pair_style command"); + + tablength = force->inumeric(FLERR,arg[1]); + if (tablength < 2) error->all(FLERR,"Illegal number of pair table entries"); + + // delete old tables, since cannot just change settings + + for (int m = 0; m < ntables; m++) free_table(&tables[m]); + memory->sfree(tables); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(tabindex); + } + allocated = 0; + + ntables = 0; + tables = NULL; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::coeff(int narg, char **arg) +{ + if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_coeff command"); + + bool rx_flag = false; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style,"rx",2) == 0) rx_flag = true; + if (!rx_flag) error->all(FLERR,"PairMultiLucyRX requires a fix rx command."); + + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + int me; + MPI_Comm_rank(world,&me); + tables = (Table *) + memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables"); + Table *tb = &tables[ntables]; + null_table(tb); + if (me == 0) read_table(tb,arg[2],arg[3]); + bcast_table(tb); + + nspecies = atom->nspecies_dpd; + int n; + n = strlen(arg[3]) + 1; + site1 = new char[n]; + strcpy(site1,arg[4]); + + n = strlen(arg[4]) + 1; + site2 = new char[n]; + strcpy(site2,arg[5]); + + // set table cutoff + + if (narg == 7) tb->cut = force->numeric(FLERR,arg[6]); + else if (tb->rflag) tb->cut = tb->rhi; + else tb->cut = tb->rfile[tb->ninput-1]; + + // error check on table parameters + // insure cutoff is within table + + if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length"); + double rlo,rhi; + if (tb->rflag == 0) { + rlo = tb->rfile[0]; + rhi = tb->rfile[tb->ninput-1]; + } else { + rlo = tb->rlo; + rhi = tb->rhi; + } + rho_0 = rlo; + + tb->match = 0; + if (tabstyle == LINEAR && tb->ninput == tablength && + tb->rflag == RSQ) tb->match = 1; + + // spline read-in values and compute r,e,f vectors within table + + if (tb->match == 0) spline_table(tb); + compute_table(tb); + + // store ptr to table in tabindex + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + tabindex[i][j] = ntables; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Illegal pair_coeff command"); + ntables++; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMultiLucyRX::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + tabindex[j][i] = tabindex[i][j]; + + return tables[tabindex[i][j]].cut; +} + +/* ---------------------------------------------------------------------- + read a table section from a tabulated potential file + only called by proc 0 + this function sets these values in Table: + ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) +{ + char line[MAXLINE]; + + // open file + + FILE *fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open file %s",file); + error->one(FLERR,str); + } + + // loop until section found with matching keyword + + while (1) { + if (fgets(line,MAXLINE,fp) == NULL) + error->one(FLERR,"Did not find keyword in table file"); + if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line + if (line[0] == '#') continue; // comment + char *word = strtok(line," \t\n\r"); + if (strcmp(word,keyword) == 0) break; // matching keyword + fgets(line,MAXLINE,fp); // no match, skip section + param_extract(tb,line); + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + } + + // read args on 2nd line of section + // allocate table arrays for file values + + fgets(line,MAXLINE,fp); + param_extract(tb,line); + memory->create(tb->rfile,tb->ninput,"pair:rfile"); + memory->create(tb->efile,tb->ninput,"pair:efile"); + memory->create(tb->ffile,tb->ninput,"pair:ffile"); + + // read r,e,f table values from file + // if rflag set, compute r + // if rflag not set, use r from file + + int itmp; + double rtmp; + + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) { + fgets(line,MAXLINE,fp); + sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); + + if (tb->rflag == RLINEAR) + rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1); + else if (tb->rflag == RSQ) { + rtmp = tb->rlo*tb->rlo + + (tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1); + rtmp = sqrt(rtmp); + } + + tb->rfile[i] = rtmp; + } + + // close file + + fclose(fp); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::bcast_table(Table *tb) +{ + MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); + + int me; + MPI_Comm_rank(world,&me); + if (me > 0) { + memory->create(tb->rfile,tb->ninput,"pair:rfile"); + memory->create(tb->efile,tb->ninput,"pair:efile"); + memory->create(tb->ffile,tb->ninput,"pair:ffile"); + } + + MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world); + + MPI_Bcast(&tb->rflag,1,MPI_INT,0,world); + if (tb->rflag) { + MPI_Bcast(&tb->rlo,1,MPI_DOUBLE,0,world); + MPI_Bcast(&tb->rhi,1,MPI_DOUBLE,0,world); + } + MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world); + if (tb->fpflag) { + MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world); + MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world); + } +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in Table: e2file,f2file +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::spline_table(Table *tb) +{ + memory->create(tb->e2file,tb->ninput,"pair:e2file"); + memory->create(tb->f2file,tb->ninput,"pair:f2file"); + + double ep0 = - tb->ffile[0]; + double epn = - tb->ffile[tb->ninput-1]; + spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file); + + if (tb->fpflag == 0) { + tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]); + tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) / + (tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]); + } + + double fp0 = tb->fplo; + double fpn = tb->fphi; + spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file); +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value R/RSQ lo hi FP fplo fphi + N is required, other params are optional +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::param_extract(Table *tb, char *line) +{ + tb->ninput = 0; + tb->rflag = NONE; + tb->fpflag = 0; + + char *word = strtok(line," \t\n\r\f"); + while (word) { + if (strcmp(word,"N") == 0) { + word = strtok(NULL," \t\n\r\f"); + tb->ninput = atoi(word); + } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0) { + if (strcmp(word,"R") == 0) tb->rflag = RLINEAR; + else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ; + word = strtok(NULL," \t\n\r\f"); + tb->rlo = atof(word); + word = strtok(NULL," \t\n\r\f"); + tb->rhi = atof(word); + } else if (strcmp(word,"FP") == 0) { + tb->fpflag = 1; + word = strtok(NULL," \t\n\r\f"); + tb->fplo = atof(word); + word = strtok(NULL," \t\n\r\f"); + tb->fphi = atof(word); + } else { + printf("WORD: %s\n",word); + error->one(FLERR,"Invalid keyword in pair table parameters"); + } + word = strtok(NULL," \t\n\r\f"); + } + + if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N"); +} + +/* ---------------------------------------------------------------------- + compute r,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::compute_table(Table *tb) +{ + int tlm1 = tablength-1; + + // inner = inner table bound + // cut = outer table bound + // delta = table spacing in rsq for N-1 bins + + double inner; + if (tb->rflag) inner = tb->rlo; + else inner = tb->rfile[0]; + tb->innersq = inner*inner; + tb->delta = (tb->rhi*tb->rhi - tb->innersq) / tlm1; + tb->invdelta = 1.0/tb->delta; + + // direct lookup tables + // N-1 evenly spaced bins in rsq from inner to cut + // e,f = value at midpt of bin + // e,f are N-1 in length since store 1 value at bin midpt + // f is converted to f/r when stored in f[i] + // e,f are never a match to read-in values, always computed via spline interp + + if (tabstyle == LOOKUP) { + memory->create(tb->e,tlm1,"pair:e"); + memory->create(tb->f,tlm1,"pair:f"); + + double r,rsq; + for (int i = 0; i < tlm1; i++) { + rsq = tb->innersq + (i+0.5)*tb->delta; + r = sqrt(rsq); + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r); + } + } + + // linear tables + // N-1 evenly spaced bins in rsq from inner to cut + // rsq,e,f = value at lower edge of bin + // de,df values = delta from lower edge to upper edge of bin + // rsq,e,f are N in length so de,df arrays can compute difference + // f is converted to f/r when stored in f[i] + // e,f can match read-in values, else compute via spline interp + + if (tabstyle == LINEAR) { + memory->create(tb->rsq,tablength,"pair:rsq"); + memory->create(tb->e,tablength,"pair:e"); + memory->create(tb->f,tablength,"pair:f"); + memory->create(tb->de,tlm1,"pair:de"); + memory->create(tb->df,tlm1,"pair:df"); + + double r,rsq; + for (int i = 0; i < tablength; i++) { + rsq = tb->innersq + i*tb->delta; + r = sqrt(rsq); + tb->rsq[i] = rsq; + if (tb->match) { + tb->e[i] = tb->efile[i]; + tb->f[i] = tb->ffile[i]; + } else { + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r); + } + } + + for (int i = 0; i < tlm1; i++) { + tb->de[i] = tb->e[i+1] - tb->e[i]; + tb->df[i] = tb->f[i+1] - tb->f[i]; + } + } +} + +/* ---------------------------------------------------------------------- + set all ptrs in a table to NULL, so can be freed safely +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::null_table(Table *tb) +{ + tb->rfile = tb->efile = tb->ffile = NULL; + tb->e2file = tb->f2file = NULL; + tb->rsq = tb->drsq = tb->e = tb->de = NULL; + tb->f = tb->df = tb->e2 = tb->f2 = NULL; +} + +/* ---------------------------------------------------------------------- + free all arrays in a table +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::free_table(Table *tb) +{ + memory->destroy(tb->rfile); + memory->destroy(tb->efile); + memory->destroy(tb->ffile); + memory->destroy(tb->e2file); + memory->destroy(tb->f2file); + + memory->destroy(tb->rsq); + memory->destroy(tb->drsq); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->f); + memory->destroy(tb->df); + memory->destroy(tb->e2); + memory->destroy(tb->f2); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::spline(double *x, double *y, int n, + double yp1, double ypn, double *y2) +{ + int i,k; + double p,qn,sig,un; + double *u = new double[n]; + + if (yp1 > 0.99e30) y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1); + } + for (i = 1; i < n-1; i++) { + sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]); + p = sig*y2[i-1] + 2.0; + y2[i] = (sig-1.0) / p; + u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]); + u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p; + } + if (ypn > 0.99e30) qn = un = 0.0; + else { + qn = 0.5; + un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2])); + } + y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0); + for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k]; + + delete [] u; +} + +/* ---------------------------------------------------------------------- */ + +double PairMultiLucyRX::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo,khi,k; + double h,b,a,y; + + klo = 0; + khi = n-1; + while (khi-klo > 1) { + k = (khi+klo) >> 1; + if (xa[k] > x) khi = k; + else klo = k; + } + h = xa[khi]-xa[klo]; + a = (xa[khi]-x) / h; + b = (x-xa[klo]) / h; + y = a*ya[klo] + b*ya[khi] + + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; + return y; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::write_restart(FILE *fp) +{ + write_restart_settings(fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMultiLucyRX::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&tabstyle,sizeof(int),1,fp); + fread(&tablength,sizeof(int),1,fp); + } + MPI_Bcast(&tabstyle,1,MPI_INT,0,world); + MPI_Bcast(&tablength,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +void PairMultiLucyRX::computeLocalDensity() +{ + int i,j,m,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz; + double rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + double **x = atom->x; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + double factor; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + double pi = MathConst::MY_PI; + double *rho = atom->rho; + + // zero out density + + if (newton_pair) { + m = nlocal + atom->nghost; + for (i = 0; i < m; i++) rho[i] = 0.0; + } else for (i = 0; i < nlocal; i++) rho[i] = 0.0; + +// rho = density at each atom +// loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutsq[itype][jtype]) { + double rcut = sqrt(cutsq[itype][jtype]); + double tmpFactor = double(1.0)-sqrt(rsq)/rcut; + double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor; + factor = (double(84.0)/(double(5.0)*pi*rcut*rcut*rcut))*(double(1.0)+double(3.0)*sqrt(rsq)/(double(2.0)*rcut))*tmpFactor4; + rho[i] += factor; + if (newton_pair || j < nlocal) { + rho[j] += factor; + } + } + } + } + if (newton_pair) comm->reverse_comm_pair(this); + + comm->forward_comm_pair(this); + +} + +/* ---------------------------------------------------------------------- */ + +void PairMultiLucyRX::getParams(int id, double &fractionOld1, double &fractionOld2, double &fraction1, double &fraction2) +{ + double fractionOld, fraction; + double nTotal, nTotalOld; + + fractionOld = double(0.0); + fraction = double(0.0); + fractionOld1 = double(0.0); + fractionOld2 = double(0.0); + fraction1 = double(0.0); + fraction2 = double(0.0); + + nTotal = double(0.0); + nTotalOld = double(0.0); + for(int ispecies=0;ispeciesdvector[ispecies][id]; + nTotalOld += atom->dvector[ispecies+nspecies][id]; + } + + for (int ispecies = 0; ispecies < nspecies; ispecies++) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0){ + fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction1 = atom->dvector[ispecies][id]/nTotal; + } + if (strcmp(site2,&atom->dname[ispecies][0]) == 0){ + fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction2 = atom->dvector[ispecies][id]/nTotal; + } + } + + for (int ispecies = 0; ispecies < nspecies; ispecies++) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0){ + fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction1 = atom->dvector[ispecies][id]/nTotal; + } + if (strcmp(site2,&atom->dname[ispecies][0]) == 0){ + fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction2 = atom->dvector[ispecies][id]/nTotal; + } + + if (strcmp(site1,"all") == 0 || strcmp(site2,"all") == 0) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0 || strcmp(site2,&atom->dname[ispecies][0]) == 0) continue; + fractionOld += atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction += atom->dvector[ispecies][id]/nTotal; + } + } + if(strcmp(site1,"all") == 0){ + fractionOld1 = fractionOld; + fraction1 = fraction; + } + if(strcmp(site2,"all") == 0){ + fractionOld2 = fractionOld; + fraction2 = fraction; + } +} + +/* ---------------------------------------------------------------------- */ + +int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +{ + int i,j,m; + double *rho = atom->rho; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = rho[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairMultiLucyRX::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + double *rho = atom->rho; + + m = 0; + last = first + n; + for (i = first; i < last; i++) rho[i] = buf[m++]; +} + +/* ---------------------------------------------------------------------- */ + +int PairMultiLucyRX::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + double *rho = atom->rho; + + m = 0; + last = first + n; + for (i = first; i < last; i++) buf[m++] = rho[i]; + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairMultiLucyRX::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + double *rho = atom->rho; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + rho[j] += buf[m++]; + } +} diff --git a/src/USER-DPD/pair_multi_lucy_rx.h b/src/USER-DPD/pair_multi_lucy_rx.h new file mode 100644 index 0000000000..8600a3d2c6 --- /dev/null +++ b/src/USER-DPD/pair_multi_lucy_rx.h @@ -0,0 +1,161 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(multi/lucy/rx,PairMultiLucyRX) + +#else + +#ifndef LMP_PAIR_MULTI_LUCY_RX_H +#define LMP_PAIR_MUTLI_LUCY_RX_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMultiLucyRX : public Pair { + public: + PairMultiLucyRX(class LAMMPS *); + virtual ~PairMultiLucyRX(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + void computeLocalDensity(); + double rho_0; + + + protected: + enum{LOOKUP,LINEAR}; + + int nmax; + + int tabstyle,tablength; + struct Table { + int ninput,rflag,fpflag,match; + double rlo,rhi,fplo,fphi,cut; + double *rfile,*efile,*ffile; + double *e2file,*f2file; + double innersq,delta,invdelta,deltasq6; + double *rsq,*drsq,*e,*de,*f,*df,*e2,*f2; + }; + int ntables; + Table *tables; + + int **tabindex; + + void allocate(); + void read_table(Table *, char *, char *); + void param_extract(Table *, char *); + void bcast_table(Table *); + void spline_table(Table *); + void compute_table(Table *); + void null_table(Table *); + void free_table(Table *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + + int nspecies; + char *site1, *site2; + void getParams(int, double &, double &, double &, double &); + +/* class FixRX *fixRX; */ +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Pair multi/lucy/rx command requires atom_style with density (e.g. dpd, meso) + +Self-explanatory + +E: Density < table inner cutoff + +The local density inner is smaller than the inner cutoff + +E: Density > table inner cutoff + +The local density inner is greater than the inner cutoff + +E: Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx + +Self-explanatory + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Unknown table style in pair_style command + +Self-explanatory + +E: Illegal number of pair table entries + +There must be at least 2 table entries. + +E: Illegal pair_coeff command + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: PairMultiLucyRX requires a fix rx command + +The fix rx command must come before the pair style command in the input file + +E: There are no rx species specified + +There must be at least one species specified through the fix rx command + +E: Invalid pair table length + +Length of read-in pair table is invalid + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open file %s + +The specified file cannot be opened. Check that the path and name are +correct. + +E: Did not find keyword in table file + +Keyword used in pair_coeff command was not found in table file. + +E: Invalid keyword in pair table parameters + +Keyword used in list of table parameters is not recognized. + +E: Pair table parameters did not set N + +List of pair table parameters must include N setting. + +*/ diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp new file mode 100644 index 0000000000..71b48b2776 --- /dev/null +++ b/src/USER-DPD/pair_table_rx.cpp @@ -0,0 +1,1126 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Paul Crozier (SNL) +------------------------------------------------------------------------- */ + +#include "mpi.h" +#include +#include +#include +#include "pair_table_rx.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" +#include "modify.h" +#include "fix.h" + +using namespace LAMMPS_NS; + +enum{NONE,RLINEAR,RSQ,BMP}; + +#define MAXLINE 1024 + +/* ---------------------------------------------------------------------- */ + +PairTableRX::PairTableRX(LAMMPS *lmp) : Pair(lmp) +{ + ntables = 0; + tables = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairTableRX::~PairTableRX() +{ + for (int m = 0; m < ntables; m++) free_table(&tables[m]); + memory->sfree(tables); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(tabindex); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairTableRX::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype,itable; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair; + double rsq,factor_lj,fraction,value,a,b; + int *ilist,*jlist,*numneigh,**firstneigh; + Table *tb; + + union_int_float_t rsq_lookup; + int tlm1 = tablength - 1; + + fraction = double(0.0); + a = double(0.0); + b = double(0.0); + + evdwlOld = 0.0; + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + double fractionOld1_i, fractionOld1_j; + double fractionOld2_i, fractionOld2_j; + double fraction1_i, fraction1_j; + double fraction2_i, fraction2_j; + double *uCG = atom->uCG; + double *uCGnew = atom->uCGnew; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + getParams(i,fractionOld1_i,fractionOld2_i,fraction1_i,fraction2_i); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + getParams(j,fractionOld1_j,fractionOld2_j,fraction1_j,fraction2_j); + + tb = &tables[tabindex[itype][jtype]]; + if (rsq < tb->innersq) + error->one(FLERR,"Pair distance < table inner cutoff"); + + if (tabstyle == LOOKUP) { + itable = static_cast ((rsq - tb->innersq) * tb->invdelta); + if (itable >= tlm1) + error->one(FLERR,"Pair distance > table outer cutoff"); + fpair = factor_lj * tb->f[itable]; + } else if (tabstyle == LINEAR) { + itable = static_cast ((rsq - tb->innersq) * tb->invdelta); + if (itable >= tlm1) + error->one(FLERR,"Pair distance > table outer cutoff"); + fraction = (rsq - tb->rsq[itable]) * tb->invdelta; + value = tb->f[itable] + fraction*tb->df[itable]; + fpair = factor_lj * value; + } else if (tabstyle == SPLINE) { + itable = static_cast ((rsq - tb->innersq) * tb->invdelta); + if (itable >= tlm1) + error->one(FLERR,"Pair distance > table outer cutoff"); + b = (rsq - tb->rsq[itable]) * tb->invdelta; + a = 1.0 - b; + value = a * tb->f[itable] + b * tb->f[itable+1] + + ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * + tb->deltasq6; + fpair = factor_lj * value; + } else { + rsq_lookup.f = rsq; + itable = rsq_lookup.i & tb->nmask; + itable >>= tb->nshiftbits; + fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable]; + value = tb->f[itable] + fraction*tb->df[itable]; + fpair = factor_lj * value; + } + if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpair; + else fpair = (sqrt(fractionOld1_i*fractionOld2_j) + sqrt(fractionOld2_i*fractionOld1_j))*fpair; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (tabstyle == LOOKUP) + evdwl = tb->e[itable]; + else if (tabstyle == LINEAR || tabstyle == BITMAP){ + evdwl = tb->e[itable] + fraction*tb->de[itable]; + } + else + evdwl = a * tb->e[itable] + b * tb->e[itable+1] + + ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * + tb->deltasq6; + if (strcmp(site1,site2) == 0){ + evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwl; + evdwl = sqrt(fraction1_i*fraction2_j)*evdwl; + } else { + evdwlOld = (sqrt(fractionOld1_i*fractionOld2_j) + sqrt(fractionOld2_i*fractionOld1_j))*evdwl; + evdwl = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*evdwl; + } + evdwlOld *= factor_lj; + evdwl *= factor_lj; + uCG[i] += double(0.5)*evdwlOld; + uCG[j] += double(0.5)*evdwlOld; + uCGnew[i] += double(0.5)*evdwl; + uCGnew[j] += double(0.5)*evdwl; + evdwl = evdwlOld; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairTableRX::allocate() +{ + allocated = 1; + const int nt = atom->ntypes + 1; + + memory->create(setflag,nt,nt,"pair:setflag"); + memory->create(cutsq,nt,nt,"pair:cutsq"); + memory->create(tabindex,nt,nt,"pair:tabindex"); + + memset(&setflag[0][0],0,nt*nt*sizeof(int)); + memset(&cutsq[0][0],0,nt*nt*sizeof(double)); + memset(&tabindex[0][0],0,nt*nt*sizeof(int)); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairTableRX::settings(int narg, char **arg) +{ + if (narg < 2) error->all(FLERR,"Illegal pair_style command"); + + // new settings + + if (strcmp(arg[0],"lookup") == 0) tabstyle = LOOKUP; + else if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR; + else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE; + else if (strcmp(arg[0],"bitmap") == 0) tabstyle = BITMAP; + else error->all(FLERR,"Unknown table style in pair_style command"); + + tablength = force->inumeric(FLERR,arg[1]); + if (tablength < 2) error->all(FLERR,"Illegal number of pair table entries"); + + // optional keywords + // assert the tabulation is compatible with a specific long-range solver + + int iarg = 2; + while (iarg < narg) { + if (strcmp(arg[iarg],"ewald") == 0) ewaldflag = 1; + else if (strcmp(arg[iarg],"pppm") == 0) pppmflag = 1; + else if (strcmp(arg[iarg],"msm") == 0) msmflag = 1; + else if (strcmp(arg[iarg],"dispersion") == 0) dispersionflag = 1; + else if (strcmp(arg[iarg],"tip4p") == 0) tip4pflag = 1; + else error->all(FLERR,"Illegal pair_style command"); + iarg++; + } + + // delete old tables, since cannot just change settings + + for (int m = 0; m < ntables; m++) free_table(&tables[m]); + memory->sfree(tables); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(tabindex); + } + allocated = 0; + + ntables = 0; + tables = NULL; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairTableRX::coeff(int narg, char **arg) +{ + if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_coeff command"); + if (!allocated) allocate(); + + bool rx_flag = false; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style,"rx",2) == 0) rx_flag = true; + if (!rx_flag) error->all(FLERR,"PairTableRX requires a fix rx command."); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + int me; + MPI_Comm_rank(world,&me); + tables = (Table *) + memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables"); + Table *tb = &tables[ntables]; + null_table(tb); + if (me == 0) read_table(tb,arg[2],arg[3]); + bcast_table(tb); + + nspecies = atom->nspecies_dpd; + if(nspecies==0) error->all(FLERR,"There are no rx species specified."); + int n; + n = strlen(arg[3]) + 1; + site1 = new char[n]; + strcpy(site1,arg[4]); + + int ispecies; + for (ispecies = 0; ispecies < nspecies; ispecies++){ + if (strcmp(site1,&atom->dname[ispecies][0]) == 0) break; + } + if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) + error->all(FLERR,"Site1 name not recognized in pair coefficients"); + + n = strlen(arg[4]) + 1; + site2 = new char[n]; + strcpy(site2,arg[5]); + + for (ispecies = 0; ispecies < nspecies; ispecies++){ + if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break; + } + if (ispecies == nspecies && strcmp(site2,"1fluid") != 0) + error->all(FLERR,"Site2 name not recognized in pair coefficients"); + + // set table cutoff + + if (narg == 7) tb->cut = force->numeric(FLERR,arg[6]); + else if (tb->rflag) tb->cut = tb->rhi; + else tb->cut = tb->rfile[tb->ninput-1]; + + // error check on table parameters + // insure cutoff is within table + // for BITMAP tables, file values can be in non-ascending order + + if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length"); + double rlo,rhi; + if (tb->rflag == 0) { + rlo = tb->rfile[0]; + rhi = tb->rfile[tb->ninput-1]; + } else { + rlo = tb->rlo; + rhi = tb->rhi; + } + if (tb->cut <= rlo || tb->cut > rhi) + error->all(FLERR,"Invalid pair table cutoff"); + if (rlo <= 0.0) error->all(FLERR,"Invalid pair table cutoff"); + + // match = 1 if don't need to spline read-in tables + // this is only the case if r values needed by final tables + // exactly match r values read from file + // for tabstyle SPLINE, always need to build spline tables + + tb->match = 0; + if (tabstyle == LINEAR && tb->ninput == tablength && + tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1; + if (tabstyle == BITMAP && tb->ninput == 1 << tablength && + tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1; + if (tb->rflag == BMP && tb->match == 0) + error->all(FLERR,"Bitmapped table in file does not match requested table"); + + // spline read-in values and compute r,e,f vectors within table + + if (tb->match == 0) spline_table(tb); + compute_table(tb); + + // store ptr to table in tabindex + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + tabindex[i][j] = ntables; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Illegal pair_coeff command"); + ntables++; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairTableRX::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + tabindex[j][i] = tabindex[i][j]; + + return tables[tabindex[i][j]].cut; +} + +/* ---------------------------------------------------------------------- + read a table section from a tabulated potential file + only called by proc 0 + this function sets these values in Table: + ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi,ntablebits +------------------------------------------------------------------------- */ + +void PairTableRX::read_table(Table *tb, char *file, char *keyword) +{ + char line[MAXLINE]; + + // open file + + FILE *fp = force->open_potential(file); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open file %s",file); + error->one(FLERR,str); + } + + // loop until section found with matching keyword + + while (1) { + if (fgets(line,MAXLINE,fp) == NULL) + error->one(FLERR,"Did not find keyword in table file"); + if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line + if (line[0] == '#') continue; // comment + char *word = strtok(line," \t\n\r"); + if (strcmp(word,keyword) == 0) break; // matching keyword + fgets(line,MAXLINE,fp); // no match, skip section + param_extract(tb,line); + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + } + + // read args on 2nd line of section + // allocate table arrays for file values + + fgets(line,MAXLINE,fp); + param_extract(tb,line); + memory->create(tb->rfile,tb->ninput,"pair:rfile"); + memory->create(tb->efile,tb->ninput,"pair:efile"); + memory->create(tb->ffile,tb->ninput,"pair:ffile"); + + // setup bitmap parameters for table to read in + + tb->ntablebits = 0; + int masklo,maskhi,nmask,nshiftbits; + if (tb->rflag == BMP) { + while (1 << tb->ntablebits < tb->ninput) tb->ntablebits++; + if (1 << tb->ntablebits != tb->ninput) + error->one(FLERR,"Bitmapped table is incorrect length in table file"); + init_bitmap(tb->rlo,tb->rhi,tb->ntablebits,masklo,maskhi,nmask,nshiftbits); + } + + // read r,e,f table values from file + // if rflag set, compute r + // if rflag not set, use r from file + + int itmp; + double rtmp; + union_int_float_t rsq_lookup; + + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) { + fgets(line,MAXLINE,fp); + sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); + + if (tb->rflag == RLINEAR) + rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1); + else if (tb->rflag == RSQ) { + rtmp = tb->rlo*tb->rlo + + (tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1); + rtmp = sqrt(rtmp); + } else if (tb->rflag == BMP) { + rsq_lookup.i = i << nshiftbits; + rsq_lookup.i |= masklo; + if (rsq_lookup.f < tb->rlo*tb->rlo) { + rsq_lookup.i = i << nshiftbits; + rsq_lookup.i |= maskhi; + } + rtmp = sqrtf(rsq_lookup.f); + } + + tb->rfile[i] = rtmp; + } + + // close file + + fclose(fp); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi +------------------------------------------------------------------------- */ + +void PairTableRX::bcast_table(Table *tb) +{ + MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); + + int me; + MPI_Comm_rank(world,&me); + if (me > 0) { + memory->create(tb->rfile,tb->ninput,"pair:rfile"); + memory->create(tb->efile,tb->ninput,"pair:efile"); + memory->create(tb->ffile,tb->ninput,"pair:ffile"); + } + + MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world); + + MPI_Bcast(&tb->rflag,1,MPI_INT,0,world); + if (tb->rflag) { + MPI_Bcast(&tb->rlo,1,MPI_DOUBLE,0,world); + MPI_Bcast(&tb->rhi,1,MPI_DOUBLE,0,world); + } + MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world); + if (tb->fpflag) { + MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world); + MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world); + } +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in Table: e2file,f2file +------------------------------------------------------------------------- */ + +void PairTableRX::spline_table(Table *tb) +{ + memory->create(tb->e2file,tb->ninput,"pair:e2file"); + memory->create(tb->f2file,tb->ninput,"pair:f2file"); + + double ep0 = - tb->ffile[0]; + double epn = - tb->ffile[tb->ninput-1]; + spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file); + + if (tb->fpflag == 0) { + tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]); + tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) / + (tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]); + } + + double fp0 = tb->fplo; + double fpn = tb->fphi; + spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file); +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value R/RSQ/BITMAP lo hi FP fplo fphi + N is required, other params are optional +------------------------------------------------------------------------- */ + +void PairTableRX::param_extract(Table *tb, char *line) +{ + tb->ninput = 0; + tb->rflag = NONE; + tb->fpflag = 0; + + char *word = strtok(line," \t\n\r\f"); + while (word) { + if (strcmp(word,"N") == 0) { + word = strtok(NULL," \t\n\r\f"); + tb->ninput = atoi(word); + } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 || + strcmp(word,"BITMAP") == 0) { + if (strcmp(word,"R") == 0) tb->rflag = RLINEAR; + else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ; + else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP; + word = strtok(NULL," \t\n\r\f"); + tb->rlo = atof(word); + word = strtok(NULL," \t\n\r\f"); + tb->rhi = atof(word); + } else if (strcmp(word,"FP") == 0) { + tb->fpflag = 1; + word = strtok(NULL," \t\n\r\f"); + tb->fplo = atof(word); + word = strtok(NULL," \t\n\r\f"); + tb->fphi = atof(word); + } else { + printf("WORD: %s\n",word); + error->one(FLERR,"Invalid keyword in pair table parameters"); + } + word = strtok(NULL," \t\n\r\f"); + } + + if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N"); +} + +/* ---------------------------------------------------------------------- + compute r,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void PairTableRX::compute_table(Table *tb) +{ + int tlm1 = tablength-1; + + // inner = inner table bound + // cut = outer table bound + // delta = table spacing in rsq for N-1 bins + + double inner; + if (tb->rflag) inner = tb->rlo; + else inner = tb->rfile[0]; + tb->innersq = double(inner)*double(inner); + tb->delta = double(tb->cut*tb->cut - double(tb->innersq)) / double(tlm1); + tb->invdelta = double(1.0)/double(tb->delta); + + // direct lookup tables + // N-1 evenly spaced bins in rsq from inner to cut + // e,f = value at midpt of bin + // e,f are N-1 in length since store 1 value at bin midpt + // f is converted to f/r when stored in f[i] + // e,f are never a match to read-in values, always computed via spline interp + + if (tabstyle == LOOKUP) { + memory->create(tb->e,tlm1,"pair:e"); + memory->create(tb->f,tlm1,"pair:f"); + + double r,rsq; + for (int i = 0; i < tlm1; i++) { + rsq = tb->innersq + (i+0.5)*tb->delta; + r = sqrt(rsq); + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; + } + } + + // linear tables + // N-1 evenly spaced bins in rsq from inner to cut + // rsq,e,f = value at lower edge of bin + // de,df values = delta from lower edge to upper edge of bin + // rsq,e,f are N in length so de,df arrays can compute difference + // f is converted to f/r when stored in f[i] + // e,f can match read-in values, else compute via spline interp + + if (tabstyle == LINEAR) { + memory->create(tb->rsq,tablength,"pair:rsq"); + memory->create(tb->e,tablength,"pair:e"); + memory->create(tb->f,tablength,"pair:f"); + memory->create(tb->de,tlm1,"pair:de"); + memory->create(tb->df,tlm1,"pair:df"); + + double r,rsq; + for (int i = 0; i < tablength; i++) { + rsq = tb->innersq + i*tb->delta; + r = sqrt(rsq); + tb->rsq[i] = rsq; + if (tb->match) { + tb->e[i] = tb->efile[i]; + tb->f[i] = tb->ffile[i]/r; + } else { + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; + } + } + + for (int i = 0; i < tlm1; i++) { + tb->de[i] = tb->e[i+1] - tb->e[i]; + tb->df[i] = tb->f[i+1] - tb->f[i]; + } + } + + // cubic spline tables + // N-1 evenly spaced bins in rsq from inner to cut + // rsq,e,f = value at lower edge of bin + // e2,f2 = spline coefficient for each bin + // rsq,e,f,e2,f2 are N in length so have N-1 spline bins + // f is converted to f/r after e is splined + // e,f can match read-in values, else compute via spline interp + + if (tabstyle == SPLINE) { + memory->create(tb->rsq,tablength,"pair:rsq"); + memory->create(tb->e,tablength,"pair:e"); + memory->create(tb->f,tablength,"pair:f"); + memory->create(tb->e2,tablength,"pair:e2"); + memory->create(tb->f2,tablength,"pair:f2"); + + tb->deltasq6 = tb->delta*tb->delta / 6.0; + + double r,rsq; + for (int i = 0; i < tablength; i++) { + rsq = tb->innersq + i*tb->delta; + r = sqrt(rsq); + tb->rsq[i] = rsq; + if (tb->match) { + tb->e[i] = tb->efile[i]; + tb->f[i] = tb->ffile[i]/r; + } else { + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r); + } + } + + // ep0,epn = dh/dg at inner and at cut + // h(r) = e(r) and g(r) = r^2 + // dh/dg = (de/dr) / 2r = -f/2r + + double ep0 = - tb->f[0] / (2.0 * sqrt(tb->innersq)); + double epn = - tb->f[tlm1] / (2.0 * tb->cut); + spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2); + + // fp0,fpn = dh/dg at inner and at cut + // h(r) = f(r)/r and g(r) = r^2 + // dh/dg = (1/r df/dr - f/r^2) / 2r + // dh/dg in secant approx = (f(r2)/r2 - f(r1)/r1) / (g(r2) - g(r1)) + + double fp0,fpn; + double secant_factor = 0.1; + if (tb->fpflag) fp0 = (tb->fplo/sqrt(tb->innersq) - tb->f[0]/tb->innersq) / + (2.0 * sqrt(tb->innersq)); + else { + double rsq1 = tb->innersq; + double rsq2 = rsq1 + secant_factor*tb->delta; + fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) / + sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta); + } + + if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn = + (tb->fphi/tb->cut - tb->f[tlm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut); + else { + double rsq2 = tb->cut * tb->cut; + double rsq1 = rsq2 - secant_factor*tb->delta; + fpn = (tb->f[tlm1] / sqrt(rsq2) - + splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) / + sqrt(rsq1)) / (secant_factor*tb->delta); + } + + for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]); + spline(tb->rsq,tb->f,tablength,fp0,fpn,tb->f2); + } + + // bitmapped linear tables + // 2^N bins from inner to cut, spaced in bitmapped manner + // f is converted to f/r when stored in f[i] + // e,f can match read-in values, else compute via spline interp + + if (tabstyle == BITMAP) { + double r; + union_int_float_t rsq_lookup; + int masklo,maskhi; + + // linear lookup tables of length ntable = 2^n + // stored value = value at lower edge of bin + + init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits); + int ntable = 1 << tablength; + int ntablem1 = ntable - 1; + + memory->create(tb->rsq,ntable,"pair:rsq"); + memory->create(tb->e,ntable,"pair:e"); + memory->create(tb->f,ntable,"pair:f"); + memory->create(tb->de,ntable,"pair:de"); + memory->create(tb->df,ntable,"pair:df"); + memory->create(tb->drsq,ntable,"pair:drsq"); + + union_int_float_t minrsq_lookup; + minrsq_lookup.i = 0 << tb->nshiftbits; + minrsq_lookup.i |= maskhi; + + for (int i = 0; i < ntable; i++) { + rsq_lookup.i = i << tb->nshiftbits; + rsq_lookup.i |= masklo; + if (rsq_lookup.f < tb->innersq) { + rsq_lookup.i = i << tb->nshiftbits; + rsq_lookup.i |= maskhi; + } + r = sqrtf(rsq_lookup.f); + tb->rsq[i] = rsq_lookup.f; + if (tb->match) { + tb->e[i] = tb->efile[i]; + tb->f[i] = tb->ffile[i]/r; + } else { + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; + } + minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f); + } + + tb->innersq = minrsq_lookup.f; + + for (int i = 0; i < ntablem1; i++) { + tb->de[i] = tb->e[i+1] - tb->e[i]; + tb->df[i] = tb->f[i+1] - tb->f[i]; + tb->drsq[i] = 1.0/(tb->rsq[i+1] - tb->rsq[i]); + } + + // get the delta values for the last table entries + // tables are connected periodically between 0 and ntablem1 + + tb->de[ntablem1] = tb->e[0] - tb->e[ntablem1]; + tb->df[ntablem1] = tb->f[0] - tb->f[ntablem1]; + tb->drsq[ntablem1] = 1.0/(tb->rsq[0] - tb->rsq[ntablem1]); + + // get the correct delta values at itablemax + // smallest r is in bin itablemin + // largest r is in bin itablemax, which is itablemin-1, + // or ntablem1 if itablemin=0 + + // deltas at itablemax only needed if corresponding rsq < cut*cut + // if so, compute deltas between rsq and cut*cut + // if tb->match, data at cut*cut is unavailable, so we'll take + // deltas at itablemax-1 as a good approximation + + double e_tmp,f_tmp; + int itablemin = minrsq_lookup.i & tb->nmask; + itablemin >>= tb->nshiftbits; + int itablemax = itablemin - 1; + if (itablemin == 0) itablemax = ntablem1; + int itablemaxm1 = itablemax - 1; + if (itablemax == 0) itablemaxm1 = ntablem1; + rsq_lookup.i = itablemax << tb->nshiftbits; + rsq_lookup.i |= maskhi; + if (rsq_lookup.f < tb->cut*tb->cut) { + if (tb->match) { + tb->de[itablemax] = tb->de[itablemaxm1]; + tb->df[itablemax] = tb->df[itablemaxm1]; + tb->drsq[itablemax] = tb->drsq[itablemaxm1]; + } else { + rsq_lookup.f = tb->cut*tb->cut; + r = sqrtf(rsq_lookup.f); + e_tmp = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); + f_tmp = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; + tb->de[itablemax] = e_tmp - tb->e[itablemax]; + tb->df[itablemax] = f_tmp - tb->f[itablemax]; + tb->drsq[itablemax] = 1.0/(rsq_lookup.f - tb->rsq[itablemax]); + } + } + } +} + +/* ---------------------------------------------------------------------- + set all ptrs in a table to NULL, so can be freed safely +------------------------------------------------------------------------- */ + +void PairTableRX::null_table(Table *tb) +{ + tb->rfile = tb->efile = tb->ffile = NULL; + tb->e2file = tb->f2file = NULL; + tb->rsq = tb->drsq = tb->e = tb->de = NULL; + tb->f = tb->df = tb->e2 = tb->f2 = NULL; +} + +/* ---------------------------------------------------------------------- + free all arrays in a table +------------------------------------------------------------------------- */ + +void PairTableRX::free_table(Table *tb) +{ + memory->destroy(tb->rfile); + memory->destroy(tb->efile); + memory->destroy(tb->ffile); + memory->destroy(tb->e2file); + memory->destroy(tb->f2file); + + memory->destroy(tb->rsq); + memory->destroy(tb->drsq); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->f); + memory->destroy(tb->df); + memory->destroy(tb->e2); + memory->destroy(tb->f2); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void PairTableRX::spline(double *x, double *y, int n, + double yp1, double ypn, double *y2) +{ + int i,k; + double p,qn,sig,un; + double *u = new double[n]; + + if (yp1 > 0.99e30) y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1); + } + for (i = 1; i < n-1; i++) { + sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]); + p = sig*y2[i-1] + 2.0; + y2[i] = (sig-1.0) / p; + u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]); + u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p; + } + if (ypn > 0.99e30) qn = un = 0.0; + else { + qn = 0.5; + un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2])); + } + y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0); + for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k]; + + delete [] u; +} + +/* ---------------------------------------------------------------------- */ + +double PairTableRX::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo,khi,k; + double h,b,a,y; + + klo = 0; + khi = n-1; + while (khi-klo > 1) { + k = (khi+klo) >> 1; + if (xa[k] > x) khi = k; + else klo = k; + } + h = xa[khi]-xa[klo]; + a = (xa[khi]-x) / h; + b = (x-xa[klo]) / h; + y = a*ya[klo] + b*ya[khi] + + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; + return y; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairTableRX::write_restart(FILE *fp) +{ + write_restart_settings(fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairTableRX::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairTableRX::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); + fwrite(&ewaldflag,sizeof(int),1,fp); + fwrite(&pppmflag,sizeof(int),1,fp); + fwrite(&msmflag,sizeof(int),1,fp); + fwrite(&dispersionflag,sizeof(int),1,fp); + fwrite(&tip4pflag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairTableRX::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&tabstyle,sizeof(int),1,fp); + fread(&tablength,sizeof(int),1,fp); + fread(&ewaldflag,sizeof(int),1,fp); + fread(&pppmflag,sizeof(int),1,fp); + fread(&msmflag,sizeof(int),1,fp); + fread(&dispersionflag,sizeof(int),1,fp); + fread(&tip4pflag,sizeof(int),1,fp); + } + MPI_Bcast(&tabstyle,1,MPI_INT,0,world); + MPI_Bcast(&tablength,1,MPI_INT,0,world); + MPI_Bcast(&ewaldflag,1,MPI_INT,0,world); + MPI_Bcast(&pppmflag,1,MPI_INT,0,world); + MPI_Bcast(&msmflag,1,MPI_INT,0,world); + MPI_Bcast(&dispersionflag,1,MPI_INT,0,world); + MPI_Bcast(&tip4pflag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairTableRX::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + int itable; + double fraction,value,a,b,phi; + int tlm1 = tablength - 1; + + Table *tb = &tables[tabindex[itype][jtype]]; + double fraction1_i, fraction1_j; + double fraction2_i, fraction2_j; + double fractionOld1_i, fractionOld1_j; + double fractionOld2_i, fractionOld2_j; + + fraction = double(0.0); + a = double(0.0); + b = double(0.0); + + getParams(i,fractionOld1_i,fractionOld2_i,fraction1_i,fraction2_i); + getParams(j,fractionOld1_j,fractionOld2_j,fraction1_j,fraction2_j); + + if (rsq < tb->innersq) error->one(FLERR,"Pair distance < table inner cutoff"); + + if (tabstyle == LOOKUP) { + itable = static_cast ((rsq-tb->innersq) * tb->invdelta); + if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); + fforce = factor_lj * tb->f[itable]; + } else if (tabstyle == LINEAR) { + itable = static_cast ((rsq-tb->innersq) * tb->invdelta); + if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); + fraction = (rsq - tb->rsq[itable]) * tb->invdelta; + value = tb->f[itable] + fraction*tb->df[itable]; + fforce = factor_lj * value; + } else if (tabstyle == SPLINE) { + itable = static_cast ((rsq-tb->innersq) * tb->invdelta); + if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); + b = (rsq - tb->rsq[itable]) * tb->invdelta; + a = 1.0 - b; + value = a * tb->f[itable] + b * tb->f[itable+1] + + ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * + tb->deltasq6; + fforce = factor_lj * value; + } else { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + itable = rsq_lookup.i & tb->nmask; + itable >>= tb->nshiftbits; + fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable]; + value = tb->f[itable] + fraction*tb->df[itable]; + fforce = factor_lj * value; + } + + if (strcmp(site1,site2) == 0) fforce = sqrt(fraction1_i*fraction2_j)*fforce; + else fforce = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*fforce; + + if (tabstyle == LOOKUP) + phi = tb->e[itable]; + else if (tabstyle == LINEAR || tabstyle == BITMAP) + phi = tb->e[itable] + fraction*tb->de[itable]; + else + phi = a * tb->e[itable] + b * tb->e[itable+1] + + ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6; + + if (strcmp(site1,site2) == 0) phi = sqrt(fraction1_i*fraction2_j)*phi; + else phi = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*phi; + + return factor_lj*phi; +} + +/* ---------------------------------------------------------------------- + return the Coulomb cutoff for tabled potentials + called by KSpace solvers which require that all pairwise cutoffs be the same + loop over all tables not just those indexed by tabindex[i][j] since + no way to know which tables are active since pair::init() not yet called +------------------------------------------------------------------------- */ + +void *PairTableRX::extract(const char *str, int &dim) +{ + if (strcmp(str,"cut_coul") != 0) return NULL; + if (ntables == 0) error->all(FLERR,"All pair coeffs are not set"); + + double cut_coul = tables[0].cut; + for (int m = 1; m < ntables; m++) + if (tables[m].cut != cut_coul) + error->all(FLERR, + "Pair table cutoffs must all be equal to use with KSpace"); + dim = 0; + return &tables[0].cut; +} + +/* ---------------------------------------------------------------------- */ + +void PairTableRX::getParams(int id, double &fractionOld1, double &fractionOld2, double &fraction1, double &fraction2) +{ + double fractionOld, fraction; + double nTotal, nTotalOld; + + fractionOld = double(0.0); + fraction = double(0.0); + fractionOld1 = double(0.0); + fractionOld2 = double(0.0); + fraction1 = double(0.0); + fraction2 = double(0.0); + + nTotal = double(0.0); + nTotalOld = double(0.0); + for(int ispecies=0;ispeciesdvector[ispecies][id]; + nTotalOld += atom->dvector[ispecies+nspecies][id]; + } + if(nTotal < 1e-8 || nTotalOld < 1e-8) + error->all(FLERR,"The number of molecules in CG particle is less than 1e-8."); + + for (int ispecies = 0; ispecies < nspecies; ispecies++) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0){ + fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction1 = atom->dvector[ispecies][id]/nTotal; + } + if (strcmp(site2,&atom->dname[ispecies][0]) == 0){ + fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction2 = atom->dvector[ispecies][id]/nTotal; + } + } + + for (int ispecies = 0; ispecies < nspecies; ispecies++) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0){ + fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction1 = atom->dvector[ispecies][id]/nTotal; + } + if (strcmp(site2,&atom->dname[ispecies][0]) == 0){ + fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction2 = atom->dvector[ispecies][id]/nTotal; + } + + if (strcmp(site1,"1fluid") == 0 || strcmp(site2,"1fluid") == 0) { + if (strcmp(site1,&atom->dname[ispecies][0]) == 0 || strcmp(site2,&atom->dname[ispecies][0]) == 0) continue; + fractionOld += atom->dvector[ispecies+nspecies][id]/nTotalOld; + fraction += atom->dvector[ispecies][id]/nTotal; + } + } + if(strcmp(site1,"1fluid") == 0){ + fractionOld1 = fractionOld; + fraction1 = fraction; + } + if(strcmp(site2,"1fluid") == 0){ + fractionOld2 = fractionOld; + fraction2 = fraction; + } +} + diff --git a/src/USER-DPD/pair_table_rx.h b/src/USER-DPD/pair_table_rx.h new file mode 100644 index 0000000000..00b83bafb7 --- /dev/null +++ b/src/USER-DPD/pair_table_rx.h @@ -0,0 +1,172 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(table/rx,PairTableRX) + +#else + +#ifndef LMP_PAIR_TABLE_RX_H +#define LMP_PAIR_TABLE_RX_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairTableRX : public Pair { + public: + PairTableRX(class LAMMPS *); + virtual ~PairTableRX(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + enum{LOOKUP,LINEAR,SPLINE,BITMAP}; + + int tabstyle,tablength; + struct Table { + int ninput,rflag,fpflag,match,ntablebits; + int nshiftbits,nmask; + double rlo,rhi,fplo,fphi,cut; + double *rfile,*efile,*ffile; + double *e2file,*f2file; + double innersq,delta,invdelta,deltasq6; + double *rsq,*drsq,*e,*de,*f,*df,*e2,*f2; + }; + int ntables; + Table *tables; + + int **tabindex; + + void allocate(); + void read_table(Table *, char *, char *); + void param_extract(Table *, char *); + void bcast_table(Table *); + void spline_table(Table *); + void compute_table(Table *); + void null_table(Table *); + void free_table(Table *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + + int nspecies; + char *site1, *site2; + void getParams(int, double &, double &, double &, double &); + +/* class FixRX *fixRX; */ +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Pair distance < table inner cutoff + +Two atoms are closer together than the pairwise table allows. + +E: Pair distance > table outer cutoff + +Two atoms are further apart than the pairwise table allows. + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Unknown table style in pair_style command + +Style of table is invalid for use with pair_style table command. + +E: PairTableRX requires a fix rx command + +The fix rx command must come before the pair style command in the input file + +E: There are no rx species specified + +There must be at least one species specified through the fix rx command + +E: Site1 name not recognized in pair coefficients + +The site1 keyword does not match the species keywords specified throug the fix rx command + +E: Illegal number of pair table entries + +There must be at least 2 table entries. + +E: Invalid pair table length + +Length of read-in pair table is invalid + +E: Invalid pair table cutoff + +Cutoffs in pair_coeff command are not valid with read-in pair table. + +E: Bitmapped table in file does not match requested table + +Setting for bitmapped table in pair_coeff command must match table +in file exactly. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open file %s + +The specified file cannot be opened. Check that the path and name are +correct. If the file is a compressed file, also check that the gzip +executable can be found and run. + +E: Did not find keyword in table file + +Keyword used in pair_coeff command was not found in table file. + +E: Bitmapped table is incorrect length in table file + +Number of table entries is not a correct power of 2. + +E: Invalid keyword in pair table parameters + +Keyword used in list of table parameters is not recognized. + +E: Pair table parameters did not set N + +List of pair table parameters must include N setting. + +E: Pair table cutoffs must all be equal to use with KSpace + +When using pair style table with a long-range KSpace solver, the +cutoffs for all atom type pairs must all be the same, since the +long-range solver starts at that cutoff. + +E: The number of molecules in CG particle is less than 1e-8 + +Self-explanatory. Check the species concentrations have been properly set +and check the reaction kinetic solver parameters in fix rx to more for +sufficient accuracy. + +*/ From 7cb2b01ebd97a6e030ea5f9389df62032e3cc5ee Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:29:39 +0000 Subject: [PATCH 076/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15120 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/Section_commands.txt | 5 + doc/src/atom_style.txt | 10 +- doc/src/compute_dpd.txt | 4 +- doc/src/compute_dpd_atom.txt | 14 +- doc/src/fix_eos_table_rx.txt | 138 ++++++++++++++++++++ doc/src/fix_rx.txt | 143 ++++++++++++++++++++ doc/src/pair_exp6_rx.txt | 114 ++++++++++++++++ doc/src/pair_multi_lucy_rx.txt | 207 +++++++++++++++++++++++++++++ doc/src/pair_table_rx.txt | 231 +++++++++++++++++++++++++++++++++ 9 files changed, 855 insertions(+), 11 deletions(-) create mode 100644 doc/src/fix_eos_table_rx.txt create mode 100644 doc/src/fix_rx.txt create mode 100644 doc/src/pair_exp6_rx.txt create mode 100644 doc/src/pair_multi_lucy_rx.txt create mode 100644 doc/src/pair_table_rx.txt diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 1aed719d73..3a3ef81916 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -618,6 +618,7 @@ package"_Section_start.html#start_3. "drude/transform/reverse"_fix_drude_transform.html, "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, +"eos/table/rx"_fix_eos_table_rx.html, "gle"_fix_gle.html, "imd"_fix_imd.html, "ipi"_fix_ipi.html, @@ -646,6 +647,7 @@ package"_Section_start.html#start_3. "qtb"_fix_qtb.html, "reax/c/bonds"_fix_reax_bonds.html, "reax/c/species"_fix_reaxc_species.html, +"rx"_fix_rx.html, "saed/vtk"_fix_saed_vtk.html, "shardlow"_fix_shardlow.html, "smd"_fix_smd.html, @@ -934,6 +936,7 @@ package"_Section_start.html#start_3. "eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, "eff/cut"_pair_eff.html, +"exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, "lennard/mdf"_pair_mdf.html, "list"_pair_list.html, @@ -955,6 +958,7 @@ package"_Section_start.html#start_3. "morse/smooth/linear"_pair_morse.html, "morse/soft"_pair_morse.html, "multi/lucy"_pair_multi_lucy.html, +"multi/lucy/rx"_pair_multi_lucy_rx.html, "quip"_pair_quip.html, "reax/c"_pair_reax_c.html, "smd/hertz"_pair_smd_hertz.html, @@ -969,6 +973,7 @@ package"_Section_start.html#start_3. "sph/taitwater"_pair_sph_taitwater.html, "sph/taitwater/morris"_pair_sph_taitwater_morris.html, "srp"_pair_srp.html, +"table/rx"_pair_table_rx.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 6415542230..95038b74fb 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -132,9 +132,13 @@ position, which is represented by the eradius = electron size. For the {peri} style, the particles are spherical and each stores a per-particle mass and volume. -The {dpd} style is for dissipative particle dynamics (DPD) particles -which store the particle internal temperature (dpdTheta), internal -conductive energy (uCond) and internal mechanical energy (uMech). +The {dpd} style is for dissipative particle dynamics (DPD) particles. +Note that it is part of the USER-DPD package, and is not for use with +the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can +simply use atom_style atomic. Atom_style dpd extends DPD particle +properties with internal temperature (dpdTheta), internal conductive +energy (uCond), internal mechanical energy (uMech), and internal +chemical energy (uChem). The {meso} style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt index d1e1d270fb..fb0493d8e2 100644 --- a/doc/src/compute_dpd.txt +++ b/doc/src/compute_dpd.txt @@ -23,7 +23,7 @@ compute 1 all dpd :pre Define a computation that accumulates the total internal conductive energy (U_cond), the total internal mechanical energy (U_mech), the -total internal energy (U) and the {harmonic} average of the internal +total chemical energy (U_chem) and the {harmonic} average of the internal temperature (dpdTheta) for the entire system of particles. See the "compute dpd/atom"_compute_dpd_atom.html command if you want per-particle internal energies and internal temperatures. @@ -40,7 +40,7 @@ where N is the number of particles in the system [Output info:] This compute calculates a global vector of length 5 (U_cond, U_mech, -U, dpdTheta, N_particles), which can be accessed by indices 1-5. See +U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index c4be61b45f..7be083dca4 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -22,23 +22,25 @@ compute 1 all dpd/atom [Description:] Define a computation that accesses the per-particle internal -conductive energy (u_cond), internal mechanical energy (u_mech) and +conductive energy (u_cond), internal mechanical energy (u_mech), +internal chemical energy (u_chem) and internal temperatures (dpdTheta) for each particle in a group. See the "compute dpd"_compute_dpd.html command if you want the total -internal conductive energy, the total internal mechanical energy, and +internal conductive energy, the total internal mechanical energy, the +total chemical energy and average internal temperature of the entire system or group of dpd particles. [Output info:] -This compute calculates a per-particle array with 3 columns (u_cond, -u_mech, dpdTheta), which can be accessed by indices 1-3 by any command +This compute calculates a per-particle array with 4 columns (u_cond, +u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See "Section_howto15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle array values will be in energy (u_cond, u_mech) and -temperature (dpdTheta) "units"_units.html. +The per-particle array values will be in energy (u_cond, u_mech, u_chem) +and temperature (dpdTheta) "units"_units.html. [Restrictions:] diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt new file mode 100644 index 0000000000..b2a0051889 --- /dev/null +++ b/doc/src/fix_eos_table_rx.txt @@ -0,0 +1,138 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix eos/table/rx command :h3 + +[Syntax:] + +fix ID group-ID eos/table/rx style file1 N keyword file2 :pre + +ID, group-ID are documented in "fix"_fix.html command +eos/table/rx = style name of this fix command +style = {linear} = method of interpolation +file1 = filename containing the tabulated equation of state +N = use N values in {linear} tables +keyword = name of table keyword correponding to table file +file2 = filename containing the heats of formation of each species :ul + +[Examples:] + +fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre + +[Description:] + +Fix {eos/table/rx} applies a tabulated mesoparticle equation +of state to relate the concentration-dependent particle internal +energy (u_i) to the particle internal temperature (dpdTheta_i). + +The concentration-dependent particle internal energy (u_i) is +computed according to the following relation: + +:c,image(Eqs/fix_eos_table_rx.jpg) + +where {m} is the number of species, {c_i,j} is the concentration of +species {j} in particle {i}, {u_j} is the internal energy of species j, +{DeltaH_f,j} is the heat of formation of species {j}, N is the number of +molecules represented by the coarse-grained particle, kb is the +Boltzmann constant, and T is the temperature of the system. + +Fix {eos/table/rx} creates interpolation tables of length {N} from {m} +internal energy values of each species {u_j} listed in a file as a +function of internal temperature. During a simulation, these tables +are used to interpolate internal energy or temperature values as needed. +The interpolation is done with the {linear} style. For the {linear} style, +the internal temperature is used to find 2 surrounding table values from +which an internal energy is computed by linear interpolation. A secant +solver is used to determine the internal temperature from the internal energy. + +The first filename specifies a file containing tabulated internal +temperature and {m} internal energy values for each species {u_j}. +The keyword specifies a section of the file. The format of this +file is described below. + +The second filename specifies a file containing heat of formation +{DeltaH_f,j} for each species. + +:line + +The format of a tabulated file is as follows (without the +parenthesized comments): + +# EOS TABLE (one or more comment or blank lines) :pre + +KEYWORD (keyword is first text on line) +N 500 h2 no2 n2 ... no (N parameter species1 species2 ... speciesN) + (blank) +1 1.00 0.000 ... 0.0000 (index, internal temperature, internal energy of species 1, ..., internal energy of species m) +2 1.02 0.001 ... 0.0002 +... +500 10.0 0.500 ... 1.0000 :pre + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the fix command. + +The next line lists the number of table entries and the species names +that correspond with all the species listed in the reaction equations +through the {fix rx} command. +The parameter "N" is required and its value is the number of table +entries that follow. Let Nfile = "N" in the tabulated file. +What LAMMPS does is a preliminary interpolation by creating splines +using the Nfile tabulated values as nodal points. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the internal temperature (in temperature units), the 3rd value until +the {m+3} value are the internal energies of the m species (in energy units). + +Note that all internal temperature and internal energy values must +increase from one line to the next. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + +:line + +The format of a heat of formation file is as follows (without the +parenthesized comments): + +# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre + (blank) +h2 0.00 (species name, heat of formation) +no2 0.34 +n2 0.00 +... +no 0.93 :pre + +Note that the species can be listed in any order. The tag that is +used as the species name must correspond with the tags used to define +the reactions with the "fix rx"_fix_rx.html command. + +:line + +[Restrictions:] + +The fix {eos/table/rx} is only available if LAMMPS is built with the +USER-DPD package. + +The equation of state must be a monotonically increasing function. + +An exit error will occur if the internal temperature or internal +energies are not within the table cutoffs. + +[Related commands:] + +"fix rx"_fix_rx.html, +"pair dpd/fdt"_dpd_fdt.html + +[Default:] none + +:line diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt new file mode 100644 index 0000000000..a32290d366 --- /dev/null +++ b/doc/src/fix_rx.txt @@ -0,0 +1,143 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix rx command :h3 + +[Syntax:] + +fix ID group-ID rx file localTemp solver ... :pre + +ID, group-ID are documented in "fix"_fix.html command +rx = style name of this fix command +file = filename containing the reaction kinetic equations and Arrhenius parameters +localTemp = {none,lucy} = no local temperature averaging or local temperature defined through Lucy weighting function +solver = {lammps_rk4} = Explicit 4th order Runge-Kutta method +minSteps = # of steps for rk4 solver :ul + +[Examples:] + +fix 1 all rx kinetics.rx none lammps_rk4 +fix 1 all rx kinetics.rx none lammps_rk4 1 +fix 1 all rx kinetics.rx lucy lammps_rk4 10 :pre + +[Description:] + +Fix {rx} solves the reaction kinetic ODEs for a given reaction set that is +defined within the file associated with this command. + +For a general reaction such that + +:c,image(Eqs/fix_rx_reaction.jpg) + +the reaction rate equation is defined to be of the form + +:c,image(Eqs/fix_rx_reactionRate.jpg) + +In the current implementation, the exponents are defined to be equal to the +stoichiometric coefficients. A given reaction set consisting of {n} reaction +equations will contain a total of {m} species. A set of {m} ordinary +differential equations (ODEs) that describe the change in concentration of a +given species as a function of time are then constructed based on the {n} +reaction rate equations. + +The ODE systems are solved over the full DPD timestep {dt} using a 4th order +Runge-Kutta {rk4} method with a fixed step-size {h}, specified by the +{lammps_rk4} keyword. The number of ODE steps per DPD timestep for the rk4 method +is optionally specified immediately after the rk4 keyword. The ODE step-size is set as +{dt/num_steps}. Smaller step-sizes tend to yield more accurate results but there +is not control on the error. + +:line + +The filename specifies a file that contains the entire set of reaction +kinetic equations and corresponding Arrhenius parameters. The format of +this file is described below. + +There is no restriction on the total number or reaction equations that are +specified. The species names are arbitrary string names that are associated +with the species concentrations. +Each species in a given reaction must be preceded by it's stoichiometric +coefficient. The only delimiters that are recognized between the species are +either a {+} or {=} character. The {=} character corresponds to an +irreversible reaction. After specifying the reaction, the reaction rate +constant is determined through the temperature dependent Arrhenius equation: + +:c,image(Eqs/fix_rx.jpg) + +where {A} is the Arrhenius factor in time units or concentration/time units, +{n} is the unitless exponent of the temperature dependence, and {E_a} is the +activation energy in energy units. The temperature dependence can be removed +by specifying the exponent as zero. + +The internal temperature of the coarse-grained particles can be used in constructing the +reaction rate constants at every DPD timestep by specifying the keyword {none}. +Alternatively, the keyword {lucy} can be specified to compute a local-average particle +internal temperature for use in the reaction rate constant expressions. +The local-average particle internal temperature is defined as: + +:c,image(Eqs/fix_rx_localTemp.jpg) + +where the Lucy function is expressed as: + +:c,image(Eqs/fix_rx_localTemp2.jpg) + +The self-particle interaction is included in the above equation. + +:line + +The format of a tabulated file is as follows (without the parenthesized comments): + +# Rxn equations and parameters (one or more comment or blank lines) :pre +1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49E+01 0.0 1.34 (rxn equation, A, n, Ea) +1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 2.16E+00 0.0 1.52 +... +1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69 :pre + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. + +Following a blank line, the next N lines list the N reaction equations. +Each species within the reaction equation is specified through its +stoichiometric coefficient and a species tag. Reactant species are specified +on the left-hand side of the equation and product species are specified on the +right-hand side of the equation. After specifying the reactant and product +species, the final three arguments of each line represent the Arrhenius +parameter {A}, the temperature exponent {n}, and the activation energy {Ea}. + +Note that the species tags that are defined in the reaction equations are +used by the "fix eos/table/rx"_fix_eos_table_rx.html command to define the +thermodynamic properties of each species. Furthermore, the number of species +molecules (i.e., concentration) can be specified either with the "set"_set.html +command using the "d_" prefix or by reading directly the concentrations from a +data file. For the latter case, the "read_data"_read_data.html command with the +fix keyword should be specified, where the fix-ID will be the "fix rx" ID with a +"_SPECIES" suffix, e.g. + +fix foo all rx reaction.file ... +read_data data.dpd fix foo_SPECIES NULL Species + +:line + +[Restrictions:] + +The fix {rx} is only available if LAMMPS is built with the USER-DPD package. + +The fix {rx} must be used with the "atom_style dpd"_atom_style.html command. + +The fix {rx} can only be used with a constant energy or constant enthalpy DPD simulation. + +[Related commands:] + +"fix eos/table/rx"_fix_eos_table_rx.html, +"fix shardlow"_fix_shardlow.html, +"pair dpd/fdt/energy"_dpd_fdt_energy.html + +[Default:] none + +:line diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt new file mode 100644 index 0000000000..5e65fee84c --- /dev/null +++ b/doc/src/pair_exp6_rx.txt @@ -0,0 +1,114 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style exp6/rx command :h3 + +[Syntax:] + +pair_style exp6/rx cutoff :pre + +cutoff = global cutoff for DPD interactions (distance units) :ul + +[Examples:] + +pair_style exp6/rx 10.0 +pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 +pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 +pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre + +[Description:] + +Style {exp6/rx} is used in reaction DPD simulations, where the coarse-grained (CG) +particles are composed of {m} species whose reaction rate kinetics are determined +from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. The {exp6/rx} style +computes an exponential-6 potential given by + +:c,image(Eqs/pair_exp6_rx.jpg) + +where the {epsilon} parameter determines the depth of the potential +minimum located at {Rm}, and {alpha} determines the softness of the repulsion. + +The coefficients must be defined for each species in a given particle type +via the "pair_coeff"_pair_coeff.html command as in the examples above, where +the first argument is the filename that includes the exponential-6 parameters +for each species. The file includes the species tag followed by the {alpha}, +{epsilon} and {Rm} parameters. The format of the file is described below. + +The second and third arguments specify the site-site interaction +potential between two species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the "fix rx"_fix_rx.html command +or they must correspond to the tag "1fluid", signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the +difference is defined to be the internal chemical energy (uChem). + +The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents. + +The final argument specifies the interaction cutoff. + +:line + +The format of a tabulated file is as follows (without the parenthesized comments): + +# exponential-6 parameters for various species (one or more comment or blank lines) :pre +h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon) +no2 exp6 13.60 0.01 3.70 +... +co2 exp6 13.00 0.03 3.20 :pre + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. + +Following a blank line, the next N lines list the species and their +corresponding parameters. The first argument is the species tag, +the second argument is the exp6 tag, the 3rd argument is the {alpha} +parameter (energy units), the 4th argument is the {epsilon} parameter +(energy-distance^6 units), and the 5th argument is the {Rm} +parameter (distance units). If a species tag of "1fluid" is listed as a +pair coefficient, a one-fluid approximation is specified where a +concentration-dependent combination of the parameters is computed +through the following equations: + +:c,image(Eqs/pair_exp6_rx_oneFluid.jpg) + +where + +:c,image(Eqs/pair_exp6_rx_oneFluid2.jpg) + +and xa and xb are the mole fractions of a and b, respectively, which +comprise the gas mixture. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This style does not support the "pair_modify"_pair_modify.html shift option +for the energy of the exp() and 1/r^6 portion of the pair interaction. + +This style does not support the pair_modify tail option for adding long-range +tail corrections to energy and pressure for the A,C terms in the +pair interaction. + +[Restrictions:] + +None + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt new file mode 100644 index 0000000000..f1c33e9711 --- /dev/null +++ b/doc/src/pair_multi_lucy_rx.txt @@ -0,0 +1,207 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style multi/lucy/rx command :h3 + +[Syntax:] + +pair_style multi/lucy/rx style N keyword ... :pre + +style = {lookup} or {linear} = method of interpolation +N = use N values in {lookup}, {linear} tables :ul + +[Examples:] + +pair_style multi/lucy/rx linear 1000 +pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 +pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre + +[Description:] + +Style {multi/lucy/rx} is used in reaction DPD simulations, where the coarse-grained +(CG) particles are composed of {m} species whose reaction rate kinetics are determined +from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. +The species of one CG particle can interact with a species in a neighboring CG particle +through a site-site interaction potential model. Style {multi/lucy/rx} computes the +site-site density-dependent force following from the many-body form described in +"(Moore)"_#Moore and "(Warren)"_#Warren as + +:c,image(Eqs/pair_multi_lucy.jpg) + +which consists of a density-dependent function, A(rho), and a radial-dependent weight +function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken +as the Lucy function: + +:c,image(Eqs/pair_multi_lucy2.jpg) + +The density-dependent energy for a given particle is given by: + +:c,image(Eqs/pair_multi_lucy_energy.jpg) + +See the supporting information of "(Brennan)"_#Brennan or the publication by "(Moore)"_#Moore +for more details on the functional form. + +An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). +Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will +have units of energy / length^4. + +The interpolation table is created as a pre-computation by fitting cubic splines to +the file values and interpolating the density-dependent energy and force at each of {N} densities. +During a simulation, the tables are used to interpolate the density-dependent energy and force as +needed for each pair of particles separated by a distance {R}. The interpolation is done in +one of 2 styles: {lookup} and {linear}. + +For the {lookup} style, the density is used to find the nearest table entry, which is the +density-dependent energy and force. + +For the {linear} style, the density is used to find the 2 surrounding table values from +which the density-dependent energy and force are computed by linear interpolation. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above. + +filename +keyword +species1 +species2 +cutoff (distance units) :ul + +The filename specifies a file containing the tabulated density-dependent +energy and force. The keyword specifies a section of the file. +The cutoff is an optional coefficient. If not specified, the outer cutoff in the +table itself (see below) will be used to build an interpolation table +that extend to the largest tabulated distance. If specified, only +file values up to the cutoff are used to create the interpolation +table. The format of this file is described below. + +The species tags define the site-site interaction potential between two +species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the "fix rx"_fix_rx.html command +or they must correspond to the tag "1fluid", signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential +is stored before and after the reaction kinetics solver is applied, where +the difference is defined to be the internal chemical energy (uChem). + +:line + +The format of a tabulated file is a series of one or more sections, +defined as follows (without the parenthesized comments): + +# Density-dependent function (one or more comment or blank lines) :pre + +DD-FUNCTION (keyword is first text on line) +N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) +1 1.0 25.5 102.34 (index, density, energy/r^4, force) +2 1.02 23.4 98.5 +... +500 10.0 0.001 0.003 :pre + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the pair_coeff +command. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the {N} +specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html command. Let +Ntable = {N} in the pair_style command, and Nfile = "N" in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate the density-dependent energy and force at Ntable different +points. The resulting tables of length Ntable are then used as +described above, when computing the density-dependent energy and force. +This means that if you want the interpolation tables of +length Ntable to match exactly what is in the tabulated file (with +effectively no preliminary interpolation), you should set Ntable = +Nfile, and use the "RSQ" parameter. This is because the +internal table abscissa is always RSQ (separation distance squared), +for efficient lookup. + +All other parameters are optional. If "R" or "RSQ" does +not appear, then the distances in each line of the table are used +as-is to perform spline interpolation. In this case, the table values +can be spaced in {density} uniformly or however you wish to position table +values in regions of large gradients. + +If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} +and {rhi}. If specified, the density associated with each density-dependent +energy and force value is computed from these 2 values (at high accuracy), rather +than using the (low-accuracy) value listed in each line of the table. +The density values in the table file are ignored in this case. +For "R", distances uniformly spaced between {rlo} and {rhi} are +computed; for "RSQ", squared distances uniformly spaced between +{rlo*rlo} and {rhi*rhi} are computed. + +NOTE: If you use "R" or "RSQ", the tabulated distance values in the +file are effectively ignored, and replaced by new values as described +in the previous paragraph. If the density value in the table is not +very close to the new value (i.e. round-off difference), then you will +be assigning density-dependent energy and force values to a different density, +which is probably not what you want. LAMMPS will warn if this is occurring. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +r (in density units), the 3rd value is the density-dependent function value +(in energy units / length^4), and the 4th is the force (in force units). The +density values must increase from one line to the next. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +The "pair_modify"_pair_modify.html shift, table, and tail options are +not relevant for this pair style. + +This pair style writes the settings for the "pair_style multi/lucy/rx" command +to "binary restart files"_restart.html, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] none + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Warren) +[(Warren)] Warren, Phys Rev E, 68, 066702 (2003). + +:link(Brennan) +[(Brennan)] Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). + +:link(Moore) +[(Moore)] Moore, J Chem Phys, 144, 104501 (2016). + diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt new file mode 100644 index 0000000000..b33ef1196d --- /dev/null +++ b/doc/src/pair_table_rx.txt @@ -0,0 +1,231 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style table/rx command :h3 + +[Syntax:] + +pair_style table style N :pre + +style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation +N = use N values in {lookup}, {linear}, {spline} tables +N = use 2^N values in {bitmap} tables + +[Examples:] + +pair_style table/rx linear 1000 +pair_style table/rx bitmap 12 +pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0 +pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0 +pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre + +[Description:] + +Style {table/rx} is used in reaction DPD simulations,where the coarse-grained (CG) +particles are composed of {m} species whose reaction rate kinetics are determined +from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style {table/rx} creates +interpolation tables of length {N} from pair potential and force values listed in a +file(s) as a function of distance. The files are read by the +"pair_coeff"_pair_coeff.html command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and force values at each of {N} +distances. During a simulation, these tables are used to interpolate +energy and force values as needed. The interpolation is done in one +of 4 styles: {lookup}, {linear}, {spline}, or {bitmap}. + +For the {lookup} style, the distance between 2 atoms is used to find +the nearest table entry, which is the energy or force. + +For the {linear} style, the pair distance is used to find 2 +surrounding table values from which an energy or force is computed by +linear interpolation. + +For the {spline} style, a cubic spline coefficients are computed and +stored at each of the {N} values in the table. The pair distance is +used to find the appropriate set of coefficients which are used to +evaluate a cubic polynomial which computes the energy or force. + +For the {bitmap} style, the N means to create interpolation tables +that are 2^N in length. Date: Tue, 7 Jun 2016 15:31:35 +0000 Subject: [PATCH 077/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15121 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Section_commands.html | 97 +++--- doc/html/_sources/Section_commands.txt | 90 +++--- doc/html/_sources/atom_style.txt | 10 +- doc/html/_sources/compute_dpd.txt | 4 +- doc/html/_sources/compute_dpd_atom.txt | 14 +- doc/html/atom_style.html | 10 +- doc/html/compute_dpd.html | 4 +- doc/html/compute_dpd_atom.html | 14 +- doc/html/fix_eos_table_rx.html | 311 ++++++++++++++++++++ doc/html/genindex.html | 24 +- doc/html/pair_exp6_rx.html | 286 ++++++++++++++++++ doc/html/pair_multi_lucy.html | 4 +- doc/html/pair_multi_lucy_rx.html | 367 +++++++++++++++++++++++ doc/html/pair_table_rx.html | 389 +++++++++++++++++++++++++ doc/html/searchindex.js | 2 +- 15 files changed, 1509 insertions(+), 117 deletions(-) create mode 100644 doc/html/fix_eos_table_rx.html create mode 100644 doc/html/pair_exp6_rx.html create mode 100644 doc/html/pair_multi_lucy_rx.html create mode 100644 doc/html/pair_table_rx.html diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 999710b03a..7faafd009c 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -769,12 +769,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

    LAMMPS is built with the appropriate package.

    ++---+ @@ -788,57 +788,57 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

    + - - + + - - + + - - + + - - + + - - + + + - - - + + + - - - + + + - -
    adapt/fep drude/transform/reverse eos/cv eos/tableeos/table/rx gleimd
    ipi
    imdipi langevin/drude langevin/eff lb/fluid lb/momentumlb/pc
    lb/rigid/pc/sphere
    lb/pclb/rigid/pc/sphere lb/viscous meso manifoldforce meso/stationarynve/manifold/rattle
    nvt/manifold/rattle
    nve/manifold/rattlenvt/manifold/rattle nph/eff npt/eff nve/eff nvt/effnvt/sllod/eff
    phonon
    nvt/sllod/effphonon pimd qbmsst qeq/reax qmmmqtb
    reax/c/bonds
    qtbreax/c/bonds reax/c/speciesrx saed/vtk shardlowsmdsmd/adjust/dt
    smd/integrate/tlsph
    smdsmd/adjust/dtsmd/integrate/tlsph smd/integrate/ulsph smd/move/triangulated/surface smd/setvelsmd/tlsph/reference/configurationsmd/wall/surface
    temp/rescale/eff
    smd/tlsph/reference/configurationsmd/wall/surfacetemp/rescale/eff ti/rs ti/spring ttm/mod  
    @@ -1182,10 +1182,10 @@ KOKKOS, o = USER-OMP, t = OPT.

    if LAMMPS is built with the appropriate package.

    ---+++ @@ -1200,53 +1200,58 @@ if + - - + + - - + + - - + + - - + + - - + + + + - - + - + + - - + - + + - - + - - - - + + + + + + +
    awpmd/cutedip (o) eff/cutexp6/rx gauss/cutlennard/mdf
    list
    lennard/mdflist lj/charmm/coul/long/soft (o) lj/cut/coul/cut/soft (o)lj/cut/coul/long/soft (o)
    lj/cut/dipole/sf (go)
    lj/cut/coul/long/soft (o)lj/cut/dipole/sf (go) lj/cut/soft (o) lj/cut/thole/long (o)lj/cut/tip4p/long/soft (o)
    lj/mdf
    lj/cut/tip4p/long/soft (o)lj/mdf lj/sdk (gko) lj/sdk/coul/long (go)lj/sdk/coul/msm (o)
    lj/sf (o)
    lj/sdk/coul/msm (o)lj/sf (o) meam/spline meam/sw/splinemgpt
    morse/smooth/linear
    mgptmorse/smooth/linear morse/soft multi/lucy
    multi/lucy/rx quip
    reax/creax/c smd/hertzsmd/tlsph
    smd/tlsph smd/triangulated/surface
    smd/ulsphsmd/ulsph smtbqsph/heatconduction
    sph/heatconduction sph/idealgas
    sph/ljsph/lj sph/rhosumsph/taitwatersph/taitwater/morris
    srptersoff/table (o)
    sph/taitwatersph/taitwater/morrissrptable/rx
    tersoff/table (o) thole tip4p/long/soft (o) 
    diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt index f19aa4047c..095bb5c4bc 100644 --- a/doc/html/_sources/Section_commands.txt +++ b/doc/html/_sources/Section_commands.txt @@ -492,25 +492,25 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. These are additional fix styles in USER packages, which can be used if :ref:`LAMMPS is built with the appropriate package `. -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`adapt/fep ` | :doc:`addtorque ` | :doc:`atc ` | :doc:`ave/correlate/long ` | :doc:`colvars ` | :doc:`drude ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`gle ` | :doc:`imd ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`ipi ` | :doc:`langevin/drude ` | :doc:`langevin/eff ` | :doc:`lb/fluid ` | :doc:`lb/momentum ` | :doc:`lb/pc ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`lb/rigid/pc/sphere ` | :doc:`lb/viscous ` | :doc:`meso ` | :doc:`manifoldforce ` | :doc:`meso/stationary ` | :doc:`nve/manifold/rattle ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`nvt/manifold/rattle ` | :doc:`nph/eff ` | :doc:`npt/eff ` | :doc:`nve/eff ` | :doc:`nvt/eff ` | :doc:`nvt/sllod/eff ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`phonon ` | :doc:`pimd ` | :doc:`qbmsst ` | :doc:`qeq/reax ` | :doc:`qmmm ` | :doc:`qtb ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`reax/c/bonds ` | :doc:`reax/c/species ` | :doc:`saed/vtk ` | :doc:`shardlow ` | :doc:`smd ` | :doc:`smd/adjust/dt ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`smd/integrate/tlsph ` | :doc:`smd/integrate/ulsph ` | :doc:`smd/move/triangulated/surface ` | :doc:`smd/setvel ` | :doc:`smd/tlsph/reference/configuration ` | :doc:`smd/wall/surface ` | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ -| :doc:`temp/rescale/eff ` | :doc:`ti/rs ` | :doc:`ti/spring ` | :doc:`ttm/mod ` | | | -+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+ ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`adapt/fep ` | :doc:`addtorque ` | :doc:`atc ` | :doc:`ave/correlate/long ` | :doc:`colvars ` | :doc:`drude ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`eos/table/rx ` | :doc:`gle ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`imd ` | :doc:`ipi ` | :doc:`langevin/drude ` | :doc:`langevin/eff ` | :doc:`lb/fluid ` | :doc:`lb/momentum ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`lb/pc ` | :doc:`lb/rigid/pc/sphere ` | :doc:`lb/viscous ` | :doc:`meso ` | :doc:`manifoldforce ` | :doc:`meso/stationary ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`nve/manifold/rattle ` | :doc:`nvt/manifold/rattle ` | :doc:`nph/eff ` | :doc:`npt/eff ` | :doc:`nve/eff ` | :doc:`nvt/eff ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`nvt/sllod/eff ` | :doc:`phonon ` | :doc:`pimd ` | :doc:`qbmsst ` | :doc:`qeq/reax ` | :doc:`qmmm ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`qtb ` | :doc:`reax/c/bonds ` | :doc:`reax/c/species ` | :doc:`rx ` | :doc:`saed/vtk ` | :doc:`shardlow ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`smd ` | :doc:`smd/adjust/dt ` | :doc:`smd/integrate/tlsph ` | :doc:`smd/integrate/ulsph ` | :doc:`smd/move/triangulated/surface ` | :doc:`smd/setvel ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ +| :doc:`smd/tlsph/reference/configuration ` | :doc:`smd/wall/surface ` | :doc:`temp/rescale/eff ` | :doc:`ti/rs ` | :doc:`ti/spring ` | :doc:`ttm/mod ` | ++----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+ ---------- @@ -648,31 +648,33 @@ KOKKOS, o = USER-OMP, t = OPT. These are additional pair styles in USER packages, which can be used if :ref:`LAMMPS is built with the appropriate package `. -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`awpmd/cut ` | :doc:`buck/mdf ` | :doc:`coul/cut/soft (o) ` | :doc:`coul/diel (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`coul/long/soft (o) ` | :doc:`dpd/fdt ` | :doc:`dpd/fdt/energy ` | :doc:`eam/cd (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`edip (o) ` | :doc:`eff/cut ` | :doc:`gauss/cut ` | :doc:`lennard/mdf ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`list ` | :doc:`lj/charmm/coul/long/soft (o) ` | :doc:`lj/cut/coul/cut/soft (o) ` | :doc:`lj/cut/coul/long/soft (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`lj/cut/dipole/sf (go) ` | :doc:`lj/cut/soft (o) ` | :doc:`lj/cut/thole/long (o) ` | :doc:`lj/cut/tip4p/long/soft (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`lj/mdf ` | :doc:`lj/sdk (gko) ` | :doc:`lj/sdk/coul/long (go) ` | :doc:`lj/sdk/coul/msm (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`lj/sf (o) ` | :doc:`meam/spline ` | :doc:`meam/sw/spline ` | :doc:`mgpt ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`morse/smooth/linear ` | :doc:`morse/soft ` | :doc:`multi/lucy ` | :doc:`quip ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`reax/c ` | :doc:`smd/hertz ` | :doc:`smd/tlsph ` | :doc:`smd/triangulated/surface ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`smd/ulsph ` | :doc:`smtbq ` | :doc:`sph/heatconduction ` | :doc:`sph/idealgas ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`sph/lj ` | :doc:`sph/rhosum ` | :doc:`sph/taitwater ` | :doc:`sph/taitwater/morris ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ -| :doc:`srp ` | :doc:`tersoff/table (o) ` | :doc:`thole ` | :doc:`tip4p/long/soft (o) ` | -+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`awpmd/cut ` | :doc:`buck/mdf ` | :doc:`coul/cut/soft (o) ` | :doc:`coul/diel (o) ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`coul/long/soft (o) ` | :doc:`dpd/fdt ` | :doc:`dpd/fdt/energy ` | :doc:`eam/cd (o) ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`edip (o) ` | :doc:`eff/cut ` | :doc:`exp6/rx ` | :doc:`gauss/cut ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`lennard/mdf ` | :doc:`list ` | :doc:`lj/charmm/coul/long/soft (o) ` | :doc:`lj/cut/coul/cut/soft (o) ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`lj/cut/coul/long/soft (o) ` | :doc:`lj/cut/dipole/sf (go) ` | :doc:`lj/cut/soft (o) ` | :doc:`lj/cut/thole/long (o) ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`lj/cut/tip4p/long/soft (o) ` | :doc:`lj/mdf ` | :doc:`lj/sdk (gko) ` | :doc:`lj/sdk/coul/long (go) ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`lj/sdk/coul/msm (o) ` | :doc:`lj/sf (o) ` | :doc:`meam/spline ` | :doc:`meam/sw/spline ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`mgpt ` | :doc:`morse/smooth/linear ` | :doc:`morse/soft ` | :doc:`multi/lucy ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`multi/lucy/rx ` | :doc:`quip ` | :doc:`reax/c ` | :doc:`smd/hertz ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`smd/tlsph ` | :doc:`smd/triangulated/surface ` | :doc:`smd/ulsph ` | :doc:`smtbq ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`sph/heatconduction ` | :doc:`sph/idealgas ` | :doc:`sph/lj ` | :doc:`sph/rhosum ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`sph/taitwater ` | :doc:`sph/taitwater/morris ` | :doc:`srp ` | :doc:`table/rx ` | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ +| :doc:`tersoff/table (o) ` | :doc:`thole ` | :doc:`tip4p/long/soft (o) ` | | ++-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ ---------- diff --git a/doc/html/_sources/atom_style.txt b/doc/html/_sources/atom_style.txt index cfa9c1208a..30ecaa9d5e 100644 --- a/doc/html/_sources/atom_style.txt +++ b/doc/html/_sources/atom_style.txt @@ -154,9 +154,13 @@ position, which is represented by the eradius = electron size. For the *peri* style, the particles are spherical and each stores a per-particle mass and volume. -The *dpd* style is for dissipative particle dynamics (DPD) particles -which store the particle internal temperature (dpdTheta), internal -conductive energy (uCond) and internal mechanical energy (uMech). +The *dpd* style is for dissipative particle dynamics (DPD) particles. +Note that it is part of the USER-DPD package, and is not for use with +the :doc:`pair_style dpd or dpd/stat ` commands, which can +simply use atom_style atomic. Atom_style dpd extends DPD particle +properties with internal temperature (dpdTheta), internal conductive +energy (uCond), internal mechanical energy (uMech), and internal +chemical energy (uChem). The *meso* style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity diff --git a/doc/html/_sources/compute_dpd.txt b/doc/html/_sources/compute_dpd.txt index 5028ed787c..5975dfd4c4 100644 --- a/doc/html/_sources/compute_dpd.txt +++ b/doc/html/_sources/compute_dpd.txt @@ -25,7 +25,7 @@ Description Define a computation that accumulates the total internal conductive energy (U_cond), the total internal mechanical energy (U_mech), the -total internal energy (U) and the *harmonic* average of the internal +total chemical energy (U_chem) and the *harmonic* average of the internal temperature (dpdTheta) for the entire system of particles. See the :doc:`compute dpd/atom ` command if you want per-particle internal energies and internal temperatures. @@ -45,7 +45,7 @@ where N is the number of particles in the system **Output info:** This compute calculates a global vector of length 5 (U_cond, U_mech, -U, dpdTheta, N_particles), which can be accessed by indices 1-5. See +U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See :ref:`this section ` for an overview of LAMMPS output options. diff --git a/doc/html/_sources/compute_dpd_atom.txt b/doc/html/_sources/compute_dpd_atom.txt index 1cdf02264e..ba36cfacbe 100644 --- a/doc/html/_sources/compute_dpd_atom.txt +++ b/doc/html/_sources/compute_dpd_atom.txt @@ -22,23 +22,25 @@ Description """"""""""" Define a computation that accesses the per-particle internal -conductive energy (u_cond), internal mechanical energy (u_mech) and +conductive energy (u_cond), internal mechanical energy (u_mech), +internal chemical energy (u_chem) and internal temperatures (dpdTheta) for each particle in a group. See the :doc:`compute dpd ` command if you want the total -internal conductive energy, the total internal mechanical energy, and +internal conductive energy, the total internal mechanical energy, the +total chemical energy and average internal temperature of the entire system or group of dpd particles. **Output info:** -This compute calculates a per-particle array with 3 columns (u_cond, -u_mech, dpdTheta), which can be accessed by indices 1-3 by any command +This compute calculates a per-particle array with 4 columns (u_cond, +u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See :ref:`Section_howto15 ` for an overview of LAMMPS output options. -The per-particle array values will be in energy (u_cond, u_mech) and -temperature (dpdTheta) :doc:`units `. +The per-particle array values will be in energy (u_cond, u_mech, u_chem) +and temperature (dpdTheta) :doc:`units `. Restrictions """""""""""" diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html index d3150678cb..2ed9ccbab0 100644 --- a/doc/html/atom_style.html +++ b/doc/html/atom_style.html @@ -309,9 +309,13 @@ Gaussians with a specified position and bandwidth or uncertainty in position, which is represented by the eradius = electron size.

    For the peri style, the particles are spherical and each stores a per-particle mass and volume.

    -

    The dpd style is for dissipative particle dynamics (DPD) particles -which store the particle internal temperature (dpdTheta), internal -conductive energy (uCond) and internal mechanical energy (uMech).

    +

    The dpd style is for dissipative particle dynamics (DPD) particles. +Note that it is part of the USER-DPD package, and is not for use with +the pair_style dpd or dpd/stat commands, which can +simply use atom_style atomic. Atom_style dpd extends DPD particle +properties with internal temperature (dpdTheta), internal conductive +energy (uCond), internal mechanical energy (uMech), and internal +chemical energy (uChem).

    The meso style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv).

    diff --git a/doc/html/compute_dpd.html b/doc/html/compute_dpd.html index ddab1ca7a8..2fecd4eef0 100644 --- a/doc/html/compute_dpd.html +++ b/doc/html/compute_dpd.html @@ -146,7 +146,7 @@

    Description

    Define a computation that accumulates the total internal conductive energy (U_cond), the total internal mechanical energy (U_mech), the -total internal energy (U) and the harmonic average of the internal +total chemical energy (U_chem) and the harmonic average of the internal temperature (dpdTheta) for the entire system of particles. See the compute dpd/atom command if you want per-particle internal energies and internal temperatures.

    @@ -157,7 +157,7 @@ relations:

    Output info:

    This compute calculates a global vector of length 5 (U_cond, U_mech, -U, dpdTheta, N_particles), which can be accessed by indices 1-5. See +U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See this section for an overview of LAMMPS output options.

    The vector values will be in energy and temperature units.

    diff --git a/doc/html/compute_dpd_atom.html b/doc/html/compute_dpd_atom.html index 195981a949..d51ffc826b 100644 --- a/doc/html/compute_dpd_atom.html +++ b/doc/html/compute_dpd_atom.html @@ -143,20 +143,22 @@

    Description

    Define a computation that accesses the per-particle internal -conductive energy (u_cond), internal mechanical energy (u_mech) and +conductive energy (u_cond), internal mechanical energy (u_mech), +internal chemical energy (u_chem) and internal temperatures (dpdTheta) for each particle in a group. See the compute dpd command if you want the total -internal conductive energy, the total internal mechanical energy, and +internal conductive energy, the total internal mechanical energy, the +total chemical energy and average internal temperature of the entire system or group of dpd particles.

    Output info:

    -

    This compute calculates a per-particle array with 3 columns (u_cond, -u_mech, dpdTheta), which can be accessed by indices 1-3 by any command +

    This compute calculates a per-particle array with 4 columns (u_cond, +u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See Section_howto15 for an overview of LAMMPS output options.

    -

    The per-particle array values will be in energy (u_cond, u_mech) and -temperature (dpdTheta) units.

    +

    The per-particle array values will be in energy (u_cond, u_mech, u_chem) +and temperature (dpdTheta) units.

    Restrictions

    diff --git a/doc/html/fix_eos_table_rx.html b/doc/html/fix_eos_table_rx.html new file mode 100644 index 0000000000..c9db07b19e --- /dev/null +++ b/doc/html/fix_eos_table_rx.html @@ -0,0 +1,311 @@ + + + + + + + + + + + fix eos/table/rx command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix eos/table/rx command

    +
    +

    Syntax

    +
    fix ID group-ID eos/table/rx style file1 N keyword file2
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • eos/table/rx = style name of this fix command
      • +
    • style = linear = method of interpolation
      • +
    • file1 = filename containing the tabulated equation of state
      • +
    • N = use N values in linear tables
      • +
    • keyword = name of table keyword correponding to table file
      • +
    • file2 = filename containing the heats of formation of each species
      • +
    +
    +
    +

    Examples

    +
    fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
+
    +
    +
    +
    +

    Description

    +

    Fix eos/table/rx applies a tabulated mesoparticle equation +of state to relate the concentration-dependent particle internal +energy (u_i) to the particle internal temperature (dpdTheta_i).

    +

    The concentration-dependent particle internal energy (u_i) is +computed according to the following relation:

    +Eqs/fix_eos_table_rx.jpg +

    where m is the number of species, c_i,j is the concentration of +species j in particle i, u_j is the internal energy of species j, +DeltaH_f,j is the heat of formation of species j, N is the number of +molecules represented by the coarse-grained particle, kb is the +Boltzmann constant, and T is the temperature of the system.

    +

    Fix eos/table/rx creates interpolation tables of length N from m +internal energy values of each species u_j listed in a file as a +function of internal temperature. During a simulation, these tables +are used to interpolate internal energy or temperature values as needed. +The interpolation is done with the linear style. For the linear style, +the internal temperature is used to find 2 surrounding table values from +which an internal energy is computed by linear interpolation. A secant +solver is used to determine the internal temperature from the internal energy.

    +

    The first filename specifies a file containing tabulated internal +temperature and m internal energy values for each species u_j. +The keyword specifies a section of the file. The format of this +file is described below.

    +

    The second filename specifies a file containing heat of formation +DeltaH_f,j for each species.

    +
    +

    The format of a tabulated file is as follows (without the +parenthesized comments):

    +
    # EOS TABLE                (one or more comment or blank lines)
+
    +
    +
    KEYWORD                    (keyword is first text on line)
+N 500 h2 no2 n2 ... no     (N  parameter species1 species2 ... speciesN)
+                           (blank)
+1   1.00 0.000 ... 0.0000  (index, internal temperature, internal energy of species 1, ..., internal energy of species m)
+2   1.02 0.001 ... 0.0002
+...
+500 10.0 0.500 ... 1.0000
+
    +
    +

    A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the fix command.

    +

    The next line lists the number of table entries and the species names +that correspond with all the species listed in the reaction equations +through the fix rx command. +The parameter “N” is required and its value is the number of table +entries that follow. Let Nfile = “N” in the tabulated file. +What LAMMPS does is a preliminary interpolation by creating splines +using the Nfile tabulated values as nodal points.

    +

    Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the internal temperature (in temperature units), the 3rd value until +the m+3 value are the internal energies of the m species (in energy units).

    +

    Note that all internal temperature and internal energy values must +increase from one line to the next.

    +

    Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword.

    +
    +

    The format of a heat of formation file is as follows (without the +parenthesized comments):

    +
    # HEAT OF FORMATION TABLE  (one or more comment or blank lines)
+
    +
    +
                               (blank)
+h2      0.00               (species name, heat of formation)
+no2     0.34
+n2      0.00
+...
+no      0.93
+
    +
    +

    Note that the species can be listed in any order. The tag that is +used as the species name must correspond with the tags used to define +the reactions with the fix rx command.

    +
    +
    +
    +

    Restrictions

    +

    The fix eos/table/rx is only available if LAMMPS is built with the +USER-DPD package.

    +

    The equation of state must be a monotonically increasing function.

    +

    An exit error will occur if the internal temperature or internal +energies are not within the table cutoffs.

    +
    + +
    + + +
    +
    +
    + + +
    + +
    +

    + © Copyright 2013 Sandia Corporation. +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 47f561802e..dced39f64f 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -1070,6 +1070,10 @@ +
    fix eos/table/rx +
    + +
    fix evaporate
    @@ -1364,6 +1368,10 @@ +
    fix rx +
    + +
    fix saed/vtk
    @@ -1816,6 +1824,10 @@ +
    pair_style exp6/rx +
    + +
    pair_style gauss
    @@ -1907,12 +1919,12 @@
    pair_style lj/smooth/linear
    - -
    pair_style lj96/cut
    +
    +
    pair_style lubricate
    @@ -1942,6 +1954,10 @@ +
    pair_style multi/lucy/rx +
    + +
    pair_style nb3b/harmonic
    @@ -2042,6 +2058,10 @@ +
    pair_style table/rx +
    + +
    pair_style tersoff
    diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html new file mode 100644 index 0000000000..b6b354ed7b --- /dev/null +++ b/doc/html/pair_exp6_rx.html @@ -0,0 +1,286 @@ + + + + + + + + + + + pair_style exp6/rx command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style exp6/rx command

    +
    +

    Syntax

    +
    pair_style exp6/rx cutoff
+
    +
    +
      +
    • cutoff = global cutoff for DPD interactions (distance units)
      • +
    +
    +
    +

    Examples

    +
    pair_style exp6/rx 10.0
+pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
+pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0
+
    +
    +
    +
    +

    Description

    +

    Style exp6/rx is used in reaction DPD simulations, where the coarse-grained (CG) +particles are composed of m species whose reaction rate kinetics are determined +from a set of n reaction rate equations through the fix rx command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. The exp6/rx style +computes an exponential-6 potential given by

    +Eqs/pair_exp6_rx.jpg +

    where the epsilon parameter determines the depth of the potential +minimum located at Rm, and alpha determines the softness of the repulsion.

    +

    The coefficients must be defined for each species in a given particle type +via the pair_coeff command as in the examples above, where +the first argument is the filename that includes the exponential-6 parameters +for each species. The file includes the species tag followed by the alpha, +epsilon and Rm parameters. The format of the file is described below.

    +

    The second and third arguments specify the site-site interaction +potential between two species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the fix rx command +or they must correspond to the tag “1fluid”, signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the +difference is defined to be the internal chemical energy (uChem).

    +

    The fourth and fifth arguments specify the Rm and epsilon scaling exponents.

    +

    The final argument specifies the interaction cutoff.

    +
    +

    The format of a tabulated file is as follows (without the parenthesized comments):

    +
    # exponential-6 parameters for various species      (one or more comment or blank lines)
+
    +
    +
    h2o  exp6  11.00 0.02 3.50                          (species, exp6, alpha, Rm, epsilon)
+no2  exp6  13.60 0.01 3.70
+...
+co2  exp6  13.00 0.03 3.20
+
    +
    +

    A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections.

    +

    Following a blank line, the next N lines list the species and their +corresponding parameters. The first argument is the species tag, +the second argument is the exp6 tag, the 3rd argument is the alpha +parameter (energy units), the 4th argument is the epsilon parameter +(energy-distance^6 units), and the 5th argument is the Rm +parameter (distance units). If a species tag of “1fluid” is listed as a +pair coefficient, a one-fluid approximation is specified where a +concentration-dependent combination of the parameters is computed +through the following equations:

    +Eqs/pair_exp6_rx_oneFluid.jpg +

    where

    +Eqs/pair_exp6_rx_oneFluid2.jpg +

    and xa and xb are the mole fractions of a and b, respectively, which +comprise the gas mixture.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly.

    +

    This style does not support the pair_modify shift option +for the energy of the exp() and 1/r^6 portion of the pair interaction.

    +

    This style does not support the pair_modify tail option for adding long-range +tail corrections to energy and pressure for the A,C terms in the +pair interaction.

    +
    +
    +

    Restrictions

    +

    None

    +
    + +
    + + +
    +
    +
    + + +
    + +
    +

    + © Copyright 2013 Sandia Corporation. +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/html/pair_multi_lucy.html b/doc/html/pair_multi_lucy.html index e171de530f..43bfaeb9cc 100644 --- a/doc/html/pair_multi_lucy.html +++ b/doc/html/pair_multi_lucy.html @@ -146,7 +146,7 @@

    Description

    Style multi/lucy computes a density-dependent force following from the many-body -form described in (Moore) and (Warren) as

    +form described in (Moore) and (Warren) as

    _images/pair_multi_lucy.jpg

    which consists of a density-dependent function, A(rho), and a radial-dependent weight function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken @@ -154,7 +154,7 @@ as the Lucy function:

    _images/pair_multi_lucy2.jpg

    The density-dependent energy for a given particle is given by:

    _images/pair_multi_lucy_energy.jpg -

    See the supporting information of (Brennan) or the publication by (Moore) +

    See the supporting information of (Brennan) or the publication by (Moore) for more details on the functional form.

    An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will diff --git a/doc/html/pair_multi_lucy_rx.html b/doc/html/pair_multi_lucy_rx.html new file mode 100644 index 0000000000..7c2fbcb272 --- /dev/null +++ b/doc/html/pair_multi_lucy_rx.html @@ -0,0 +1,367 @@ + + + + + + + + + + + pair_style multi/lucy/rx command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style multi/lucy/rx command

    +
    +

    Syntax

    +
    pair_style multi/lucy/rx style N keyword ...
+
    +
    +
      +
    • style = lookup or linear = method of interpolation
      • +
    • N = use N values in lookup, linear tables
      • +
    +
    +
    +

    Examples

    +
    pair_style multi/lucy/rx linear 1000
+pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
+pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
+
    +
    +
    +
    +

    Description

    +

    Style multi/lucy/rx is used in reaction DPD simulations, where the coarse-grained +(CG) particles are composed of m species whose reaction rate kinetics are determined +from a set of n reaction rate equations through the fix rx command. +The species of one CG particle can interact with a species in a neighboring CG particle +through a site-site interaction potential model. Style multi/lucy/rx computes the +site-site density-dependent force following from the many-body form described in +(Moore) and (Warren) as

    +_images/pair_multi_lucy.jpg +

    which consists of a density-dependent function, A(rho), and a radial-dependent weight +function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken +as the Lucy function:

    +_images/pair_multi_lucy2.jpg +

    The density-dependent energy for a given particle is given by:

    +_images/pair_multi_lucy_energy.jpg +

    See the supporting information of (Brennan) or the publication by (Moore) +for more details on the functional form.

    +

    An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). +Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will +have units of energy / length^4.

    +

    The interpolation table is created as a pre-computation by fitting cubic splines to +the file values and interpolating the density-dependent energy and force at each of N densities. +During a simulation, the tables are used to interpolate the density-dependent energy and force as +needed for each pair of particles separated by a distance R. The interpolation is done in +one of 2 styles: lookup and linear.

    +

    For the lookup style, the density is used to find the nearest table entry, which is the +density-dependent energy and force.

    +

    For the linear style, the density is used to find the 2 surrounding table values from +which the density-dependent energy and force are computed by linear interpolation.

    +

    The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above.

    +
      +
    • filename
      • +
    • keyword
      • +
    • species1
      • +
    • species2
      • +
    • cutoff (distance units)
      • +
    +

    The filename specifies a file containing the tabulated density-dependent +energy and force. The keyword specifies a section of the file. +The cutoff is an optional coefficient. If not specified, the outer cutoff in the +table itself (see below) will be used to build an interpolation table +that extend to the largest tabulated distance. If specified, only +file values up to the cutoff are used to create the interpolation +table. The format of this file is described below.

    +

    The species tags define the site-site interaction potential between two +species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the fix rx command +or they must correspond to the tag “1fluid”, signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential +is stored before and after the reaction kinetics solver is applied, where +the difference is defined to be the internal chemical energy (uChem).

    +
    +

    The format of a tabulated file is a series of one or more sections, +defined as follows (without the parenthesized comments):

    +
    # Density-dependent function (one or more comment or blank lines)
+
    +
    +
    DD-FUNCTION                (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, density, energy/r^4, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
    +
    +

    A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the pair_coeff +command. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values.

    +

    The parameter “N” is required and its value is the number of table +entries that follow. Note that this may be different than the N +specified in the pair_style multi/lucy/rx command. Let +Ntable = N in the pair_style command, and Nfile = “N” in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate the density-dependent energy and force at Ntable different +points. The resulting tables of length Ntable are then used as +described above, when computing the density-dependent energy and force. +This means that if you want the interpolation tables of +length Ntable to match exactly what is in the tabulated file (with +effectively no preliminary interpolation), you should set Ntable = +Nfile, and use the “RSQ” parameter. This is because the +internal table abscissa is always RSQ (separation distance squared), +for efficient lookup.

    +

    All other parameters are optional. If “R” or “RSQ” does +not appear, then the distances in each line of the table are used +as-is to perform spline interpolation. In this case, the table values +can be spaced in density uniformly or however you wish to position table +values in regions of large gradients.

    +

    If used, the parameters “R” or “RSQ” are followed by 2 values rlo +and rhi. If specified, the density associated with each density-dependent +energy and force value is computed from these 2 values (at high accuracy), rather +than using the (low-accuracy) value listed in each line of the table. +The density values in the table file are ignored in this case. +For “R”, distances uniformly spaced between rlo and rhi are +computed; for “RSQ”, squared distances uniformly spaced between +rlo*rlo and rhi*rhi are computed.

    +
    +

    Note

    +

    If you use “R” or “RSQ”, the tabulated distance values in the +file are effectively ignored, and replaced by new values as described +in the previous paragraph. If the density value in the table is not +very close to the new value (i.e. round-off difference), then you will +be assigning density-dependent energy and force values to a different density, +which is probably not what you want. LAMMPS will warn if this is occurring.

    +
    +

    Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +r (in density units), the 3rd value is the density-dependent function value +(in energy units / length^4), and the 4th is the force (in force units). The +density values must increase from one line to the next.

    +

    Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly.

    +

    The pair_modify shift, table, and tail options are +not relevant for this pair style.

    +

    This pair style writes the settings for the “pair_style multi/lucy/rx” command +to binary restart files, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script.

    +

    This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

    +
    +
    +
    +

    Restrictions

    +
    +
    none
    +
    + +
    + + +
    +
    +
    + + +
    + +
    +

    + © Copyright 2013 Sandia Corporation. +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/html/pair_table_rx.html b/doc/html/pair_table_rx.html new file mode 100644 index 0000000000..32bb6aae19 --- /dev/null +++ b/doc/html/pair_table_rx.html @@ -0,0 +1,389 @@ + + + + + + + + + + + pair_style table/rx command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style table/rx command

    +
    +

    Syntax

    +
    pair_style table style N
+
    +
    +

    style = lookup or linear or spline or bitmap = method of interpolation +N = use N values in lookup, linear, spline tables +N = use 2^N values in bitmap tables

    +
    +
    +

    Examples

    +
    pair_style table/rx linear 1000
+pair_style table/rx bitmap 12
+pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
+pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
+pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
+
    +
    +
    +
    +

    Description

    +

    Style table/rx is used in reaction DPD simulations,where the coarse-grained (CG) +particles are composed of m species whose reaction rate kinetics are determined +from a set of n reaction rate equations through the fix rx command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style table/rx creates +interpolation tables of length N from pair potential and force values listed in a +file(s) as a function of distance. The files are read by the +pair_coeff command.

    +

    The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and force values at each of N +distances. During a simulation, these tables are used to interpolate +energy and force values as needed. The interpolation is done in one +of 4 styles: lookup, linear, spline, or bitmap.

    +

    For the lookup style, the distance between 2 atoms is used to find +the nearest table entry, which is the energy or force.

    +

    For the linear style, the pair distance is used to find 2 +surrounding table values from which an energy or force is computed by +linear interpolation.

    +

    For the spline style, a cubic spline coefficients are computed and +stored at each of the N values in the table. The pair distance is +used to find the appropriate set of coefficients which are used to +evaluate a cubic polynomial which computes the energy or force.

    +

    For the bitmap style, the N means to create interpolation tables +that are 2^N in length. <The pair distance is used to index into the +table via a fast bit-mapping technique (Wolff) and a linear +interpolation is performed between adjacent table values.

    +

    The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above.

    +
      +
    • filename
      • +
    • keyword
      • +
    • species1
      • +
    • species2
      • +
    • cutoff (distance units)
      • +
    +

    The filename specifies a file containing tabulated energy and force +values. The keyword specifies a section of the file. The cutoff is +an optional coefficient. If not specified, the outer cutoff in the +table itself (see below) will be used to build an interpolation table +that extend to the largest tabulated distance. If specified, only +file values up to the cutoff are used to create the interpolation +table. The format of this file is described below.

    +

    The species tags define the site-site interaction potential between two +species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the fix rx command +or they must correspond to the tag “1fluid”, signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential +is stored before and after the reaction kinetics solver is applied, where +the difference is defined to be the internal chemical energy (uChem).

    +
    +

    Here are some guidelines for using the pair_style table/rx command to +best effect:

    +
      +
    • Vary the number of table points; you may need to use more than you think +to get good resolution.
      • +
    • Always use the pair_write command to produce a plot +of what the final interpolated potential looks like. This can show up +interpolation “features” you may not like.
      • +
    • Start with the linear style; it’s the style least likely to have problems.
      • +
    • Use N in the pair_style command equal to the “N” in the tabulation +file, and use the “RSQ” or “BITMAP” parameter, so additional interpolation +is not needed. See discussion below.
      • +
    • Make sure that your tabulated forces and tabulated energies are consistent +(dE/dr = -F) along the entire range of r values.
      • +
    • Use as large an inner cutoff as possible. This avoids fitting splines +to very steep parts of the potential.
      • +
    +
    +

    The format of a tabulated file is a series of one or more sections, +defined as follows (without the parenthesized comments):

    +
    # Morse potential for Fe   (one or more comment or blank lines)
+
    +
    +
    MORSE_FE                   (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
    +
    +

    A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the pair_coeff +command. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values.

    +

    The parameter “N” is required and its value is the number of table +entries that follow. Note that this may be different than the N +specified in the pair_style table/rx command. Let +Ntable = N in the pair_style command, and Nfile = “N” in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate as needed to generate energy and force +values at Ntable different points. The resulting tables of length +Ntable are then used as described above, when computing energy and +force for individual pair distances. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile, and use the “RSQ” or “BITMAP” parameter. +The internal table abscissa is RSQ (separation distance squared).

    +

    All other parameters are optional. If “R” or “RSQ” or “BITMAP” does +not appear, then the distances in each line of the table are used +as-is to perform spline interpolation. In this case, the table values +can be spaced in r uniformly or however you wish to position table +values in regions of large gradients.

    +

    If used, the parameters “R” or “RSQ” are followed by 2 values rlo +and rhi. If specified, the distance associated with each energy and +force value is computed from these 2 values (at high accuracy), rather +than using the (low-accuracy) value listed in each line of the table. +The distance values in the table file are ignored in this case. +For “R”, distances uniformly spaced between rlo and rhi are +computed; for “RSQ”, squared distances uniformly spaced between +rlo*rlo and rhi*rhi are computed.

    +

    If used, the parameter “BITMAP” is also followed by 2 values rlo and +rhi. These values, along with the “N” value determine the ordering +of the N lines that follow and what distance is associated with each. +This ordering is complex, so it is not documented here, since this +file is typically produced by the pair_write command +with its bitmap option. When the table is in BITMAP format, the “N” +parameter in the file must be equal to 2^M where M is the value +specified in the pair_style command. Also, a cutoff parameter cannot +be used as an optional 3rd argument in the pair_coeff command; the +entire table extent as specified in the file must be used.

    +

    If used, the parameter “FPRIME” is followed by 2 values fplo and +fphi which are the derivative of the force at the innermost and +outermost distances listed in the table. These values are needed by +the spline construction routines. If not specified by the “FPRIME” +parameter, they are estimated (less accurately) by the first 2 and +last 2 force values in the table. This parameter is not used by +BITMAP tables.

    +

    Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +r (in distance units), the 3rd value is the energy (in energy units), +and the 4th is the force (in force units). The r values must increase +from one line to the next (unless the BITMAP parameter is specified).

    +

    Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly.

    +

    The pair_modify shift, table, and tail options are +not relevant for this pair style.

    +

    This pair style writes the settings for the “pair_style table/rx” command +to binary restart files, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script.

    +

    This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

    +
    +
    +
    +

    Restrictions

    +
    +
    none
    +
    + +
    + + +
    +
    +
    + + +
    + +
    +

    + © Copyright 2013 Sandia Corporation. +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 51f163a57c..e098f6c431 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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el:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:[],circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:[],cko:[],cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:[184,349],clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,391,416,420,452,453,491,505,507,517],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:389,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,244,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,511,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[],conducit:6,conduct:[],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,338,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,391,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterclockwis:184,counterpart:[202,315,485],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[],cst:412,cstherm:6,cstyle:487,csvr:[],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[],cut0:488,cut1:499,cut2:499,cut:[],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,422,443,479,488,489,497,500,507,517],deby:[],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,444,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[],displace_atom:[],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,1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237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,391,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,391,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[],errata:[473,475],erratum:348,erron:3,error:[],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,337,343,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,184,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:[],expand:[],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,336,337,343,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[],fennel:[405,426],fep:[],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[],fluid_veloc:259,flush:[3,206,507],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222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452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:[],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,444,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,23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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],axel:512,balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:14,custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253,511],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,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,205,206,224,246,306,311],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,306,316,334,335,345,355,393,419,423,456,457,496,510,512,522],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:391,comb3:[],comb:[],comb_1:308,comb_2:308,combiant:408,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,299,305,321,337,346,354,357,359,375,376,378,383,391,405,407,408,412,416,417,418,424,436,437,465,475,478,480,481,483,486,498,503,508,516,522,524],come:[],comfort:[12,13],comit:517,comm:[0,3,11,12,64,78,204,250,252,253,376,386,391,411,446,453,476,477,497],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,241,254,316,317,345,385,386,392,414,415,417,418,428,441,448,449,450,457,464,465,475,476,477,478,479,480,483,492,493,495,516,517,522],commerci:7,commit:[9,517],commmand:[3,6,12,62,119,294,427,489,490,492,509,526],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,370,422,431,465,478,480,495,498,507],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,298,305,307,308,309,316,321,333,345,356,373,375,387,388,389,391,412,413,452,488,492,493,504,505,522,525,527],communc:375,comp:[7,204,252,253,286,292,320,376,386,416,446,453,458,472,476,477,479],compact:[66,209,404,474],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,307,356,358,375,376,384,386,441,464,490,509,510,516,521],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:380,compass:[7,9,21,22,37,44,45,56,185,186,197,359,360,369,403,474],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,298,310,337,340,347,350,353,375,391,425,444,446,476,492,493,522],compens:[6,225,226,314,387,416],compet:344,competit:376,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,344,376,391,444,495,496,500,516,522],compl:17,complain:[11,12,17],complement:441,complementari:[7,407,429],complet:[3,6,9,11,12,15,42,62,76,206,224,229,259,299,302,305,333,344,346,357,358,374,386,391,417,461,463,482,490,495,500,503,507,509,512,516,522],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,286,329,354,373,386,416,444,476,477,493,495,498,522],compli:[340,344],complic:[6,7,9,12,13,216,245,493],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,298,299,300,303,314,316,319,320,322,326,327,330,333,336,337,338,340,347,348,353,354,355,375,378,383,384,385,386,391,411,416,421,438,439,461,463,464,465,495,496,505,513,522,523],componenet:6,composit:[6,216,256,414],compound:[406,416,417,483],compres:[76,126,218],compress:[],compris:[41,354,418,458,482],compton:[130,177],comptu:3,compuat:376,comput:[],computation:[3,6,225,226,345,397],computational:516,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,318],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,526],concav:354,concentr:[76,241,317,414,418,449,477],concept:[6,158,168,218,504],conceptu:[3,6,76,166,228,230,386,407,424,441,500],concern:[6,78,96,204,246],concetr:76,concis:[11,344],conclud:12,concret:8,concurr:[16,376,522],conden:[345,478,480],condens:[6,160,345,393,409,414,429,483],condit:[],conducit:6,conduct:[],cone:498,confer:444,confid:[3,509],config:[12,202,492],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,299,307,344,373,384,386,393,397,415,441,444,475,478,480,483,490,495,497,498,509,517],confin:[495,509],conflict:[3,12,41,203,446,493,517],conform:[3,6,13,62,227,228,269,315,322,344,368,386,416,507],confus:[3,483],conjuct:[9,411],conjug:[7,8,253,383,416,456,457],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,284,302,303,307,308,309,311,316,321,333,341,348,353,375,376,386,398,400,404,407,411,416,423,429,446,451,459,481,495,498,502,516,527],connect:[3,6,9,96,163,181,227,250,301,316,320,330,380,386,408,421,456,457,473,480,492,493,495,499,516],conner:393,connor:393,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,250,251,407,429,433,490,496,498],consequ:[1,6,216,345,428,509],conserv:[3,9,29,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,316,320,321,336,337,341,348,349,353,386,410,411,412,421,435,464,504,509],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,298,316,340,341,344,345,348,376,404,416,424,457,458,464,473,490,491,493,496,497,498,500,503,505,513,516,522],consider:[6,8,253,254,336,337,338,391,504],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,303,306,311,313,315,316,317,336,337,338,339,349,375,376,378,380,385,386,391,393,397,399,405,407,416,420,424,427,438,439,441,444,446,448,449,458,461,463,464,476,477,484,493,495,496,497,498,499,500,507,516,522],consistent_fe_initi:215,consit:316,constant:[],constantli:237,constitu:[3,6,259,316,350,354,405,458],constitut:[461,463],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,301,302,314,316,320,331,341,348,384,385,416,500,507,516],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,270,298,315,317,354,387,391,410,444,446,473,475,476,477,498,499,514,522],constructor:[8,11],consult:457,consum:[1,311,452,522],consumpt:373,contact:[],contact_stiff:[460,462],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,301,302,304,305,306,309,313,316,317,318,323,333,340,344,345,354,355,358,374,376,385,386,389,390,392,393,394,397,406,407,410,414,415,416,418,424,425,441,444,448,449,450,454,455,456,457,465,475,476,477,478,479,480,481,483,490,491,492,493,495,496,497,498,500,502,504,507,509,510,512,513,516,517,522,525,527],content:[4,8,9,12,18,457,511,513],context:[3,6,8,12,17,128,129,206,225,226,231,301,313,349,383,486,495,502,511,521,522,523],contibut:75,contigu:492,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,300,302,305,306,316,318,322,332,333,335,342,343,345,351,354,358,374,390,391,397,411,413,431,434,456,457,458,461,463,479,490,493,495,497,498,503,509,510,512,513,522,525],continuum:[6,7,9,215,345,461,463],contour_integr:215,contract:[62,228,230,270,303,316],contradictori:3,contrain:320,contraint:284,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,230,356,461,463,486,526],contrib:345,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,301,302,310,313,316,318,320,347,375,384,386,394,411,413,414,416,424,438,439,444,446,456,457,464,507,513,516,517],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,303,308,316,317,324,325,336,337,338,345,349,373,375,388,416,420,444,456,457,460,462,475,480,490,492,504,510,511],control_typ:215,controlfil:457,convect:100,conveni:[6,12,29,202,207,222,318,378,465,481,517,522],convent:[3,8,29,189,196,197,203,206,315,330,357,414,416,522],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,243,275,286,292,306,308,311,315,320,382,383,384,386,406,407,429,464,490,502,509],convers:[3,8,152,205,206,216,219,303,375,407,408,409,416,429,433,437,451,493,509,521],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,268,302,305,356,359,361,365,368,378,386,392,414,444,478,480,487,493,495,496,497,502,512,516,521,522,525,527],convex:[43,354],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,314],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:464,coordbb:464,coordiat:384,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,301,302,303,313,314,316,319,320,322,327,330,331,332,333,335,343,344,345,352,353,355,356,378,384,385,386,391,392,393,396,415,464,490,495,496,497,498,500,503,505,509,516,522,523],coordn:[126,218],coords:464,copi:[0,3,4,8,9,11,12,15,17,41,131,205,345,386,404,456,493,517],copper:487,coproccesor:16,coprocessor:[1,7,9,16,17,391,508],coproprocessor:17,copy_arrai:8,copyright:[7,8,301],coral:206,core:[],core_shel:160,cores:516,coreshel:[4,6,9],coreshell:[],cornel:[6,184,507],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,354,355,378,482,495,517],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:406,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,245,247,253,270,271,293,301,303,306,344,350,354,375,386,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,487,488,495,510,513,516,517],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,309,316,320,330,332,351,354,386,387,391,409,439,444,492,493,495,505,517,521,523],correl:[],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,298,299,303,308,316,317,319,320,340,350,351,353,354,355,357,359,360,361,362,364,365,368,370,376,381,383,385,386,392,393,395,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,417,418,419,420,421,422,423,424,427,429,430,431,432,433,434,435,436,437,438,441,442,444,446,447,449,450,451,453,454,456,457,458,459,464,465,466,475,476,477,478,479,480,481,483,485,486,487,490,492,493,495,496,498,508,509,510,512,513,516,522],correspondingli:[438,439,504],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,242,270,308,345,375,376,389,407,429,433,444,446,475,492,504],costheta0:[475,478,480,483],costheta:454,costli:[11,97,247,387],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,305,306,307,311,314,316,319,333,334,340,344,345,346,350,354,356,358,366,372,374,382,384,387,391,393,394,419,423,424,427,456,457,491,492,493,495,497,499,502,503,510,511,516,522,523],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,307,309,346,375,376,384,391,398,400,401,402,403,406,407,408,409,410,416,421,422,424,429,433,437,440,446,451,456,457,459,464,474,480,481,483,486,500,507,513,516,521],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,302,320,336,337,354,376,384,385,386,388,391,419,423,446,513,522],counter:[3,351,490,501,503,509],counteract:245,counterbal:[237,249],counterbalanc:29,counterclockwis:184,counterpart:[202,316,490],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:323,cours:[3,8,138,140,172,202,210,211,246,315,330,344,350,352,353,355,356,376,438,466,492,495,508,516,522,525],courtesi:378,cov:464,coval:[6,9,29,416,441,464,516],covari:247,cover:[6,12,76,198,206,215,256,416,482],coverag:76,cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,320],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,254,346,373,376,391,404,474,490,508,509,512,513,514,522],cpuremain:513,cpus:12,cr2:177,cr3:177,crack:[4,387],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,387,516],craympi:391,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:301,criteria:[3,128,179,205,206,225,226,227,265,384,453,482,497,500,522],criterion:[12,42,133,178,181,216,224,227,245,284,308,323,351,356,384,386,406,416,421,464,500,509,510],criterioni:509,critic:[6,49,50,268,340,345,384],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,267,269,293,316,326,330,332,341,348,360,378,386,402,411,413,414,422,423,424,429,431,433,454,459,461,463,478,480,487,495,499,505,525],crossov:1,crossterm:495,crozier:[0,7,13],crucial:306,crystal:[3,4,6,13,78,118,297,298,343,378,387,495,499,513,516],crystallin:[6,114,298,378,479,516],crystallis:340,crystallogr:[130,177],crystallograph:[378,513],crystallographi:[130,177,378],cs1:177,cs_chunk:6,cs_im:[41,495],cs_re:[41,495],csanyi:[152,455,465],cscl:441,csequ:6,csh:[11,12,404],cshrc:[11,12],csic:[415,475,478,480,483],csinfo:6,csisi:[415,475,478,480,483],csld:[],cst:414,cstherm:6,cstyle:492,csvr:[],ctcm:[392,414],ctemp_core:234,cterm:322,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:441,cube:[6,176,181,234,354,378,516],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:397,cummul:[3,6,222,225,226,227,229,242,247,253,255,333,336,337,338,339,341,348,423,513],cumul:[6,216,218,221,235,245,253,268,270,275,284,316,318,386],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,267,270,271,276,277,278,284,286,290,291,292,293,295,301,302,307,308,310,313,314,315,316,317,320,321,322,323,324,325,326,327,329,331,332,333,336,337,338,344,345,348,349,350,351,352,353,355,356,358,373,374,375,376,379,380,381,383,384,385,386,391,397,404,406,410,414,416,417,421,424,425,428,438,439,441,442,443,446,454,456,457,460,461,462,463,466,478,480,481,484,490,491,492,493,495,496,497,498,499,501,502,503,505,507,509,510,512,513,517,522,523,524,525,526,527],curv:[6,178,245,286,292,298],curvatur:[420,458,487],custom:[],cut0:493,cut1:504,cut2:504,cut:[],cuthi:[297,309],cutinn:[399,438,439],cutlo:[297,309],cutmax:454,cutoff1:[403,410,429,433,437,440,451,459],cutoff2:[398,400,401,403,409,410,429,433,437,440,451,459,481],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,241,297,306,307,309,311,313,316,321,333,346,350,354,356,373,375,376,384,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,458,459,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,493,497,500,504,516,522],cutoffa:415,cutoffc:415,cuu3:414,cval:177,cvd:340,cvel:322,cvff:[],cwiggl:[3,267,350,353,355,522],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,251,292,302,351,354,380,498],cylinder_d:380,cylindr:[6,251,330,351],cypress:391,cyrot:397,cyrstal:298,d3q15:256,d3q19:256,d_double_double:15,d_e:345,d_flag2:305,d_flag:305,d_name:[125,202,305,335,505],d_single_double:15,d_single_single:15,d_sx:305,d_sy:305,d_sz:305,daan:343,dai:12,daili:12,daivi:293,damag:[],dammak:311,damp:[3,6,209,214,253,254,255,260,270,271,275,292,303,306,307,311,316,336,337,349,351,352,383,384,386,398,400,402,407,410,416,421,429,437,451,459,474,481,509,516],damp_com:254,damp_drud:254,dampen:[316,516],dampflag:[351,421],dan:17,danger:[3,12,245,356,411,513],dangl:181,daniel:9,darden:[376,410],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:307,dash:[421,512],dat:[6,100,198,215,491],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,318],dataset:318,datatyp:3,date:[0,4,6,12,13,201,456,457,522],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:440,davi:350,david:[9,19,375,376,478,480],daw:[414,454],dbg:14,dcd:[3,6,7,202,204,205,206,207,299,496,500],dcs:9,ddim:201,deactiv:437,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,299,304,373,375,425,446,484,493,494,502,505,512,522],deby:[],decai:[101,407,487],decid:[3,6,12,16,76,267,305,316,346,510,517],decipher:378,deck:305,declar:204,declin:333,decod:205,decompos:[96,465],decomposit:[3,5,7,18,65,215,299,321],decoupl:[6,516],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,344,375],decrement:322,deepli:372,deeppink:206,deepskyblu:206,def:[12,13,493],defaul:64,defect:[6,75,176,444],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,301,302,303,305,307,309,314,316,317,318,319,320,323,327,331,333,335,336,337,338,339,341,342,343,345,347,348,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,368,369,370,371,373,375,376,378,381,383,384,385,386,387,388,389,390,391,393,394,395,396,398,399,400,401,402,403,404,405,407,408,410,411,412,413,415,416,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,444,445,446,447,448,449,450,451,453,454,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,492,493,495,496,498,499,500,501,504,505,506,507,509,510,512,513,516,518,519,520,521,522,523,524],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,251,275,318,335,347,350,353,355,357,369,373,385,394,397,405,412,416,427,454,461,463,465,482,493,495,497,504,506,521,522],defint:513,deform:[],deg2theta:177,deg:516,degener:[3,301],degrad:[8,18,298,376,504],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,315,316,320,336,337,338,343,359,361,365,368,370,384,410,414,423,505,513,516,523],degrees:198,degress:[158,218],del:509,delai:[3,6,12,387,413,513],deleg:424,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,242,245,270,318,336,337,356,358,374,385,387,390,446,473,495,496,497,498,506,507,512,517,518,520,522,523],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[317,493,522],dellago:[6,237],deloc:[271,416,464],delr:441,delt_lo:509,delta:[],delta_1:397,delta_3:397,delta_7:397,delta_conf:3,delta_ij:[441,454],delta_pi:397,delta_r:454,delta_sigma:397,deltah_f:241,delx:201,delz:201,demand:311,demo:11,demon:296,demonstr:[306,441],den:302,dendrim:423,dendtrit:380,denniston:[9,256,258,259,260,298],denomin:[7,183],denot:[130,234,237,254,298,309,311,407,422,424,457,461,463],dens:[76,227,416],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,298,302,303,305,307,345,350,378,381,385,392,393,397,414,441,442,443,448,449,454,458,464,468,470,471,472,495,504,505,513,521],density_continuity:463,density_summation:463,dent:380,depart:[0,7],departur:[268,306],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,308,311,313,316,317,319,320,321,327,333,336,337,338,340,342,344,345,347,350,353,354,355,356,358,359,360,361,362,364,365,368,370,376,378,384,385,387,388,389,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,441,442,444,445,447,448,449,450,451,453,454,456,457,458,459,464,465,466,474,475,476,478,479,480,481,483,485,486,487,490,492,495,497,498,501,505,507,509,512,513,515,522,523],dependend:6,depflags:12,dephas:[490,509],depos:231,deposit:[],deprec:[3,307,456],deprect:218,depth:[52,156,205,345,418,420,458],dequidt:9,der:[96,119,405,406,437,456,457,486],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,303,307,311,342,343,345,350,351,354,383,385,393,397,405,410,416,417,422,431,435,436,441,444,456,457,474,476,477,486,516],derjagin:486,derlet:297,descend:206,descent:[7,383],descib:[41,205,307],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,299,304,305,306,307,308,309,316,317,322,330,333,334,335,336,337,338,339,340,341,342,343,348,350,351,353,358,375,376,378,382,383,384,385,386,390,393,394,396,398,399,400,402,403,404,405,406,407,410,414,416,417,418,420,421,422,424,427,429,430,431,432,433,434,435,436,437,438,439,440,441,444,445,448,449,453,454,455,456,457,458,459,464,465,466,473,474,475,476,477,478,479,480,481,483,485,486,487,488,490,492,493,495,496,497,498,499,505,508,509,512,517,522,523,525],descript:[],descriptor:[152,202,425],deserno:376,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,270,271,297,298,318,340,345,394,395,396,399,402,407,409,416,437,438,439,442,443,454,457,476],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,301,302,303,304,307,311,316,320,333,336,337,338,339,344,351,366,372,375,376,378,382,384,385,386,411,414,423,438,439,475,478,480,491,492,493,495,499,504,509,510,512,513,522,523,525],desk:7,desktop:[4,6,7,10,12,205],despit:516,destabil:397,destre:368,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,298,301,302,303,305,306,308,309,310,316,320,321,333,336,337,338,339,340,341,343,344,345,346,347,348,349,356,358,360,369,375,376,379,384,385,387,388,391,392,393,394,396,397,399,401,402,403,404,405,406,407,410,411,416,417,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,445,446,448,449,453,456,457,458,464,465,466,474,482,485,486,488,493,495,496,497,498,500,501,504,505,507,510,513,514,517,522,523,527],detect:[2,3,12,43,64,66,95,101,244,302,344,386,406,423,428,490,492,495,506,509,522],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,299,302,303,306,313,314,315,316,317,318,319,323,325,327,333,336,337,338,340,346,347,350,351,352,353,354,355,356,369,375,376,378,385,387,388,391,393,394,401,406,410,413,414,418,419,421,424,425,433,441,444,446,449,457,458,464,473,476,477,481,486,492,495,496,498,500,502,505,509,511,512,514,521,522,523],determinist:321,detil:120,devan:[9,459],devanathan:480,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,275,301,306,307,310,393,397,416,443,444,464,483,497],devemi:9,deviat:[268,275,297,419],deviator:9,devic:[1,3,12,15,17,250,391],device_typ:391,devin:[308,406],devis:443,dfactor:205,dff:516,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,376],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,310,444],dhi:[62,201,230,302],dhug:[268,306],dhugoniot:[268,306],dia:441,diagnost:[],diagon:[3,6,92,152,153,154,228,270,303,316,348,461,463],diagonalstyl:465,diagram:[42,130,177,197,224,299],diallo:423,diam:[205,206,302,385],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,302,305,316,333,335,349,351,385,405,420,421,431,458,482,486,495,496,505],diamond:[378,416,441],diamter:[41,302],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,384,411,413,414,421,446,478,480,503],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,347,375],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,299,301,303,306,307,308,311,314,316,320,322,330,331,333,336,337,338,341,342,343,345,348,349,350,351,354,358,359,369,372,374,375,376,378,379,382,383,385,386,388,389,390,391,392,393,397,401,402,404,405,406,411,412,414,416,418,420,421,422,424,427,429,430,432,433,440,441,442,443,445,446,447,448,449,450,454,456,457,458,459,460,461,463,464,465,466,474,475,476,477,478,480,482,483,486,489,490,492,493,495,497,498,499,500,503,504,505,507,509,510,512,513,514,516,521,522,523,525],differenti:[1,3,6,29,198,317,375,407,454,479],difficult:[228,299,391,423,504],difficulti:[101,118,320,456],diffract:[7,9,130,177,318],diffus:[],diffuse:[4,6],digit:[2,3,206,358,444,522],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:416,dij:320,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,251,351,378,441,498,521,522,523],dimdim:522,dimems:298,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,298,345,378,382,386,454,495,505],dimensionless:[116,133,134,136,139,141,143,148,152,345,376,465,486],dimensions:318,diment:3,dimentionless:147,dimer:[6,316,441],dimgrai:206,dimstr:[42,224],dinola:[303,336],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,335,516],dir1:506,dir2:506,dir:[1,3,4,8,10,11,12,268,297,306,332,454,456,457,493,506,522],dirac:152,direc:454,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,247,251,256,298,317,318,337,349,351,352,353,354,378,383,391,392,393,398,400,401,407,410,414,416,429,433,446,451,459,473,493,505,506,507,513,522],directoi:14,directori:[],disabl:[3,12,16,345,428,493,508,522],disadvantag:[6,224],disallow:[202,230,270],disappear:497,discard:[2,3,42,76,220,224,346,354,492,497,498],discontinu:[198,384,435],discourag:441,discov:[13,346],discret:[6,8,41,43,205,206,253,256,292],discuss:[],disk:[6,93,94,101,171,200,231,245,302,493],disloc:[75,444],disord:[40,75,444],disp:[],dispar:458,disperion:[410,433],dispers:[3,6,7,9,176,298,375,376,401,410,433,438,446,457,476,483],displac:[],displace_atom:[],displace_box:62,displacemet:498,displai:[11,13,22,37,45,56,186,197,202,205,360,369,404,474],dispters:3,disregard:444,dissip:[6,9,41,89,90,239,246,253,298,321,342,343,399,411,412,421,438,439,474],dissolut:225,dist:[6,74,100,120,129,202,299,315,413,473,490,523],distanc:[],distinct:[6,234,313,375,458],distinguish:[6,95,152,259,416,494,522],distort:[176,392],distrbut:392,distribut:[],distro:[123,404,453,454],ditto:[8,12,14,15,16,17,18,43,127,226,487,493],div:8,divd:129,diverg:[3,12,40,316,343,393,497,516,525],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,297,341,348,353,375,384,386,417,457,464,483,504,512,522],divis:[6,256,397,427,437,492,513,522],dl_poly:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,344,495,496,500],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:505,dlmp_intel_offload:[9,16],dlo:[62,201,230,302],dlopen:6,dlvo:[7,405,486],dm_lb:256,dmax:[333,382],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,231,245,253,254,265,270,271,276,277,278,282,290,291,293,294,295,302,305,316,330,333,336,337,338,347,351,354,356,358,360,369,374,384,385,386,391,392,393,396,404,406,407,414,415,417,423,424,426,427,441,442,443,446,450,453,454,455,465,474,475,478,480,482,483,493,495,496,497,498,500,503,504,505,512,513,517,522,523,525,526],docuement:458,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,223,224,226,227,228,230,234,236,237,240,241,242,245,246,249,251,253,254,256,259,266,270,271,272,273,274,276,277,278,290,291,292,293,294,295,303,304,305,309,311,314,316,333,336,338,340,341,345,348,349,350,353,354,355,356,361,362,363,365,366,368,374,375,376,377,378,385,386,387,392,393,394,395,396,397,399,401,402,403,405,406,407,408,410,411,413,414,415,416,418,419,420,421,422,424,425,426,427,428,431,432,434,435,436,438,439,441,442,443,444,446,448,449,454,455,456,457,458,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483,485,486,487,488,490,491,492,493,495,496,497,498,499,502,503,505,506,507,508,509,512,513,516,517,522,527],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,330,385,387,391,393,406,415,426,456,457,475,478,479,480,483,495,497],dof:[3,8,124,156,157,158,171,218,316,523],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[385,495],doi:[6,229],domain:[3,6,7,12,13,18,40,42,43,61,64,65,76,130,167,177,180,201,204,205,206,209,216,224,228,230,231,249,252,256,270,271,299,311,316,321,345,350,351,375,376,386,391,413,446,490,492,495,499,512],domin:[1,416,509],don:[0,8,9,12,13,128,181,212,236,254,354,441,464,493,495,517],donadio:337,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,62,65,76,172,175,178,181,198,202,205,206,215,216,218,220,221,222,224,225,226,227,228,230,231,240,241,243,245,250,251,253,254,261,270,276,277,278,290,291,293,295,296,298,299,300,302,305,313,316,318,320,333,336,337,338,340,342,343,356,358,374,375,376,384,386,387,390,391,393,401,414,424,425,426,433,439,440,441,446,448,449,456,473,476,477,482,490,491,492,493,496,499,500,503,513,514,516,517,522,523],donor:423,dot:[153,174,212,236,248,269],doti:[397,454],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,96,184,230,243,304,354,358,374,376,390,391,397,417,422,444,456,457,491,495,499,503,508,522,523],dover:215,down:[3,6,7,8,11,40,76,228,245,253,333,349,416,446,464,494,514],downhil:[382,383],download:[5,7,8,9,11,12,13,17,250,425,455],downsid:6,downward:313,dozen:[8,9,12,119,209,456,457],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[],dpde:263,dpdtheta:[41,89,90,412],dpdtheta_i:[239,240,241],dproduct:394,dr_ewald:[130,318],drag:[],dragforc:256,drai:[268,306],drain:[249,349,384],dramat:[9,62,201,225,226,227,228,230,270,333,336,337,376,446,464,492],drautz:397,draw:205,drawback:305,drawn:[43,202,205,206,246,490],drayleigh:[268,306],dreid:[],dreiding:[],drfourth:116,drho:[125,392,414,448,449],drift:[6,114,116,237,246,247,249,253,254,266,314,333,504,512,516],drive:[11,12,213,228,230,248,270,297,303,316,352,386],driven:[6,190],driver:[6,12,14,15,209,243,250],drop:[3,206,411],droplet:424,drsquar:116,drude:[],drudes:[254,516],dry:242,dsecriptor:425,dsf:[],dsmc:[],dstyle:302,dt_collis:256,dt_lb:256,dt_md:256,dt_srd:333,dtilt:[62,230],dtneb:509,dtqm:306,dtype:[127,226],dual:[16,17,333,391],dudarev:177,due:[1,3,6,9,12,16,17,19,41,55,58,60,61,64,70,75,76,79,80,87,88,95,97,98,99,104,113,114,115,116,117,122,128,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,223,225,226,227,228,229,230,231,236,238,242,243,246,247,250,251,253,254,255,256,259,260,261,266,267,268,269,270,275,284,297,300,302,314,315,316,319,330,332,333,334,336,337,338,339,340,342,343,345,349,350,352,353,354,356,376,382,384,386,387,388,408,411,412,414,419,420,424,438,439,446,454,456,45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26,230,231,243,245,246,253,270,302,313,318,345,346,354,358,374,375,384,385,386,387,389,414,415,424,437,439,444,452,456,457,475,478,480,483,490,493,495,496,497,502,504,505,509,510,511,512,513,514,516,521,522,525,527],ethernet:18,etol:[384,386,490,509],etot0:306,etot:[6,105,107,108,122,153,164,206,234,254,268,306,512,513],eu2:177,eu3:177,euler:[384,386],eulerian:215,euqat:467,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,298,304,307,319,323,327,336,337,338,347,350,353,355,356,358,382,384,444,446,448,449,454,460,462,464,476,477,490,491,493,497,498,500,502,503,504,505,509,511,513,522,523],evaluat:[375,376,522],evalut:[358,493],evan:[166,293],evanseck:[6,20,184,402,507],evapor:[],evaul:[8,384],evdwl:[119,154,456,457,513],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,298,302,311,313,316,318,329,333,341,345,348,350,354,356,367,375,382,384,386,391,396,416,417,421,424,427,446,458,483,484,488,495,496,498,500,501,502,504,505,507,510,512,513,514,516,527],evenli:[3,42,58,153,198,224,256,427,484],event:[],eventu:[3,6,12,15,180,509],eventual:307,ever:[9,55,57,252,333],everaer:[405,420,458,474],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,302,303,304,305,306,307,308,309,311,313,314,316,317,318,320,322,333,335,336,337,338,339,340,341,344,345,346,347,348,356,358,374,376,386,387,388,391,411,413,424,437,456,457,464,470,489,490,491,495,497,499,500,502,503,504,509,510,511,513,517,522,527],everyth:[8,119,517],everywher:[128,431],eviri:416,evolut:[237,247,256,299,490],evolv:[256,299,346],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,346,375,376,384,398,400,401,407,410,416,429,433,451,459,474,476,481],ewald_disp:410,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,246,247,253,254,255,302,311,312,333,345,360,375,404,497,502,509,522,525,527],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,298,305,306,333,338,339,352,391,404,411,414,421,424,438,446,448,449,476,477,497,498,505,509,522],exager:516,examin:[6,8,17,227,298],examp:[493,522],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,242,270,298,313,318,324,325,333,384,391,495,522],exceed:[3,42,62,224,230,270,333,503],excel:416,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,299,308,309,316,319,320,330,333,339,345,353,356,357,358,359,360,361,362,364,365,368,369,370,375,376,378,381,385,386,387,389,390,391,392,393,395,398,399,400,401,402,403,404,405,406,407,409,410,411,414,415,416,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,442,447,450,451,453,456,457,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,492,493,495,497,498,500,503,504,505,506,507,509,513,516,521,522,523,526],exception:493,excess:[220,416],exchang:[2,3,6,8,64,65,209,215,216,237,245,249,253,308,316,341,345,348,375,391,416,510],exchange:375,excit:416,excite:416,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,257,266,301,314,316,340,351,356,384,385,387,399,421,424,427,438,439,446,473,507],exclude:387,exclus:[1,3,12,16,96,184,406,444,446,504,514],excurs:[270,490],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,310,358,374,377,390,491,493,503,506,509,522],exempl:464,exemplari:246,exemplifi:416,exert:[6,251,254,286,311,352,353,354,376],exhaust:[215,390,522],exhibit:[101,237,249,270,383,416,504],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,245,301,302,304,305,356,357,359,361,362,363,365,369,379,385,412,424,456,473,484,491,493,495,496,497,506,507,508,517,522,523,525],exit:[2,3,11,12,42,60,202,224,240,241,374,390,493,494,503,512,522],exlanatori:3,exp6:2,exp:[],expand:[],expans:[12,152,202,506,522],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,245,247,267,297,303,305,306,311,316,356,376,387,404,441,444,446,490,493,495,497,500,504,509,522],expens:[6,76,206,297,301,316,345,356,375,376,387,391,493],experi:[6,13,15,223,231,250,259,269,303,315,316,382,386,411,446,504,509],experienc:[6,12,258,259],experiment:[17,245,375,391,509],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,305,316,330,356,358,374,375,378,385,386,390,396,414,427,464,466,482,493,496,497,500,502,505,516,517,522,527],explan:[3,6,62,125,152,202,203,218,269,297,424,489,492,493,495,504],explanatori:[3,8,129,202,203,217,218,221,316,385,492,522],explantori:[3,312],explic:445,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,317,324,325,360,381,393,394,397,402,404,414,416,428,438,481,489,492,496,499,517],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,305,306,308,316,319,320,338,339,345,353,359,361,362,364,365,368,370,385,391,392,393,395,398,399,400,401,402,403,404,405,406,407,408,410,411,413,414,415,417,418,419,420,421,422,423,424,428,429,430,431,432,433,434,435,436,437,438,442,444,446,447,448,449,450,451,453,458,459,466,467,468,469,470,471,472,474,475,476,477,478,479,480,481,483,485,486,487,495,497,498,504,505,507,508,514,516,517],explictli:[16,508],exploit:[15,17,299],explor:[130,177],expon:[3,307,309,317,414,418,420,423,437,445,459],exponenti:[96,418,454,475,483,487,509,522],expos:11,exposit:[215,411,413],express:[6,152,164,178,210,211,228,267,297,307,317,345,351,358,397,414,416,431,441,464,465,474,522],expression:358,expressiont:397,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,314,315,316,319,322,327,330,332,336,337,338,339,340,342,343,345,347,350,354,355,420,441,444,457,458,465,512,513,521],extensiv:[66,209,513],extent:[1,3,42,43,46,60,76,176,180,202,214,224,251,352,355,375,378,393,460,462,476,477,492,495,498],exterior:[3,6,176,354],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,304,305,306,316,333,384,385,388,389,410,421,424,427,441,446,492,493,495,498,507,516,522],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,309,386,407,417,441,465,493,500,512],extract_atom:11,extract_comput:[11,493],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,270,343,416,479,516],extrema:437,extreme:416,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,347],f_a:[478,479,480],f_ave:129,f_c:479,f_f:480,f_fix_id:306,f_foo:522,f_harm:343,f_i:[29,454],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,265,335,347,513,522],f_ij:454,f_indent:222,f_int:342,f_j:29,f_jj:100,f_k:454,f_langevin:345,f_max:[306,311],f_msst:268,f_r:[254,478,479,480],f_sigma:397,f_solid:343,f_ss:6,face:[3,6,60,62,76,166,176,180,214,350,352,353,354,355,378,420,441,458,495,498],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,302,333,343,421,456,464,507],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,299,303,307,315,317,320,323,325,333,337,341,348,349,350,354,365,376,378,385,391,393,394,397,398,400,402,407,408,409,411,412,416,421,424,428,429,441,444,446,448,449,450,451,457,459,466,475,481,492,495,498,499,504,507,509,510,513,516,521,522],factori:[3,493],factoriz:375,fail:[3,9,11,12,62,182,228,231,375,384,386,409,457,493],failur:[133,461,494,522],fairli:[11,446,504,509,517],faken:78,falcon:250,fall:[3,6,206,221,302,493,522],fals:[95,356,464,522],fame:8,famili:[483,492],familiar:[0,11,517],fan:454,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,270,297,315,316,333,350,361,365,382,386,387,482,493,495,500,513],farago:253,farrel:[478,480],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,305,306,308,316,322,326,332,335,343,345,349,350,351,353,355,386,424,438,498,507,522,526],fasolino:426,fast:[6,7,9,12,13,17,40,202,203,281,306,346,375,376,399,438,439,444,474,476,477,497,502,504,513,523,527],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,303,307,308,316,319,320,333,340,342,345,349,353,359,361,362,364,365,368,370,375,376,388,389,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,498,504,508,516],fastest:[1,6,14,17,166,345,346,391,492],fatal:[3,512],fault:[75,457],faulti:12,fava:420,favor:227,favorit:7,fbmc:340,fcc:[],fcm:[287,522],fcold:237,fdirect:234,fdotr:425,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:414,feedback:[7,250],feel:[7,250,251,259,297,354,356,386,446],felling:443,felt:354,femtosecond:521,fene:[],fennel:[407,429],fep:[],ferguson:[6,184,507],fermi:[1,9,10,12,15,164,391,480],fermion:416,fernando:440,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,254,270,302,305,307,320,347,375,384,385,386,393,464,492,495,500,504,506,514,525],fewer:[1,3,11,15,16,64,259,504],fewest:3,fextern:243,feynman:299,fff:493,ffield:[406,417,456,457,464],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,298,375,376,504],fft_inc:[12,376],fft_lib:12,fft_path:12,fftbench:[375,514],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:473,fictiti:[6,212,213,236,243,247,299,315,407,429,433,473],field1:[496,500],field2:496,field:[],fifth:[6,330,418,450],figur:[1,3,8,12,306,492,493,517],fij:410,file0:297,file1:[11,13,241,297,344,358,385,500,502,506],file2:[11,13,241,344,358,385,500,502,506],file:[],file_from:204,filen:385,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,301,304,307,308,309,312,313,316,317,318,344,345,372,373,374,385,386,392,393,397,407,414,415,417,418,426,441,442,443,448,449,450,454,455,456,457,464,465,475,476,477,478,479,480,483,491,492,493,496,497,502,506,513,522,525,526,527],filennam:502,filep:[3,202,203,206,497,502,527],filepo:313,fill:[7,9,178,205,302,345,378,387,397,444,457,498,517],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,409],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,242,245,269,297,302,303,311,315,382,384,386,387,407,424,429,433,441,448,449,464,474,476,477,516,517,522],find_custom:8,fine:[16,17,182,212,236,343,387,391,517,522],finer:[152,178,522],finest:375,finger:[178,201,267,498],finish:[6,11,42,224,358,372,374,375,388,390,391,482,500,522,523],finit:[],finni:[7,414,474],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,299,304,305,306,308,313,316,320,322,330,331,333,334,335,342,343,344,345,347,351,356,358,359,366,378,384,385,386,387,390,391,392,393,396,397,398,400,402,404,406,407,414,416,417,418,421,422,424,425,426,427,428,429,433,438,439,441,443,444,446,448,449,450,454,456,457,464,465,473,475,476,477,478,479,480,483,487,490,491,492,493,495,496,497,500,502,504,507,508,509,512,513,516,517,522,523,524,525,527],fischer:[6,9,19,20,184,402,507],fit:[3,6,9,12,38,57,198,240,315,333,393,397,426,441,446,448,449,469,476,477,479,503,517,522],five:[78,164,306,385,397,442,495,509],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,303,306],fix_manifoldforc:517,fix_modifi:[],fix_nh:8,fix_nv:517,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:320,fix_reax_bond:456,fix_saed_vtk:318,fix_setforc:8,fix_shak:320,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:410,flag1:[233,389],flag2:[233,389],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,298,305,316,330,332,333,340,344,353,356,371,373,376,385,389,390,391,393,423,428,441,444,473,488,490,492,493,495,496,497,499,500,501,505,517,522],flag_buck:401,flag_coul:[401,410,433],flag_lj:[410,433],flagfld:[399,438,439],flaghi:[3,399,438,439],flaglog:[399,438,439],flagn:233,flagvf:[399,438,439],flat:[6,345,350,351,355],flavor:[2,7,12],fld:[350,438,439],flen:394,flex_press:394,flexibl:[3,6,8,179,205,218,229,247,271,341,348,416,479,513],flip:[3,6,230,270,352,353],floor:522,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,245,246,253,256,270,275,297,298,303,321,343,345,368,412],fluid:[],fluid_veloc:260,flush:[3,206,512],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,316,320,346,397,444,513,516],fmackai:9,fmag:232,fmass:299,fmax:[384,513],fmomentum:234,fmsec:[2,206,253,254,267,270,303,316,336,337,504,515,521,523],fname:374,fno:[9,16],fnorm:[384,513],fnpt:234,fnve:237,fnvt:234,foce:424,fock:394,focu:320,fogarti:[9,309,457],foil:[152,297,465],fold:[331,504],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,298,299,301,304,305,306,307,309,311,313,315,316,317,318,320,335,336,337,338,341,342,343,344,345,347,348,356,357,361,362,363,364,365,368,370,373,378,381,384,385,386,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447,448,449,450,451,453,454,455,456,457,458,459,461,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483,485,486,487,488,490,492,493,495,496,498,500,502,503,504,507,509,510,511,516,517,522,523,526],foo:[4,8,11,12,202,205,243,317,493,506,522],foo_species:317,foot:6,footprint:[12,391],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[315,423],forcegroup:256,forcezero:382,ford:410,forestgreen:206,forev:76,forget:[254,516],forgiv:270,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,298,309,311,315,316,317,345,350,354,359,360,363,368,381,383,385,386,393,394,397,404,412,414,416,419,423,424,428,440,441,443,444,448,449,450,451,454,456,457,458,464,465,466,474,476,478,479,480,486,489,492,493,495,500,505,512,516,522],formal:[6,83,86,100,246,247,253,270,299,333,341,464],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,298,301,305,307,309,312,316,317,318,329,344,345,356,357,360,381,385,386,392,393,397,404,414,417,418,428,441,443,448,449,455,456,457,459,465,476,477,483,484,492,493,495,496,497,500,511,512,513,522,524,525],formation:241,former:[6,12,16,40,42,206,224,345,349,397,399,501,507,522],formerli:[7,13],formul:[1,6,9,41,67,153,212,236,253,270,293,307,309,315,320,344,375,393,397,414,416,420,441,453],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,304,313,319,327,331,333,336,337,338,347,350,353,355,356,358,359,360,362,369,378,385,393,394,396,397,402,403,404,405,410,411,414,415,420,421,422,423,425,428,429,431,432,433,435,436,438,439,441,445,446,447,458,459,466,474,475,476,478,479,480,483,485,486,491,495,498,505,512,513,521,522,523],forth:[1,6,11,12,13,14,15,390,493,498,502],fortran:[3,6,9,11,12,13,243,414,424,441,456,457],fortun:8,forward:[3,8,96,374,386,391],foster:[397,453,454],foul:181,found:[3,6,9,12,78,172,202,227,229,237,245,250,256,262,298,340,346,358,374,387,404,407,410,490,496,497,512],four:[6,11,55,88,114,115,152,174,268,345,368,385,386,444,490],fourier:[],fourth:[6,116,315,330,340,402,418,450,464],fox:[6,130,184,472,507],fphi:[38,57,476,477],fpic:12,fplo:[38,57,476,477],fprime:[476,477],fqdn:252,fqq:410,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,225,226,227,228,268,302,306,313,314,333,338,339,378,386,391,397,399,418,421,438,439,500,505],fragment:[43,250,313],fraig:43,frame:[92,152,206,215,268,306,352,420],framer:[205,206],framework:[5,247,392,465],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,297,333,342,343,344,345,383,386,394,416,437,444,447,454,486,492],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,316,320,336,337,338,343,384,410,513,516,523],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[6,237,245,343],freq:214,frequenc:[3,6,16,40,114,206,220,284,298,299,306,311,373,411,416,457,464,490,504,509,522,526],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,225,226,237,242,341,348,446,481,502],fri:[268,306],friction:[4,5,6,9,10,43,209,247,253,306,311,316,345,349,351,421,505],friedrich:323,from:[],front:[268,306,352],frontend:[205,310],frozen:[6,124,182,244,246,254,387,419],fs2:[6,100],fscale:250,fstr:522,fstring:493,ftol:[384,386,490,509],fuchsia:206,fuction:407,fudg:320,fugac:245,fugacity_coeff:245,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,100,205,219,220,229,237,256,297,317,375,376,391,397,414,416,417,420,481,495,497,502,503,507,509,514,516,526],full_energi:[3,245],fuller:384,fulli:[3,6,83,247,252,297,384,386,407,454,455,495,517,524,525],fulton:414,fumi:398,func:[493,522],funcfl:414,functionaliri:229,fund:[0,7],fundament:[333,521],funnel_flow:329,funrol:444,further:[3,4,6,8,12,13,64,66,68,73,76,84,95,102,116,119,128,205,206,209,218,221,222,225,231,235,256,260,299,307,318,321,323,333,345,347,356,376,382,384,385,386,387,392,396,406,444,464,490,509,510,522],furthermor:[27,187,237,317,412,416],furthest:64,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:454,g_p:345,ga3:177,gaa:397,gahler:383,gai:[3,420,474],gain:340,gainsboro:206,galindo:445,game:250,gamma0:29,gamma:[3,6,29,253,256,260,298,306,307,309,311,349,411,412,415,420,441,445,468,471,472,475,478,480,483,513],gamma_:[3,345,351],gamma_ijk:478,gamma_n:[351,421],gamma_p:[3,345],gamma_t:[351,421],gammaa: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1,335],input:[],input_doubl:3,inquir:323,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,245,251,302,375,465,473,493,499,516],insertion:[3,231,245,302],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,242,245,251,256,259,302,316,333,350,352,353,354,355,356,373,378,493,494,495,497,498,505,522],inside:[256,431,493,509],insight:[6,13],instabl:[256,410,463],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,376,386,401,402,425,429,433,437,444,490,496,497,502,510,517,527],install:[],instanc:[6,9,11,210,229,247,352,419,424,446,454,493,516],instantan:[6,66,227,228,246,247,270,275,298,303,306,311,313,316,340,501,513],instanti:[6,11,12,215,424,492],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,245,253,256,259,260,298,304,305,314,316,335,353,373,375,376,379,387,391,400,401,414,428,430,437,441,444,447,474,481,490,498,502,509,511,516,522],institut:[9,250,301],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,308,316,319,320,353,359,361,362,364,365,368,370,376,391,392,393,395,398,399,400,401,402,403,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,475,476,478,479,480,481,483,485,486,487,498,504,516],instruction:11,insuffici:[3,6,12],insult:270,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,231,236,238,242,243,245,248,253,266,304,305,314,316,333,345,350,354,355,356,358,374,385,387,391,405,420,424,452,458,476,488,492,493,495,496,500,503,504,512,513,522,523],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,243,245,246,247,250,253,254,255,256,298,301,302,305,306,311,316,333,335,337,340,344,345,364,375,378,399,411,412,413,427,441,456,457,461,463,465,490,492,493,494,495,503,504,505,509,512,522,523],integer:[3,495],integr:[],integral:[299,448,449],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,246,455,495],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,242,249,259,268,270,275,313,316,318,333,341,345,347,348,512,513,521],intensiv:[66,209,513],intepol:522,inter:[14,18,43,64,65,158,181,182,202,227,253,255,269,308,316,375,386,397,505,516,522,525,527],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,244,245,250,251,253,255,259,284,297,299,301,302,307,309,315,316,317,324,325,333,334,340,345,349,350,351,354,355,360,361,362,363,365,367,369,375,376,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,451,452,453,454,457,458,459,461,463,464,465,466,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,490,493,495,497,499,500,504,505,507,512,513,516,525],interatom:[3,4,7,9,10,178,202,269,342,343,392,397,414,416,425,441,444,464,479,522],intercept:130,interchang:6,interconnect:18,interconvert:416,intereract:40,interesect:354,interest:[1,5,7,8,9,11,13,76,177,299,340,343,376,415,439,456,457,493,522],interf:[391,517],interfac:[],interfer:[12,270,393],interg:[6,516],intergr:504,interi:439,interior:[3,6,42,354,498],interlac:441,interleav:[6,178,503],intermedi:[6,12,62,205,269,297,368,386,493,494,503,507],intermix:490,intermolecular:[154,393],intern:[],internal:[3,205,211,302,522],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:252,interpenetr:441,interpentr:[468,469,471],interpol:[6,15,38,57,111,198,205,206,215,240,241,256,297,375,376,386,397,446,448,449,457,470,476,477,478],interpret:[2,6,11,205,221,421,466,490,493,509,522],interrupt:306,intersect:[3,6,130,206,354,356,498],intersert:354,interspers:384,interstiti:[176,444],intertia:[3,104],interv:[3,6,100,204,219,253,270,306,311,312,325,464,470,490,509,522],intestieti:130,intial:[6,391,393],intiial:[42,500],intiti:[3,332],intra:316,intra_energi:245,intramolecular:[29,154,245],introduc:[6,9,101,118,205,237,270,306,311,316,368,375,392,407,416,429,433,437,475,509,522],introduct:[],intuit:378,inv:[130,177,318],invalid:[3,12,76,98,181,284,386,438,439,497],invari:[118,145,150,152],invent:320,invers:[],inverse:516,invert:[1,6,182,298],invis:354,invoc:[176,227,391,461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244,245,246,247,248,249,250,251,253,254,255,265,267,270,272,273,274,275,276,277,278,279,280,284,287,288,290,291,293,294,295,298,299,301,302,303,305,307,308,311,314,315,316,319,320,322,330,332,333,334,336,337,338,339,341,342,343,344,345,347,348,349,350,351,353,354,355,356,358,359,361,362,364,365,366,368,370,374,375,376,378,381,383,384,385,386,387,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,483,485,486,487,489,490,491,492,493,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,512,513,514,516,517,521,522,523,524,525,527],young:[421,460,462],your:[],yourself:[6,8,12,13,228,385,517],yplane:351,ypo:178,ysu:[3,202,203,335,496],yuan:9,yukawa:[],yukawa_1_1:484,yxz:492,yzx:492,z_i:[416,480,487],z_j:[480,487],z_meam:441,zachari:13,zannoni:420,zbl:[],zblcut:480,zblcutinn:465,zblcutout:465,zblexpscal:480,zblz:465,zcm:316,zcylind:351,zepeda:216,zero:[],zeta:[3,256,307,417],zfactor:205,zflag:[165,166,257,259,266,316,340],zhang:[316,341,421],zhi:[3,6,180,202,214,344,350,353,355,495,498,513],zhi_bound:[6,202],zhou:[13,397,417,454,478,480],zhu:472,ziegenhain:13,ziegler:[301,441,474,480,487],zimmerman2004:215,zimmerman2010:215,zimmerman:[9,75,215,397],zlat:[230,251,513],zlib:[9,202],zlim:464,zlo:[3,6,180,202,214,344,350,352,353,355,495,498,513],zlo_bound:[6,202],zmax:[214,256,522],zmin:[256,522],zn2:177,zone:[130,318],zoom:[3,202,205,206],zorig:76,zplane:351,zr4:177,zrest:332,zsu:[3,202,203,335,496],zwall:350,zwall_veloc:256,zxy:492,zybin:457,zyx:492},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,298,299,302,303,304,305,306,308,311,313,314,316,318,333,335,340,341,342,343,346,348,350,352,356,369,373,375,376,378,379,382,383,385,387,388,389,391,394,397,399,416,438,439,444,446,456,457,473,474,490,491,492,495,496,498,500,502,503,504,507,509,511,512,513,514,515,521,523,525,526],"function":522,"long":[220,398,400,401,402,403,407,409,410,429,433,437,451,459,481],"new":8,"static":12,acceler:1,account:517,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:517,addition:[12,13,517],addtorqu:213,adiabat:6,adjust_dt:323,adp:392,after:517,airebo:393,alloi:414,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,305,522],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,394],axel:517,balanc:[42,224],barostat:6,basal:71,beck:395,berendsen:[303,336],between:6,binary2txt:13,bodi:[6,8,43,72,157,273,277,282,291,396],body:9,bond:[8,13,73,74,225,226,227,312],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:397,born:[398,409],boundari:[7,60],box:[6,61,228],branch:517,brownian:399,buck:[400,401,409,440],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:517,change_box:62,charmm:[6,20,184,402,437],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,359,403],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,350,405,486],colvar:[13,229],colvars:9,com:[79,80,159],comb3:406,comb:[308,406],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,522],compute_modifi:113,condit:7,conduct:[6,341],constant:[6,522],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:361,coul:[398,400,401,402,403,407,408,409,422,429,433,437,451,459],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:337,csvr:337,cubic:431,cuda:14,custom:[8,202,203],cut:[50,394,400,403,407,410,416,419,429,430,437,445,451,481],cvff:362,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[407,429],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],diagnost:7,diel:408,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,410],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:363,distribut:[7,12],document:0,dpd:[9,89,90,411,412],drag:232,dreid:423,dreiding:6,drude:[6,9,163,233,234,254,516],dsf:[407,429],dsmc:413,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:307,eam:[13,414],echo:208,edip:415,eff:[9,13,107,108,162,164,169,255,271,283,294,339,416],efield:236,ehex:237,eim:417,elastic:6,emac:13,energi:[135,412],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:242,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],exp6:418,exp:[27,187],expand:[47,432],extend:[8,11],extern:243,fcc:297,fdt:412,featur:[7,8,517,522],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:307,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246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\ No newline at end of file From 946de18d47bec7013ab1ff1d57c992dbabf935b4 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:32:00 +0000 Subject: [PATCH 078/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15122 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/fix_eos_table_rx.txt | 166 +++++++++++++++ doc/html/_sources/fix_rx.txt | 170 +++++++++++++++ doc/html/_sources/pair_exp6_rx.txt | 136 ++++++++++++ doc/html/_sources/pair_multi_lucy_rx.txt | 242 ++++++++++++++++++++++ doc/html/_sources/pair_table_rx.txt | 252 +++++++++++++++++++++++ 5 files changed, 966 insertions(+) create mode 100644 doc/html/_sources/fix_eos_table_rx.txt create mode 100644 doc/html/_sources/fix_rx.txt create mode 100644 doc/html/_sources/pair_exp6_rx.txt create mode 100644 doc/html/_sources/pair_multi_lucy_rx.txt create mode 100644 doc/html/_sources/pair_table_rx.txt diff --git a/doc/html/_sources/fix_eos_table_rx.txt b/doc/html/_sources/fix_eos_table_rx.txt new file mode 100644 index 0000000000..0e6f6854c7 --- /dev/null +++ b/doc/html/_sources/fix_eos_table_rx.txt @@ -0,0 +1,166 @@ +.. index:: fix eos/table/rx + +fix eos/table/rx command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID eos/table/rx style file1 N keyword file2 + +* ID, group-ID are documented in :doc:`fix ` command +* eos/table/rx = style name of this fix command +* style = *linear* = method of interpolation +* file1 = filename containing the tabulated equation of state +* N = use N values in *linear* tables +* keyword = name of table keyword correponding to table file +* file2 = filename containing the heats of formation of each species + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table + +Description +""""""""""" + +Fix *eos/table/rx* applies a tabulated mesoparticle equation +of state to relate the concentration-dependent particle internal +energy (u_i) to the particle internal temperature (dpdTheta_i). + +The concentration-dependent particle internal energy (u_i) is +computed according to the following relation: + +.. image:: Eqs/fix_eos_table_rx.jpg + :align: center + +where *m* is the number of species, *c_i,j* is the concentration of +species *j* in particle *i*\ , *u_j* is the internal energy of species j, +*DeltaH_f,j* is the heat of formation of species *j*\ , N is the number of +molecules represented by the coarse-grained particle, kb is the +Boltzmann constant, and T is the temperature of the system. + +Fix *eos/table/rx* creates interpolation tables of length *N* from *m* +internal energy values of each species *u_j* listed in a file as a +function of internal temperature. During a simulation, these tables +are used to interpolate internal energy or temperature values as needed. +The interpolation is done with the *linear* style. For the *linear* style, +the internal temperature is used to find 2 surrounding table values from +which an internal energy is computed by linear interpolation. A secant +solver is used to determine the internal temperature from the internal energy. + +The first filename specifies a file containing tabulated internal +temperature and *m* internal energy values for each species *u_j*\ . +The keyword specifies a section of the file. The format of this +file is described below. + +The second filename specifies a file containing heat of formation +*DeltaH_f,j* for each species. + + +---------- + + +The format of a tabulated file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # EOS TABLE (one or more comment or blank lines) + +.. parsed-literal:: + + KEYWORD (keyword is first text on line) + N 500 h2 no2 n2 ... no (N parameter species1 species2 ... speciesN) + (blank) + 1 1.00 0.000 ... 0.0000 (index, internal temperature, internal energy of species 1, ..., internal energy of species m) + 2 1.02 0.001 ... 0.0002 + ... + 500 10.0 0.500 ... 1.0000 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the fix command. + +The next line lists the number of table entries and the species names +that correspond with all the species listed in the reaction equations +through the *fix rx* command. +The parameter "N" is required and its value is the number of table +entries that follow. Let Nfile = "N" in the tabulated file. +What LAMMPS does is a preliminary interpolation by creating splines +using the Nfile tabulated values as nodal points. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the internal temperature (in temperature units), the 3rd value until +the *m+3* value are the internal energies of the m species (in energy units). + +Note that all internal temperature and internal energy values must +increase from one line to the next. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +The format of a heat of formation file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # HEAT OF FORMATION TABLE (one or more comment or blank lines) + +.. parsed-literal:: + + (blank) + h2 0.00 (species name, heat of formation) + no2 0.34 + n2 0.00 + ... + no 0.93 + +Note that the species can be listed in any order. The tag that is +used as the species name must correspond with the tags used to define +the reactions with the :doc:`fix rx ` command. + + +---------- + + +Restrictions +"""""""""""" + + +The fix *eos/table/rx* is only available if LAMMPS is built with the +USER-DPD package. + +The equation of state must be a monotonically increasing function. + +An exit error will occur if the internal temperature or internal +energies are not within the table cutoffs. + +Related commands +"""""""""""""""" + +:doc:`fix rx `, +:doc:`pair dpd/fdt ` + +**Default:** none + + +---------- + + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/fix_rx.txt b/doc/html/_sources/fix_rx.txt new file mode 100644 index 0000000000..8ad193cd02 --- /dev/null +++ b/doc/html/_sources/fix_rx.txt @@ -0,0 +1,170 @@ +.. index:: fix rx + +fix rx command +============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID rx file localTemp solver ... + +* ID, group-ID are documented in :doc:`fix ` command +* rx = style name of this fix command +* file = filename containing the reaction kinetic equations and Arrhenius parameters +* localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function +* solver = *lammps_rk4* = Explicit 4th order Runge-Kutta method +* minSteps = # of steps for rk4 solver + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all rx kinetics.rx none lammps_rk4 + fix 1 all rx kinetics.rx none lammps_rk4 1 + fix 1 all rx kinetics.rx lucy lammps_rk4 10 + +Description +""""""""""" + +Fix *rx* solves the reaction kinetic ODEs for a given reaction set that is +defined within the file associated with this command. + +For a general reaction such that + +.. image:: Eqs/fix_rx_reaction.jpg + :align: center + +the reaction rate equation is defined to be of the form + +.. image:: Eqs/fix_rx_reactionRate.jpg + :align: center + +In the current implementation, the exponents are defined to be equal to the +stoichiometric coefficients. A given reaction set consisting of *n* reaction +equations will contain a total of *m* species. A set of *m* ordinary +differential equations (ODEs) that describe the change in concentration of a +given species as a function of time are then constructed based on the *n* +reaction rate equations. + +The ODE systems are solved over the full DPD timestep *dt* using a 4th order +Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified by the +*lammps_rk4* keyword. The number of ODE steps per DPD timestep for the rk4 method +is optionally specified immediately after the rk4 keyword. The ODE step-size is set as +*dt/num_steps*\ . Smaller step-sizes tend to yield more accurate results but there +is not control on the error. + + +---------- + + +The filename specifies a file that contains the entire set of reaction +kinetic equations and corresponding Arrhenius parameters. The format of +this file is described below. + +There is no restriction on the total number or reaction equations that are +specified. The species names are arbitrary string names that are associated +with the species concentrations. +Each species in a given reaction must be preceded by it's stoichiometric +coefficient. The only delimiters that are recognized between the species are +either a *+* or *=* character. The *=* character corresponds to an +irreversible reaction. After specifying the reaction, the reaction rate +constant is determined through the temperature dependent Arrhenius equation: + +.. image:: Eqs/fix_rx.jpg + :align: center + +where *A* is the Arrhenius factor in time units or concentration/time units, +*n* is the unitless exponent of the temperature dependence, and *E_a* is the +activation energy in energy units. The temperature dependence can be removed +by specifying the exponent as zero. + +The internal temperature of the coarse-grained particles can be used in constructing the +reaction rate constants at every DPD timestep by specifying the keyword *none*\ . +Alternatively, the keyword *lucy* can be specified to compute a local-average particle +internal temperature for use in the reaction rate constant expressions. +The local-average particle internal temperature is defined as: + +.. image:: Eqs/fix_rx_localTemp.jpg + :align: center + +where the Lucy function is expressed as: + +.. image:: Eqs/fix_rx_localTemp2.jpg + :align: center + +The self-particle interaction is included in the above equation. + + +---------- + + +The format of a tabulated file is as follows (without the parenthesized comments): + +.. parsed-literal:: + + # Rxn equations and parameters (one or more comment or blank lines) + +.. parsed-literal:: + + 1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49E+01 0.0 1.34 (rxn equation, A, n, Ea) + 1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 2.16E+00 0.0 1.52 + ... + 1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. + +Following a blank line, the next N lines list the N reaction equations. +Each species within the reaction equation is specified through its +stoichiometric coefficient and a species tag. Reactant species are specified +on the left-hand side of the equation and product species are specified on the +right-hand side of the equation. After specifying the reactant and product +species, the final three arguments of each line represent the Arrhenius +parameter *A*\ , the temperature exponent *n*\ , and the activation energy *Ea*\ . + +Note that the species tags that are defined in the reaction equations are +used by the :doc:`fix eos/table/rx ` command to define the +thermodynamic properties of each species. Furthermore, the number of species +molecules (i.e., concentration) can be specified either with the :doc:`set ` +command using the "d_" prefix or by reading directly the concentrations from a +data file. For the latter case, the :doc:`read_data ` command with the +fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. + +fix foo all rx reaction.file ... +read_data data.dpd fix foo_SPECIES NULL Species + + +---------- + + +Restrictions +"""""""""""" + + +The fix *rx* is only available if LAMMPS is built with the USER-DPD package. + +The fix *rx* must be used with the :doc:`atom_style dpd ` command. + +The fix *rx* can only be used with a constant energy or constant enthalpy DPD simulation. + +Related commands +"""""""""""""""" + +:doc:`fix eos/table/rx `, +:doc:`fix shardlow `, +:doc:`pair dpd/fdt/energy ` + +**Default:** none + + +---------- + + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/pair_exp6_rx.txt b/doc/html/_sources/pair_exp6_rx.txt new file mode 100644 index 0000000000..0a5576911c --- /dev/null +++ b/doc/html/_sources/pair_exp6_rx.txt @@ -0,0 +1,136 @@ +.. index:: pair_style exp6/rx + +pair_style exp6/rx command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + pair_style exp6/rx cutoff + +* cutoff = global cutoff for DPD interactions (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + pair_style exp6/rx 10.0 + pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 + pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 + pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 + +Description +""""""""""" + +Style *exp6/rx* is used in reaction DPD simulations, where the coarse-grained (CG) +particles are composed of *m* species whose reaction rate kinetics are determined +from a set of *n* reaction rate equations through the :doc:`fix rx ` command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. The *exp6/rx* style +computes an exponential-6 potential given by + +.. image:: Eqs/pair_exp6_rx.jpg + :align: center + +where the *epsilon* parameter determines the depth of the potential +minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion. + +The coefficients must be defined for each species in a given particle type +via the :doc:`pair_coeff ` command as in the examples above, where +the first argument is the filename that includes the exponential-6 parameters +for each species. The file includes the species tag followed by the *alpha*\ , +*epsilon* and *Rm* parameters. The format of the file is described below. + +The second and third arguments specify the site-site interaction +potential between two species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the :doc:`fix rx ` command +or they must correspond to the tag "1fluid", signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the +difference is defined to be the internal chemical energy (uChem). + +The fourth and fifth arguments specify the *Rm* and *epsilon* scaling exponents. + +The final argument specifies the interaction cutoff. + + +---------- + + +The format of a tabulated file is as follows (without the parenthesized comments): + +.. parsed-literal:: + + # exponential-6 parameters for various species (one or more comment or blank lines) + +.. parsed-literal:: + + h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon) + no2 exp6 13.60 0.01 3.70 + ... + co2 exp6 13.00 0.03 3.20 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. + +Following a blank line, the next N lines list the species and their +corresponding parameters. The first argument is the species tag, +the second argument is the exp6 tag, the 3rd argument is the *alpha* +parameter (energy units), the 4th argument is the *epsilon* parameter +(energy-distance^6 units), and the 5th argument is the *Rm* +parameter (distance units). If a species tag of "1fluid" is listed as a +pair coefficient, a one-fluid approximation is specified where a +concentration-dependent combination of the parameters is computed +through the following equations: + +.. image:: Eqs/pair_exp6_rx_oneFluid.jpg + :align: center + +where + +.. image:: Eqs/pair_exp6_rx_oneFluid2.jpg + :align: center + +and xa and xb are the mole fractions of a and b, respectively, which +comprise the gas mixture. + + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This style does not support the :doc:`pair_modify ` shift option +for the energy of the exp() and 1/r^6 portion of the pair interaction. + +This style does not support the pair_modify tail option for adding long-range +tail corrections to energy and pressure for the A,C terms in the +pair interaction. + +Restrictions +"""""""""""" + + +None + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/pair_multi_lucy_rx.txt b/doc/html/_sources/pair_multi_lucy_rx.txt new file mode 100644 index 0000000000..b134a14b4d --- /dev/null +++ b/doc/html/_sources/pair_multi_lucy_rx.txt @@ -0,0 +1,242 @@ +.. index:: pair_style multi/lucy/rx + +pair_style multi/lucy/rx command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + pair_style multi/lucy/rx style N keyword ... + +* style = *lookup* or *linear* = method of interpolation +* N = use N values in *lookup*\ , *linear* tables + +Examples +"""""""" + +.. parsed-literal:: + + pair_style multi/lucy/rx linear 1000 + pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 + pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 + +Description +""""""""""" + +Style *multi/lucy/rx* is used in reaction DPD simulations, where the coarse-grained +(CG) particles are composed of *m* species whose reaction rate kinetics are determined +from a set of *n* reaction rate equations through the :doc:`fix rx ` command. +The species of one CG particle can interact with a species in a neighboring CG particle +through a site-site interaction potential model. Style *multi/lucy/rx* computes the +site-site density-dependent force following from the many-body form described in +:ref:`(Moore) ` and :ref:`(Warren) ` as + +.. image:: Eqs/pair_multi_lucy.jpg + :align: center + +which consists of a density-dependent function, A(rho), and a radial-dependent weight +function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken +as the Lucy function: + +.. image:: Eqs/pair_multi_lucy2.jpg + :align: center + +The density-dependent energy for a given particle is given by: + +.. image:: Eqs/pair_multi_lucy_energy.jpg + :align: center + +See the supporting information of :ref:`(Brennan) ` or the publication by :ref:`(Moore) ` +for more details on the functional form. + +An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). +Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will +have units of energy / length^4. + +The interpolation table is created as a pre-computation by fitting cubic splines to +the file values and interpolating the density-dependent energy and force at each of *N* densities. +During a simulation, the tables are used to interpolate the density-dependent energy and force as +needed for each pair of particles separated by a distance *R*\ . The interpolation is done in +one of 2 styles: *lookup* and *linear*\ . + +For the *lookup* style, the density is used to find the nearest table entry, which is the +density-dependent energy and force. + +For the *linear* style, the density is used to find the 2 surrounding table values from +which the density-dependent energy and force are computed by linear interpolation. + +The following coefficients must be defined for each pair of atoms +types via the :doc:`pair_coeff ` command as in the examples +above. + +* filename +* keyword +* species1 +* species2 +* cutoff (distance units) + +The filename specifies a file containing the tabulated density-dependent +energy and force. The keyword specifies a section of the file. +The cutoff is an optional coefficient. If not specified, the outer cutoff in the +table itself (see below) will be used to build an interpolation table +that extend to the largest tabulated distance. If specified, only +file values up to the cutoff are used to create the interpolation +table. The format of this file is described below. + +The species tags define the site-site interaction potential between two +species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the :doc:`fix rx ` command +or they must correspond to the tag "1fluid", signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential +is stored before and after the reaction kinetics solver is applied, where +the difference is defined to be the internal chemical energy (uChem). + + +---------- + + +The format of a tabulated file is a series of one or more sections, +defined as follows (without the parenthesized comments): + +.. parsed-literal:: + + # Density-dependent function (one or more comment or blank lines) + +.. parsed-literal:: + + DD-FUNCTION (keyword is first text on line) + N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) + 1 1.0 25.5 102.34 (index, density, energy/r^4, force) + 2 1.02 23.4 98.5 + ... + 500 10.0 0.001 0.003 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the pair_coeff +command. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the :doc:`pair_style multi/lucy/rx ` command. Let +Ntable = *N* in the pair_style command, and Nfile = "N" in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate the density-dependent energy and force at Ntable different +points. The resulting tables of length Ntable are then used as +described above, when computing the density-dependent energy and force. +This means that if you want the interpolation tables of +length Ntable to match exactly what is in the tabulated file (with +effectively no preliminary interpolation), you should set Ntable = +Nfile, and use the "RSQ" parameter. This is because the +internal table abscissa is always RSQ (separation distance squared), +for efficient lookup. + +All other parameters are optional. If "R" or "RSQ" does +not appear, then the distances in each line of the table are used +as-is to perform spline interpolation. In this case, the table values +can be spaced in *density* uniformly or however you wish to position table +values in regions of large gradients. + +If used, the parameters "R" or "RSQ" are followed by 2 values *rlo* +and *rhi*\ . If specified, the density associated with each density-dependent +energy and force value is computed from these 2 values (at high accuracy), rather +than using the (low-accuracy) value listed in each line of the table. +The density values in the table file are ignored in this case. +For "R", distances uniformly spaced between *rlo* and *rhi* are +computed; for "RSQ", squared distances uniformly spaced between +*rlo*rlo* and *rhi*rhi* are computed. + +.. note:: + + If you use "R" or "RSQ", the tabulated distance values in the + file are effectively ignored, and replaced by new values as described + in the previous paragraph. If the density value in the table is not + very close to the new value (i.e. round-off difference), then you will + be assigning density-dependent energy and force values to a different density, + which is probably not what you want. LAMMPS will warn if this is occurring. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +r (in density units), the 3rd value is the density-dependent function value +(in energy units / length^4), and the 4th is the force (in force units). The +density values must increase from one line to the next. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +The :doc:`pair_modify ` shift, table, and tail options are +not relevant for this pair style. + +This pair style writes the settings for the "pair_style multi/lucy/rx" command +to :doc:`binary restart files `, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + + +---------- + + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + + +---------- + + +.. _Warren: + + + +**(Warren)** Warren, Phys Rev E, 68, 066702 (2003). + +.. _Brennan: + + + +**(Brennan)** Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). + +.. _Moore: + + + +**(Moore)** Moore, J Chem Phys, 144, 104501 (2016). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/pair_table_rx.txt b/doc/html/_sources/pair_table_rx.txt new file mode 100644 index 0000000000..e1af9b0ea4 --- /dev/null +++ b/doc/html/_sources/pair_table_rx.txt @@ -0,0 +1,252 @@ +.. index:: pair_style table/rx + +pair_style table/rx command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + pair_style table style N + +style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation +N = use N values in *lookup*\ , *linear*\ , *spline* tables +N = use 2^N values in *bitmap* tables + +Examples +"""""""" + +.. parsed-literal:: + + pair_style table/rx linear 1000 + pair_style table/rx bitmap 12 + pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0 + pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0 + pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 + +Description +""""""""""" + +Style *table/rx* is used in reaction DPD simulations,where the coarse-grained (CG) +particles are composed of *m* species whose reaction rate kinetics are determined +from a set of *n* reaction rate equations through the :doc:`fix rx ` command. +The species of one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style *table/rx* creates +interpolation tables of length *N* from pair potential and force values listed in a +file(s) as a function of distance. The files are read by the +:doc:`pair_coeff ` command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and force values at each of *N* +distances. During a simulation, these tables are used to interpolate +energy and force values as needed. The interpolation is done in one +of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ . + +For the *lookup* style, the distance between 2 atoms is used to find +the nearest table entry, which is the energy or force. + +For the *linear* style, the pair distance is used to find 2 +surrounding table values from which an energy or force is computed by +linear interpolation. + +For the *spline* style, a cubic spline coefficients are computed and +stored at each of the *N* values in the table. The pair distance is +used to find the appropriate set of coefficients which are used to +evaluate a cubic polynomial which computes the energy or force. + +For the *bitmap* style, the N means to create interpolation tables +that are 2^N in length. ` and a linear +interpolation is performed between adjacent table values. + +The following coefficients must be defined for each pair of atoms +types via the :doc:`pair_coeff ` command as in the examples +above. + +* filename +* keyword +* species1 +* species2 +* cutoff (distance units) + +The filename specifies a file containing tabulated energy and force +values. The keyword specifies a section of the file. The cutoff is +an optional coefficient. If not specified, the outer cutoff in the +table itself (see below) will be used to build an interpolation table +that extend to the largest tabulated distance. If specified, only +file values up to the cutoff are used to create the interpolation +table. The format of this file is described below. + +The species tags define the site-site interaction potential between two +species contained within two different particles. +The species tags must either correspond to the species defined in the reaction +kinetics files specified with the :doc:`fix rx ` command +or they must correspond to the tag "1fluid", signifying interaction +with a product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential +is stored before and after the reaction kinetics solver is applied, where +the difference is defined to be the internal chemical energy (uChem). + + +---------- + + +Here are some guidelines for using the pair_style table/rx command to +best effect: + +* Vary the number of table points; you may need to use more than you think + to get good resolution. +* Always use the :doc:`pair_write ` command to produce a plot + of what the final interpolated potential looks like. This can show up + interpolation "features" you may not like. +* Start with the linear style; it's the style least likely to have problems. +* Use *N* in the pair_style command equal to the "N" in the tabulation + file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation + is not needed. See discussion below. +* Make sure that your tabulated forces and tabulated energies are consistent + (dE/dr = -F) along the entire range of r values. +* Use as large an inner cutoff as possible. This avoids fitting splines + to very steep parts of the potential. + +---------- + + +The format of a tabulated file is a series of one or more sections, +defined as follows (without the parenthesized comments): + +.. parsed-literal:: + + # Morse potential for Fe (one or more comment or blank lines) + +.. parsed-literal:: + + MORSE_FE (keyword is first text on line) + N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters) + (blank) + 1 1.0 25.5 102.34 (index, r, energy, force) + 2 1.02 23.4 98.5 + ... + 500 10.0 0.001 0.003 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the pair_coeff +command. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the :doc:`pair_style table/rx ` command. Let +Ntable = *N* in the pair_style command, and Nfile = "N" in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate as needed to generate energy and force +values at Ntable different points. The resulting tables of length +Ntable are then used as described above, when computing energy and +force for individual pair distances. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter. +The internal table abscissa is RSQ (separation distance squared). + +All other parameters are optional. If "R" or "RSQ" or "BITMAP" does +not appear, then the distances in each line of the table are used +as-is to perform spline interpolation. In this case, the table values +can be spaced in *r* uniformly or however you wish to position table +values in regions of large gradients. + +If used, the parameters "R" or "RSQ" are followed by 2 values *rlo* +and *rhi*\ . If specified, the distance associated with each energy and +force value is computed from these 2 values (at high accuracy), rather +than using the (low-accuracy) value listed in each line of the table. +The distance values in the table file are ignored in this case. +For "R", distances uniformly spaced between *rlo* and *rhi* are +computed; for "RSQ", squared distances uniformly spaced between +*rlo*rlo* and *rhi*rhi* are computed. + +If used, the parameter "BITMAP" is also followed by 2 values *rlo* and +*rhi*\ . These values, along with the "N" value determine the ordering +of the N lines that follow and what distance is associated with each. +This ordering is complex, so it is not documented here, since this +file is typically produced by the :doc:`pair_write ` command +with its *bitmap* option. When the table is in BITMAP format, the "N" +parameter in the file must be equal to 2^M where M is the value +specified in the pair_style command. Also, a cutoff parameter cannot +be used as an optional 3rd argument in the pair_coeff command; the +entire table extent as specified in the file must be used. + +If used, the parameter "FPRIME" is followed by 2 values *fplo* and +*fphi* which are the derivative of the force at the innermost and +outermost distances listed in the table. These values are needed by +the spline construction routines. If not specified by the "FPRIME" +parameter, they are estimated (less accurately) by the first 2 and +last 2 force values in the table. This parameter is not used by +BITMAP tables. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +r (in distance units), the 3rd value is the energy (in energy units), +and the 4th is the force (in force units). The r values must increase +from one line to the next (unless the BITMAP parameter is specified). + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +The :doc:`pair_modify ` shift, table, and tail options are +not relevant for this pair style. + +This pair style writes the settings for the "pair_style table/rx" command +to :doc:`binary restart files `, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + + +---------- + + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + + +---------- + + +.. _Wolff: + + + +**(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm From 63c80930f1cede549a7228a1dfa8c6048072fe3d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:32:15 +0000 Subject: [PATCH 079/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15123 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/fix_rx.html | 307 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 307 insertions(+) create mode 100644 doc/html/fix_rx.html diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html new file mode 100644 index 0000000000..752afbe7ef --- /dev/null +++ b/doc/html/fix_rx.html @@ -0,0 +1,307 @@ + + + + + + + + + + + fix rx command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix rx command

    +
    +

    Syntax

    +
    fix ID group-ID rx file localTemp solver ...
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • rx = style name of this fix command
      • +
    • file = filename containing the reaction kinetic equations and Arrhenius parameters
      • +
    • localTemp = none,lucy = no local temperature averaging or local temperature defined through Lucy weighting function
      • +
    • solver = lammps_rk4 = Explicit 4th order Runge-Kutta method
      • +
    • minSteps = # of steps for rk4 solver
      • +
    +
    +
    +

    Examples

    +
    fix 1 all rx kinetics.rx none lammps_rk4
+fix 1 all rx kinetics.rx none lammps_rk4 1
+fix 1 all rx kinetics.rx lucy lammps_rk4 10
+
    +
    +
    +
    +

    Description

    +

    Fix rx solves the reaction kinetic ODEs for a given reaction set that is +defined within the file associated with this command.

    +

    For a general reaction such that

    +Eqs/fix_rx_reaction.jpg +

    the reaction rate equation is defined to be of the form

    +Eqs/fix_rx_reactionRate.jpg +

    In the current implementation, the exponents are defined to be equal to the +stoichiometric coefficients. A given reaction set consisting of n reaction +equations will contain a total of m species. A set of m ordinary +differential equations (ODEs) that describe the change in concentration of a +given species as a function of time are then constructed based on the n +reaction rate equations.

    +

    The ODE systems are solved over the full DPD timestep dt using a 4th order +Runge-Kutta rk4 method with a fixed step-size h, specified by the +lammps_rk4 keyword. The number of ODE steps per DPD timestep for the rk4 method +is optionally specified immediately after the rk4 keyword. The ODE step-size is set as +dt/num_steps. Smaller step-sizes tend to yield more accurate results but there +is not control on the error.

    +
    +

    The filename specifies a file that contains the entire set of reaction +kinetic equations and corresponding Arrhenius parameters. The format of +this file is described below.

    +

    There is no restriction on the total number or reaction equations that are +specified. The species names are arbitrary string names that are associated +with the species concentrations. +Each species in a given reaction must be preceded by it’s stoichiometric +coefficient. The only delimiters that are recognized between the species are +either a + or = character. The = character corresponds to an +irreversible reaction. After specifying the reaction, the reaction rate +constant is determined through the temperature dependent Arrhenius equation:

    +Eqs/fix_rx.jpg +

    where A is the Arrhenius factor in time units or concentration/time units, +n is the unitless exponent of the temperature dependence, and E_a is the +activation energy in energy units. The temperature dependence can be removed +by specifying the exponent as zero.

    +

    The internal temperature of the coarse-grained particles can be used in constructing the +reaction rate constants at every DPD timestep by specifying the keyword none. +Alternatively, the keyword lucy can be specified to compute a local-average particle +internal temperature for use in the reaction rate constant expressions. +The local-average particle internal temperature is defined as:

    +Eqs/fix_rx_localTemp.jpg +

    where the Lucy function is expressed as:

    +Eqs/fix_rx_localTemp2.jpg +

    The self-particle interaction is included in the above equation.

    +
    +

    The format of a tabulated file is as follows (without the parenthesized comments):

    +
    # Rxn equations and parameters                                               (one or more comment or blank lines)
+
    +
    +
    1.0 hcn + 1.0 no2 = 1.0  no + 0.5 n2  + 0.5 h2 + 1.0 co   2.49E+01 0.0 1.34  (rxn equation, A, n, Ea)
+1.0 hcn + 1.0  no = 1.0  co + 1.0 n2  + 0.5 h2            2.16E+00 0.0 1.52
+...
+1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     1.66E+06 0.0 0.69
+
    +
    +

    A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections.

    +

    Following a blank line, the next N lines list the N reaction equations. +Each species within the reaction equation is specified through its +stoichiometric coefficient and a species tag. Reactant species are specified +on the left-hand side of the equation and product species are specified on the +right-hand side of the equation. After specifying the reactant and product +species, the final three arguments of each line represent the Arrhenius +parameter A, the temperature exponent n, and the activation energy Ea.

    +

    Note that the species tags that are defined in the reaction equations are +used by the fix eos/table/rx command to define the +thermodynamic properties of each species. Furthermore, the number of species +molecules (i.e., concentration) can be specified either with the set +command using the “d_” prefix or by reading directly the concentrations from a +data file. For the latter case, the read_data command with the +fix keyword should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g.

    +

    fix foo all rx reaction.file ... +read_data data.dpd fix foo_SPECIES NULL Species

    +
    +
    +
    +

    Restrictions

    +

    The fix rx is only available if LAMMPS is built with the USER-DPD package.

    +

    The fix rx must be used with the atom_style dpd command.

    +

    The fix rx can only be used with a constant energy or constant enthalpy DPD simulation.

    +
    + +
    + + +
    +
    +
    + + +
    + +
    +

    + © Copyright 2013 Sandia Corporation. +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From 7c55da3879cfd36c7cf28116cd000340fbf3a3b7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:37:34 +0000 Subject: [PATCH 080/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15124 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/Eqs/compute_dpd.jpg | Bin 11073 -> 21381 bytes doc/src/Eqs/compute_dpd.tex | 3 ++- doc/src/Eqs/fix_eos_table_rx.jpg | Bin 0 -> 17367 bytes doc/src/Eqs/fix_eos_table_rx.tex | 9 +++++++++ doc/src/Eqs/fix_rx.jpg | Bin 0 -> 2427 bytes doc/src/Eqs/fix_rx.tex | 9 +++++++++ doc/src/Eqs/fix_rx_localTemp.jpg | Bin 0 -> 16562 bytes doc/src/Eqs/fix_rx_localTemp.tex | 9 +++++++++ doc/src/Eqs/fix_rx_localTemp2.jpg | Bin 0 -> 16284 bytes doc/src/Eqs/fix_rx_localTemp2.tex | 9 +++++++++ doc/src/Eqs/fix_rx_reaction.jpg | Bin 0 -> 2896 bytes doc/src/Eqs/fix_rx_reaction.tex | 9 +++++++++ doc/src/Eqs/fix_rx_reactionRate.jpg | Bin 0 -> 2939 bytes doc/src/Eqs/fix_rx_reactionRate.tex | 9 +++++++++ doc/src/Eqs/pair_exp6_rx.jpg | Bin 0 -> 9372 bytes doc/src/Eqs/pair_exp6_rx.tex | 9 +++++++++ doc/src/Eqs/pair_exp6_rx_oneFluid.jpg | Bin 0 -> 16062 bytes doc/src/Eqs/pair_exp6_rx_oneFluid.tex | 11 +++++++++++ doc/src/Eqs/pair_exp6_rx_oneFluid2.jpg | Bin 0 -> 7629 bytes doc/src/Eqs/pair_exp6_rx_oneFluid2.tex | 11 +++++++++++ doc/src/Eqs/pair_multi_lucy.jpg | Bin 6756 -> 18222 bytes doc/src/Eqs/pair_multi_lucy2.jpg | Bin 5494 -> 16516 bytes doc/src/Eqs/pair_multi_lucy_energy.jpg | Bin 5006 -> 15425 bytes 23 files changed, 87 insertions(+), 1 deletion(-) create mode 100644 doc/src/Eqs/fix_eos_table_rx.jpg create mode 100644 doc/src/Eqs/fix_eos_table_rx.tex create mode 100644 doc/src/Eqs/fix_rx.jpg create mode 100644 doc/src/Eqs/fix_rx.tex create mode 100644 doc/src/Eqs/fix_rx_localTemp.jpg create mode 100644 doc/src/Eqs/fix_rx_localTemp.tex create mode 100644 doc/src/Eqs/fix_rx_localTemp2.jpg create mode 100644 doc/src/Eqs/fix_rx_localTemp2.tex create mode 100644 doc/src/Eqs/fix_rx_reaction.jpg create mode 100644 doc/src/Eqs/fix_rx_reaction.tex create mode 100644 doc/src/Eqs/fix_rx_reactionRate.jpg create mode 100644 doc/src/Eqs/fix_rx_reactionRate.tex create mode 100644 doc/src/Eqs/pair_exp6_rx.jpg create mode 100644 doc/src/Eqs/pair_exp6_rx.tex create mode 100644 doc/src/Eqs/pair_exp6_rx_oneFluid.jpg create mode 100644 doc/src/Eqs/pair_exp6_rx_oneFluid.tex create mode 100644 doc/src/Eqs/pair_exp6_rx_oneFluid2.jpg create mode 100644 doc/src/Eqs/pair_exp6_rx_oneFluid2.tex diff --git a/doc/src/Eqs/compute_dpd.jpg b/doc/src/Eqs/compute_dpd.jpg index 42ed03db156bbe8abe0d39229d439618d44b8d2c..549f259c6cbbb89c8c6a8218b5b43af2a688ce3d 100644 GIT binary patch literal 21381 zcmbq)WmFx(mhQnlA-KD{y99!}ySuvtPjEX(aChh69NgW59$bS%a1ZcuXWq=*ch{X? zue#P=UEOQd>aMP;{e9ow{l5IZ4M3NZl9d8LK|uim{vLq$HNcmDwEn-!doKV55sD28 z4GQWL;C&E441fYa!~CO5z<(74L^yaPWLRjJzqiHE0npIUFaRiMI4EcoSQG#N4jvZa 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ZeXZm_@cHfL&wsAgyiHU7XVATw`G3P{)tmqT diff --git a/doc/src/Eqs/compute_dpd.tex b/doc/src/Eqs/compute_dpd.tex index 3d4338db08..e46b0b4dd6 100644 --- a/doc/src/Eqs/compute_dpd.tex +++ b/doc/src/Eqs/compute_dpd.tex @@ -5,7 +5,8 @@ \begin{eqnarray*} U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ - U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech}) \\ + U^{chem} = \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\ + U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\ \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\ \end{eqnarray*} diff --git a/doc/src/Eqs/fix_eos_table_rx.jpg b/doc/src/Eqs/fix_eos_table_rx.jpg new file mode 100644 index 0000000000000000000000000000000000000000..0172281b6ccfb25e31b923f8e0a2c7f027812caf GIT binary patch literal 17367 zcmeHu2RNMFy7sHLAVlv$LNIzKL=r86=$+^-y3rXVdM5}GM2R4X-i<^jh#uV_L^tYa 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b/doc/html/Section_perf.html index f4c504ff9d..963ec4afa9 100644 --- a/doc/html/Section_perf.html +++ b/doc/html/Section_perf.html @@ -149,11 +149,8 @@ below:

    The 5 standard problems are as follow:

      -
    1. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
      2. -
    -
    -
    neighbors per atom), NVE integration
    -
      +
    1. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 +neighbors per atom), NVE integration
    2. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per atom), NVE integration
      3. diff --git a/doc/html/_sources/Section_intro.txt b/doc/html/_sources/Section_intro.txt index c7ce42c26b..7a583e4f3d 100644 --- a/doc/html/_sources/Section_intro.txt +++ b/doc/html/_sources/Section_intro.txt @@ -493,6 +493,7 @@ items. Leave on desk. VISA also accepted. Chocolate chip cookies encouraged. + ---------- diff --git a/doc/html/_sources/Section_perf.txt b/doc/html/_sources/Section_perf.txt index fa44adb3b0..e398d5245e 100644 --- a/doc/html/_sources/Section_perf.txt +++ b/doc/html/_sources/Section_perf.txt @@ -14,7 +14,7 @@ below: The 5 standard problems are as follow: #. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 - neighbors per atom), NVE integration + neighbors per atom), NVE integration #. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per atom), NVE integration @@ -26,6 +26,7 @@ The 5 standard problems are as follow: field with a 10 Angstrom LJ cutoff (440 neighbors per atom), particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT integration + Input files for these 5 problems are provided in the bench directory of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 timesteps. The size of the problem (number of atoms) can be varied diff --git a/doc/html/_sources/bond_write.txt b/doc/html/_sources/bond_write.txt index 66cf5884bc..8d06fab28b 100644 --- a/doc/html/_sources/bond_write.txt +++ b/doc/html/_sources/bond_write.txt @@ -16,7 +16,7 @@ Syntax * file = name of file to write values to * keyword = section name in file for this set of tabulated values * itype,jtype = 2 atom types (optional) -* +* Examples """""""" diff --git a/doc/html/_sources/dihedral_harmonic.txt b/doc/html/_sources/dihedral_harmonic.txt index 78805e27d0..211beaf4dd 100644 --- a/doc/html/_sources/dihedral_harmonic.txt +++ b/doc/html/_sources/dihedral_harmonic.txt @@ -54,6 +54,7 @@ or :doc:`read_restart ` commands: * Some force fields let *n* be positive or negative which corresponds to *d* = 1 or -1 for the harmonic style. + ---------- diff --git a/doc/html/_sources/dump_image.txt b/doc/html/_sources/dump_image.txt index 1662ae18b6..133b465207 100644 --- a/doc/html/_sources/dump_image.txt +++ b/doc/html/_sources/dump_image.txt @@ -584,6 +584,7 @@ Load the animated GIF file additional libraries, purchasing a license, or may not be supported. + ---------- diff --git a/doc/html/_sources/fix_gle.txt b/doc/html/_sources/fix_gle.txt index 3c4f7c6f87..d3deb93361 100644 --- a/doc/html/_sources/fix_gle.txt +++ b/doc/html/_sources/fix_gle.txt @@ -23,7 +23,6 @@ keyword = *noneq* and/or *every* of the integration of the GLE, but has *no effect* on the accuracy of equilibrium sampling. It might change sampling properties when used together with *noneq*\ . - Examples """""""" diff --git a/doc/html/_sources/suffix.txt b/doc/html/_sources/suffix.txt index 6f31d935ee..2e407852ea 100644 --- a/doc/html/_sources/suffix.txt +++ b/doc/html/_sources/suffix.txt @@ -55,6 +55,7 @@ These are the variants these packages provide: * OPT = a handful of pair styles, cache-optimized for faster CPU performance * HYBRID = a combination of two packages can be specified (see below) + As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, lj/cut/gpu, lj/cut/intel, or lj/cut/kk. A variant styles can be specified explicitly in your input script, e.g. pair_style diff --git a/doc/html/pair_modify.html b/doc/html/pair_modify.html index 21313080f0..fe24147bb1 100644 --- a/doc/html/pair_modify.html +++ b/doc/html/pair_modify.html @@ -228,7 +228,7 @@ see the doc page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a -bit-mapping technique       (Wolff) and a linear interpolation is +bit-mapping technique (Wolff) and a linear interpolation is performed between adjacent table values. In our experiments with different table styles (lookup, linear, spline), this method typically gave the best performance in terms of speed and accuracy.

      diff --git a/doc/html/pair_table.html b/doc/html/pair_table.html index 0b323dd8ac..7dd8b8ecf1 100644 --- a/doc/html/pair_table.html +++ b/doc/html/pair_table.html @@ -188,7 +188,7 @@ computes the energy or force.

      For the bitmap style, the specified N is used to create interpolation tables that are 2^N in length. The distance R is used to index into the table via a fast bit-mapping technique due to -(Wolff), and a linear interpolation is performed between +(Wolff), and a linear interpolation is performed between adjacent table values.

      The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index e098f6c431..5d3b7b60fc 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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,205,206,224,246,306,311],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,306,316,334,335,345,355,393,419,423,456,457,496,510,512,522],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:391,comb3:[],comb:[],comb_1:308,comb_2:308,combiant:408,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,299,305,321,337,346,354,357,359,375,376,378,383,391,405,407,408,412,416,417,418,424,436,437,465,475,478,480,481,483,486,498,503,508,516,522,524],come:[],comfort:[12,13],comit:517,comm:[0,3,11,12,64,78,204,250,252,253,376,386,391,411,446,453,476,477,497],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,241,254,316,317,345,385,386,392,414,415,417,418,428,441,448,449,450,457,464,465,475,476,477,478,479,480,483,492,493,495,516,517,522],commerci:7,commit:[9,517],commmand:[3,6,12,62,119,294,427,489,490,492,509,526],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,370,422,431,465,478,480,495,498,507],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,298,305,307,308,309,316,321,333,345,356,373,375,387,388,389,391,412,413,452,488,492,493,504,505,522,525,527],communc:375,comp:[7,204,252,253,286,292,320,376,386,416,446,453,458,472,476,477,479],compact:[66,209,404,474],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,307,356,358,375,376,384,386,441,464,490,509,510,516,521],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:380,compass:[7,9,21,22,37,44,45,56,185,186,197,359,360,369,403,474],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,298,310,337,340,347,350,353,375,391,425,444,446,476,492,493,522],compens:[6,225,226,314,387,416],compet:344,competit:376,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,344,376,391,444,495,496,500,516,522],compl:17,complain:[11,12,17],complement:441,complementari:[7,407,429],complet:[3,6,9,11,12,15,42,62,76,206,224,229,259,299,302,305,333,344,346,357,358,374,386,391,417,461,463,482,490,495,500,503,507,509,512,516,522],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,286,329,354,373,386,416,444,476,477,493,495,498,522],compli:[340,344],complic:[6,7,9,12,13,216,245,493],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,298,299,300,303,314,316,319,320,322,326,327,330,333,336,337,338,340,347,348,353,354,355,375,378,383,384,385,386,391,411,416,421,438,439,461,463,464,465,495,496,505,513,522,523],componenet:6,composit:[6,216,256,414],compound:[406,416,417,483],compres:[76,126,218],compress:[],compris:[41,354,418,458,482],compton:[130,177],comptu:3,compuat:376,comput:[],computation:[3,6,225,226,345,397],computational:516,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,318],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,526],concav:354,concentr:[76,241,317,414,418,449,477],concept:[6,158,168,218,504],conceptu:[3,6,76,166,228,230,386,407,424,441,500],concern:[6,78,96,204,246],concetr:76,concis:[11,344],conclud:12,concret:8,concurr:[16,376,522],conden:[345,478,480],condens:[6,160,345,393,409,414,429,483],condit:[],conducit:6,conduct:[],cone:498,confer:444,confid:[3,509],config:[12,202,492],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,299,307,344,373,384,386,393,397,415,441,444,475,478,480,483,490,495,497,498,509,517],confin:[495,509],conflict:[3,12,41,203,446,493,517],conform:[3,6,13,62,227,228,269,315,322,344,368,386,416,507],confus:[3,483],conjuct:[9,411],conjug:[7,8,253,383,416,456,457],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,284,302,303,307,308,309,311,316,321,333,341,348,353,375,376,386,398,400,404,407,411,416,423,429,446,451,459,481,495,498,502,516,527],connect:[3,6,9,96,163,181,227,250,301,316,320,330,380,386,408,421,456,457,473,480,492,493,495,499,516],conner:393,connor:393,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,250,251,407,429,433,490,496,498],consequ:[1,6,216,345,428,509],conserv:[3,9,29,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,316,320,321,336,337,341,348,349,353,386,410,411,412,421,435,464,504,509],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,298,316,340,341,344,345,348,376,404,416,424,457,458,464,473,490,491,493,496,497,498,500,503,505,513,516,522],consider:[6,8,253,254,336,337,338,391,504],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,303,306,311,313,315,316,317,336,337,338,339,349,375,376,378,380,385,386,391,393,397,399,405,407,416,420,424,427,438,439,441,444,446,448,449,458,461,463,464,476,477,484,493,495,496,497,498,499,500,507,516,522],consistent_fe_initi:215,consit:316,constant:[],constantli:237,constitu:[3,6,259,316,350,354,405,458],constitut:[461,463],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,301,302,314,316,320,331,341,348,384,385,416,500,507,516],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,270,298,315,317,354,387,391,410,444,446,473,475,476,477,498,499,514,522],constructor:[8,11],consult:457,consum:[1,311,452,522],consumpt:373,contact:[],contact_stiff:[460,462],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,301,302,304,305,306,309,313,316,317,318,323,333,340,344,345,354,355,358,374,376,385,386,389,390,392,393,394,397,406,407,410,414,415,416,418,424,425,441,444,448,449,450,454,455,456,457,465,475,476,477,478,479,480,481,483,490,491,492,493,495,496,497,498,500,502,504,507,509,510,512,513,516,517,522,525,527],content:[4,8,9,12,18,457,511,513],context:[3,6,8,12,17,128,129,206,225,226,231,301,313,349,383,486,495,502,511,521,522,523],contibut:75,contigu:492,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,300,302,305,306,316,318,322,332,333,335,342,343,345,351,354,358,374,390,391,397,411,413,431,434,456,457,458,461,463,479,490,493,495,497,498,503,509,510,512,513,522,525],continuum:[6,7,9,215,345,461,463],contour_integr:215,contract:[62,228,230,270,303,316],contradictori:3,contrain:320,contraint:284,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,230,356,461,463,486,526],contrib:345,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,301,302,310,313,316,318,320,347,375,384,386,394,411,413,414,416,424,438,439,444,446,456,457,464,507,513,516,517],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,303,308,316,317,324,325,336,337,338,345,349,373,375,388,416,420,444,456,457,460,462,475,480,490,492,504,510,511],control_typ:215,controlfil:457,convect:100,conveni:[6,12,29,202,207,222,318,378,465,481,517,522],convent:[3,8,29,189,196,197,203,206,315,330,357,414,416,522],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,243,275,286,292,306,308,311,315,320,382,383,384,386,406,407,429,464,490,502,509],convers:[3,8,152,205,206,216,219,303,375,407,408,409,416,429,433,437,451,493,509,521],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,268,302,305,356,359,361,365,368,378,386,392,414,444,478,480,487,493,495,496,497,502,512,516,521,522,525,527],convex:[43,354],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,314],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[],coordb:464,coordbb:464,coordiat:384,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,301,302,303,313,314,316,319,320,322,327,330,331,332,333,335,343,344,345,352,353,355,356,378,384,385,386,391,392,393,396,415,464,490,495,496,497,498,500,503,505,509,516,522,523],coordn:[126,218],coords:464,copi:[0,3,4,8,9,11,12,15,17,41,131,205,345,386,404,456,493,517],copper:487,coproccesor:16,coprocessor:[1,7,9,16,17,391,508],coproprocessor:17,copy_arrai:8,copyright:[7,8,301],coral:206,core:[],core_shel:160,cores:516,coreshel:[4,6,9],coreshell:[],cornel:[6,184,507],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,354,355,378,482,495,517],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:406,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,184,203,205,230,237,245,247,253,270,271,293,301,303,306,344,350,354,375,386,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,487,488,495,510,513,516,517],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,309,316,320,330,332,351,354,386,387,391,409,439,444,492,493,495,505,517,521,523],correl:[],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,298,299,303,308,316,317,319,320,340,350,351,353,354,355,357,359,360,361,362,364,365,368,370,376,381,383,385,386,392,393,395,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,417,418,419,420,421,422,423,424,427,429,430,431,432,433,434,435,436,437,438,441,442,444,446,447,449,450,451,453,454,456,457,458,459,464,465,466,475,476,477,478,479,480,481,483,485,486,487,490,492,493,495,496,498,508,509,510,512,513,516,522],correspondingli:[438,439,504],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,242,270,308,345,375,376,389,407,429,433,444,446,475,492,504],costheta0:[475,478,480,483],costheta:454,costli:[11,97,247,387],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,305,306,307,311,314,316,319,333,334,340,344,345,346,350,354,356,358,366,372,374,382,384,387,391,393,394,419,423,424,427,456,457,491,492,493,495,497,499,502,503,510,511,516,522,523],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,307,309,346,375,376,384,391,398,400,401,402,403,406,407,408,409,410,416,421,422,424,429,433,437,440,446,451,456,457,459,464,474,480,481,483,486,500,507,513,516,521],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,302,320,336,337,354,376,384,385,386,388,391,419,423,446,513,522],counter:[3,351,490,501,503,509],counteract:245,counterbal:[237,249],counterbalanc:29,counterclockwis:184,counterpart:[202,316,490],counterproduct:18,coupl:[],couple:[4,6,11,12],courant:323,cours:[3,8,138,140,172,202,210,211,246,315,330,344,350,352,353,355,356,376,438,466,492,495,508,516,522,525],courtesi:378,cov:464,coval:[6,9,29,416,441,464,516],covari:247,cover:[6,12,76,198,206,215,256,416,482],coverag:76,cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,320],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,254,346,373,376,391,404,474,490,508,509,512,513,514,522],cpuremain:513,cpus:12,cr2:177,cr3:177,crack:[4,387],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,387,516],craympi:391,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:301,criteria:[3,128,179,205,206,225,226,227,265,384,453,482,497,500,522],criterion:[12,42,133,178,181,216,224,227,245,284,308,323,351,356,384,386,406,416,421,464,500,509,510],criterioni:509,critic:[6,49,50,268,340,345,384],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,267,269,293,316,326,330,332,341,348,360,378,386,402,411,413,414,422,423,424,429,431,433,454,459,461,463,478,480,487,495,499,505,525],crossov:1,crossterm:495,crozier:[0,7,13],crucial:306,crystal:[3,4,6,13,78,118,297,298,343,378,387,495,499,513,516],crystallin:[6,114,298,378,479,516],crystallis:340,crystallogr:[130,177],crystallograph:[378,513],crystallographi:[130,177,378],cs1:177,cs_chunk:6,cs_im:[41,495],cs_re:[41,495],csanyi:[152,455,465],cscl:441,csequ:6,csh:[11,12,404],cshrc:[11,12],csic:[415,475,478,480,483],csinfo:6,csisi:[415,475,478,480,483],csld:[],cst:414,cstherm:6,cstyle:492,csvr:[],ctcm:[392,414],ctemp_core:234,cterm:322,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:441,cube:[6,176,181,234,354,378,516],cubes:[42,224],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:397,cummul:[3,6,222,225,226,227,229,242,247,253,255,333,336,337,338,339,341,348,423,513],cumul:[6,216,218,221,235,245,253,268,270,275,284,316,318,386],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,267,270,271,276,277,278,284,286,290,291,292,293,295,301,302,307,308,310,313,314,315,316,317,320,321,322,323,324,325,326,327,329,331,332,333,336,337,338,344,345,348,349,350,351,352,353,355,356,358,373,374,375,376,379,380,381,383,384,385,386,391,397,404,406,410,414,416,417,421,424,425,428,438,439,441,442,443,446,454,456,457,460,461,462,463,466,478,480,481,484,490,491,492,493,495,496,497,498,499,501,502,503,505,507,509,510,512,513,517,522,523,524,525,526,527],curv:[6,178,245,286,292,298],curvatur:[420,458,487],custom:[],cut0:493,cut1:504,cut2:504,cut:[],cuthi:[297,309],cutinn:[399,438,439],cutlo:[297,309],cutmax:454,cutoff1:[403,410,429,433,437,440,451,459],cutoff2:[398,400,401,403,409,410,429,433,437,440,451,459,481],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,241,297,306,307,309,311,313,316,321,333,346,350,354,356,373,375,376,384,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,458,459,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,493,497,500,504,516,522],cutoffa:415,cutoffc:415,cuu3:414,cval:177,cvd:340,cvel:322,cvff:[],cwiggl:[3,267,350,353,355,522],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,76,205,218,251,292,302,351,354,380,498],cylinder_d:380,cylindr:[6,251,330,351],cypress:391,cyrot:397,cyrstal:298,d3q15:256,d3q19:256,d_double_double:15,d_e:345,d_flag2:305,d_flag:305,d_name:[125,202,305,335,505],d_single_double:15,d_single_single:15,d_sx:305,d_sy:305,d_sz:305,daan:343,dai:12,daili:12,daivi:293,damag:[],dammak:311,damp:[3,6,209,214,253,254,255,260,270,271,275,292,303,306,307,311,316,336,337,349,351,352,383,384,386,398,400,402,407,410,416,421,429,437,451,459,474,481,509,516],damp_com:254,damp_drud:254,dampen:[316,516],dampflag:[351,421],dan:17,danger:[3,12,245,356,411,513],dangl:181,daniel:9,darden:[376,410],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:307,dash:[421,512],dat:[6,100,198,215,491],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,318],dataset:318,datatyp:3,date:[0,4,6,12,13,201,456,457,522],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:440,davi:350,david:[9,19,375,376,478,480],daw:[414,454],dbg:14,dcd:[3,6,7,202,204,205,206,207,299,496,500],dcs:9,ddim:201,deactiv:437,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,299,304,373,375,425,446,484,493,494,502,505,512,522],deby:[],decai:[101,407,487],decid:[3,6,12,16,76,267,305,316,346,510,517],decipher:378,deck:305,declar:204,declin:333,decod:205,decompos:[96,465],decomposit:[3,5,7,18,65,215,299,321],decoupl:[6,516],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,344,375],decrement:322,deepli:372,deeppink:206,deepskyblu:206,def:[12,13,493],defaul:64,defect:[6,75,176,444],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,301,302,303,305,307,309,314,316,317,318,319,320,323,327,331,333,335,336,337,338,339,341,342,343,345,347,348,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,368,369,370,371,373,375,376,378,381,383,384,385,386,387,388,389,390,391,393,394,395,396,398,399,400,401,402,403,404,405,407,408,410,411,412,413,415,416,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,444,445,446,447,448,449,450,451,453,454,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,492,493,495,496,498,499,500,501,504,505,506,507,509,510,512,513,516,518,519,520,521,522,523,524],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,251,275,318,335,347,350,353,355,357,369,373,385,394,397,405,412,416,427,454,461,463,465,482,493,495,497,504,506,521,522],defint:513,deform:[],deg2theta:177,deg:516,degener:[3,301],degrad:[8,18,298,376,504],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,315,316,320,336,337,338,343,359,361,365,368,370,384,410,414,423,505,513,516,523],degrees:198,degress:[158,218],del:509,delai:[3,6,12,387,413,513],deleg:424,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,242,245,270,318,336,337,356,358,374,385,387,390,446,473,495,496,497,498,506,507,512,517,518,520,522,523],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[317,493,522],dellago:[6,237],deloc:[271,416,464],delr:441,delt_lo:509,delta:[],delta_1:397,delta_3:397,delta_7:397,delta_conf:3,delta_ij:[441,454],delta_pi:397,delta_r:454,delta_sigma:397,deltah_f:241,delx:201,delz:201,demand:311,demo:11,demon:296,demonstr:[306,441],den:302,dendrim:423,dendtrit:380,denniston:[9,256,258,259,260,298],denomin:[7,183],denot:[130,234,237,254,298,309,311,407,422,424,457,461,463],dens:[76,227,416],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,298,302,303,305,307,345,350,378,381,385,392,393,397,414,441,442,443,448,449,454,458,464,468,470,471,472,495,504,505,513,521],density_continuity:463,density_summation:463,dent:380,depart:[0,7],departur:[268,306],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,308,311,313,316,317,319,320,321,327,333,336,337,338,340,342,344,345,347,350,353,354,355,356,358,359,360,361,362,364,365,368,370,376,378,384,385,387,388,389,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,441,442,444,445,447,448,449,450,451,453,454,456,457,458,459,464,465,466,474,475,476,478,479,480,481,483,485,486,487,490,492,495,497,498,501,505,507,509,512,513,515,522,523],dependend:6,depflags:12,dephas:[490,509],depos:231,deposit:[],deprec:[3,307,456],deprect:218,depth:[52,156,205,345,418,420,458],dequidt:9,der:[96,119,405,406,437,456,457,486],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,303,307,311,342,343,345,350,351,354,383,385,393,397,405,410,416,417,422,431,435,436,441,444,456,457,474,476,477,486,516],derjagin:486,derlet:297,descend:206,descent:[7,383],descib:[41,205,307],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,299,304,305,306,307,308,309,316,317,322,330,333,334,335,336,337,338,339,340,341,342,343,348,350,351,353,358,375,376,378,382,383,384,385,386,390,393,394,396,398,399,400,402,403,404,405,406,407,410,414,416,417,418,420,421,422,424,427,429,430,431,432,433,434,435,436,437,438,439,440,441,444,445,448,449,453,454,455,456,457,458,459,464,465,466,473,474,475,476,477,478,479,480,481,483,485,486,487,488,490,492,493,495,496,497,498,499,505,508,509,512,517,522,523,525],descript:[],descriptor:[152,202,425],deserno:376,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,270,271,297,298,318,340,345,394,395,396,399,402,407,409,416,437,438,439,442,443,454,457,476],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,301,302,303,304,307,311,316,320,333,336,337,338,339,344,351,366,372,375,376,378,382,384,385,386,411,414,423,438,439,475,478,480,491,492,493,495,499,504,509,510,512,513,522,523,525],desk:7,desktop:[4,6,7,10,12,205],despit:516,destabil:397,destre:368,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,298,301,302,303,305,306,308,309,310,316,320,321,333,336,337,338,339,340,341,343,344,345,346,347,348,349,356,358,360,369,375,376,379,384,385,387,388,391,392,393,394,396,397,399,401,402,403,404,405,406,407,410,411,416,417,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,445,446,448,449,453,456,457,458,464,465,466,474,482,485,486,488,493,495,496,497,498,500,501,504,505,507,510,513,514,517,522,523,527],detect:[2,3,12,43,64,66,95,101,244,302,344,386,406,423,428,490,492,495,506,509,522],determ:[],determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,299,302,303,306,313,314,315,316,317,318,319,323,325,327,333,336,337,338,340,346,347,350,351,352,353,354,355,356,369,375,376,378,385,387,388,391,393,394,401,406,410,413,414,418,419,421,424,425,433,441,444,446,449,457,458,464,473,476,477,481,486,492,495,496,498,500,502,505,509,511,512,514,521,522,523],determinist:321,detil:120,devan:[9,459],devanathan:480,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,275,301,306,307,310,393,397,416,443,444,464,483,497],devemi:9,deviat:[268,275,297,419],deviator:9,devic:[1,3,12,15,17,250,391],device_typ:391,devin:[308,406],devis:443,dfactor:205,dff:516,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,376],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,310,444],dhi:[62,201,230,302],dhug:[268,306],dhugoniot:[268,306],dia:441,diagnost:[],diagon:[3,6,92,152,153,154,228,270,303,316,348,461,463],diagonalstyl:465,diagram:[42,130,177,197,224,299],diallo:423,diam:[205,206,302,385],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,302,305,316,333,335,349,351,385,405,420,421,431,458,482,486,495,496,505],diamond:[378,416,441],diamter:[41,302],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,384,411,413,414,421,446,478,480,503],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,347,375],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,299,301,303,306,307,308,311,314,316,320,322,330,331,333,336,337,338,341,342,343,345,348,349,350,351,354,358,359,369,372,374,375,376,378,379,382,383,385,386,388,389,390,391,392,393,397,401,402,404,405,406,411,412,414,416,418,420,421,422,424,427,429,430,432,433,440,441,442,443,445,446,447,448,449,450,454,456,457,458,459,460,461,463,464,465,466,474,475,476,477,478,480,482,483,486,489,490,492,493,495,497,498,499,500,503,504,505,507,509,510,512,513,514,516,521,522,523,525],differenti:[1,3,6,29,198,317,375,407,454,479],difficult:[228,299,391,423,504],difficulti:[101,118,320,456],diffract:[7,9,130,177,318],diffus:[],diffuse:[4,6],digit:[2,3,206,358,444,522],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:416,dij:320,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,251,351,378,441,498,521,522,523],dimdim:522,dimems:298,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,298,345,378,382,386,454,495,505],dimensionless:[116,133,134,136,139,141,143,148,152,345,376,465,486],dimensions:318,diment:3,dimentionless:147,dimer:[6,316,441],dimgrai:206,dimstr:[42,224],dinola:[303,336],dintel_offload_noaffinity:16,dipol:[],dipolar:[4,29,41,202,203,335,516],dir1:506,dir2:506,dir:[1,3,4,8,10,11,12,268,297,306,332,454,456,457,493,506,522],dirac:152,direc:454,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,247,251,256,298,317,318,337,349,351,352,353,354,378,383,391,392,393,398,400,401,407,410,414,416,429,433,446,451,459,473,493,505,506,507,513,522],directoi:14,directori:[],disabl:[3,12,16,345,428,493,508,522],disadvantag:[6,224],disallow:[202,230,270],disappear:497,discard:[2,3,42,76,220,224,346,354,492,497,498],discontinu:[198,384,435],discourag:441,discov:[13,346],discret:[6,8,41,43,205,206,253,256,292],discuss:[],disk:[6,93,94,101,171,200,231,245,302,493],disloc:[75,444],disord:[40,75,444],disp:[],dispar:458,disperion:[410,433],dispers:[3,6,7,9,176,298,375,376,401,410,433,438,446,457,476,483],displac:[],displace_atom:[],displace_box:62,displacemet:498,displai:[11,13,22,37,45,56,186,197,202,205,360,369,404,474],dispters:3,disregard:444,dissip:[6,9,41,89,90,239,246,253,298,321,342,343,399,411,412,421,438,439,474],dissolut:225,dist:[6,74,100,120,129,202,299,315,413,473,490,523],distanc:[],distinct:[6,234,313,375,458],distinguish:[6,95,152,259,416,494,522],distort:[176,392],distrbut:392,distribut:[],distro:[123,404,453,454],ditto:[8,12,14,15,16,17,18,43,127,226,487,493],div:8,divd:129,diverg:[3,12,40,316,343,393,497,516,525],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,297,341,348,353,375,384,386,417,457,464,483,504,512,522],divis:[6,256,397,427,437,492,513,522],dl_poly:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,344,495,496,500],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:505,dlmp_intel_offload:[9,16],dlo:[62,201,230,302],dlopen:6,dlvo:[7,405,486],dm_lb:256,dmax:[333,382],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,231,245,253,254,265,270,271,276,277,278,282,290,291,293,294,295,302,305,316,330,333,336,337,338,347,351,354,356,358,360,369,374,384,385,386,391,392,393,396,404,406,407,414,415,417,423,424,426,427,441,442,443,446,450,453,454,455,465,474,475,478,480,482,483,493,495,496,497,498,500,503,504,505,512,513,517,522,523,525,526],docuement:458,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,223,224,226,227,228,230,234,236,237,240,241,242,245,246,249,251,253,254,256,259,266,270,271,272,273,274,276,277,278,290,291,292,293,294,295,303,304,305,309,311,314,316,333,336,338,340,341,345,348,349,350,353,354,355,356,361,362,363,365,366,368,374,375,376,377,378,385,386,387,392,393,394,395,396,397,399,401,402,403,405,406,407,408,410,411,413,414,415,416,418,419,420,421,422,424,425,426,427,428,431,432,434,435,436,438,439,441,442,443,444,446,448,449,454,455,456,457,458,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483,485,486,487,488,490,491,492,493,495,496,497,498,499,502,503,505,506,507,508,509,512,513,516,517,522,527],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,330,385,387,391,393,406,415,426,456,457,475,478,479,480,483,495,497],dof:[3,8,124,156,157,158,171,218,316,523],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[385,495],doi:[6,229],domain:[3,6,7,12,13,18,40,42,43,61,64,65,76,130,167,177,180,201,204,205,206,209,216,224,228,230,231,249,252,256,270,271,299,311,316,321,345,350,351,375,376,386,391,413,446,490,492,495,499,512],domin:[1,416,509],don:[0,8,9,12,13,128,181,212,236,254,354,441,464,493,495,517],donadio:337,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,62,65,76,172,175,178,181,198,202,205,206,215,216,218,220,221,222,224,225,226,227,228,230,231,240,241,243,245,250,251,253,254,261,270,276,277,278,290,291,293,295,296,298,299,300,302,305,313,316,318,320,333,336,337,338,340,342,343,356,358,374,375,376,384,386,387,390,391,393,401,414,424,425,426,433,439,440,441,446,448,449,456,473,476,477,482,490,491,492,493,496,499,500,503,513,514,516,517,522,523],donor:423,dot:[153,174,212,236,248,269],doti:[397,454],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,96,184,230,243,304,354,358,374,376,390,391,397,417,422,444,456,457,491,495,499,503,508,522,523],dover:215,down:[3,6,7,8,11,40,76,228,245,253,333,349,416,446,464,494,514],downhil:[382,383],download:[5,7,8,9,11,12,13,17,250,425,455],downsid:6,downward:313,dozen:[8,9,12,119,209,456,457],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[],dpde:263,dpdtheta:[41,89,90,412],dpdtheta_i:[239,240,241],dproduct:394,dr_ewald:[130,318],drag:[],dragforc:256,drai:[268,306],drain:[249,349,384],dramat:[9,62,201,225,226,227,228,230,270,333,336,337,376,446,464,492],drautz:397,draw:205,drawback:305,drawn:[43,202,205,206,246,490],drayleigh:[268,306],dreid:[],dreiding:[],drfourth:116,drho:[125,392,414,448,449],drift:[6,114,116,237,246,247,249,253,254,266,314,333,504,512,516],drive:[11,12,213,228,230,248,270,297,303,316,352,386],driven:[6,190],driver:[6,12,14,15,209,243,250],drop:[3,206,411],droplet:424,drsquar:116,drude:[],drudes:[254,516],dry:242,dsecriptor:425,dsf:[],dsmc:[],dstyle:302,dt_collis:256,dt_lb:256,dt_md:256,dt_srd:333,dtilt:[62,230],dtneb:509,dtqm:306,dtype:[127,226],dual:[16,17,333,391],dudarev:177,due:[1,3,6,9,12,16,17,19,41,55,58,60,61,64,70,75,76,79,80,87,88,95,97,98,99,104,113,114,115,116,117,122,128,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,223,225,226,227,228,229,230,231,236,238,242,243,246,247,250,251,253,254,255,256,259,260,261,266,267,268,269,270,275,284,297,300,302,314,315,316,319,330,332,333,334,336,337,338,339,340,342,343,345,349,350,352,353,354,356,376,382,384,386,387,388,408,411,412,414,419,420,424,438,439,446,454,456,45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26,230,231,243,245,246,253,270,302,313,318,345,346,354,358,374,375,384,385,386,387,389,414,415,424,437,439,444,452,456,457,475,478,480,483,490,493,495,496,497,502,504,505,509,510,511,512,513,514,516,521,522,525,527],ethernet:18,etol:[384,386,490,509],etot0:306,etot:[6,105,107,108,122,153,164,206,234,254,268,306,512,513],eu2:177,eu3:177,euler:[384,386],eulerian:215,euqat:467,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,298,304,307,319,323,327,336,337,338,347,350,353,355,356,358,382,384,444,446,448,449,454,460,462,464,476,477,490,491,493,497,498,500,502,503,504,505,509,511,513,522,523],evaluat:[375,376,522],evalut:[358,493],evan:[166,293],evanseck:[6,20,184,402,507],evapor:[],evaul:[8,384],evdwl:[119,154,456,457,513],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,298,302,311,313,316,318,329,333,341,345,348,350,354,356,367,375,382,384,386,391,396,416,417,421,424,427,446,458,483,484,488,495,496,498,500,501,502,504,505,507,510,512,513,514,516,527],evenli:[3,42,58,153,198,224,256,427,484],event:[],eventu:[3,6,12,15,180,509],eventual:307,ever:[9,55,57,252,333],everaer:[405,420,458,474],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,302,303,304,305,306,307,308,309,311,313,314,316,317,318,320,322,333,335,336,337,338,339,340,341,344,345,346,347,348,356,358,374,376,386,387,388,391,411,413,424,437,456,457,464,470,489,490,491,495,497,499,500,502,503,504,509,510,511,513,517,522,527],everyth:[8,119,517],everywher:[128,431],eviri:416,evolut:[237,247,256,299,490],evolv:[256,299,346],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,346,375,376,384,398,400,401,407,410,416,429,433,451,459,474,476,481],ewald_disp:410,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,246,247,253,254,255,302,311,312,333,345,360,375,404,497,502,509,522,525,527],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,298,305,306,333,338,339,352,391,404,411,414,421,424,438,446,448,449,476,477,497,498,505,509,522],exager:516,examin:[6,8,17,227,298],examp:[493,522],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,242,270,298,313,318,324,325,333,384,391,495,522],exceed:[3,42,62,224,230,270,333,503],excel:416,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,299,308,309,316,319,320,330,333,339,345,353,356,357,358,359,360,361,362,364,365,368,369,370,375,376,378,381,385,386,387,389,390,391,392,393,395,398,399,400,401,402,403,404,405,406,407,409,410,411,414,415,416,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,442,447,450,451,453,456,457,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,492,493,495,497,498,500,503,504,505,506,507,509,513,516,521,522,523,526],exception:493,excess:[220,416],exchang:[2,3,6,8,64,65,209,215,216,237,245,249,253,308,316,341,345,348,375,391,416,510],exchange:375,excit:416,excite:416,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,257,266,301,314,316,340,351,356,384,385,387,399,421,424,427,438,439,446,473,507],exclude:387,exclus:[1,3,12,16,96,184,406,444,446,504,514],excurs:[270,490],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,310,358,374,377,390,491,493,503,506,509,522],exempl:464,exemplari:246,exemplifi:416,exert:[6,251,254,286,311,352,353,354,376],exhaust:[215,390,522],exhibit:[101,237,249,270,383,416,504],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,245,301,302,304,305,356,357,359,361,362,363,365,369,379,385,412,424,456,473,484,491,493,495,496,497,506,507,508,517,522,523,525],exit:[2,3,11,12,42,60,202,224,240,241,374,390,493,494,503,512,522],exlanatori:3,exp6:2,exp:[],expand:[],expans:[12,152,202,506,522],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,245,247,267,297,303,305,306,311,316,356,376,387,404,441,444,446,490,493,495,497,500,504,509,522],expens:[6,76,206,297,301,316,345,356,375,376,387,391,493],experi:[6,13,15,223,231,250,259,269,303,315,316,382,386,411,446,504,509],experienc:[6,12,258,259],experiment:[17,245,375,391,509],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,305,316,330,356,358,374,375,378,385,386,390,396,414,427,464,466,482,493,496,497,500,502,505,516,517,522,527],explan:[3,6,62,125,152,202,203,218,269,297,424,489,492,493,495,504],explanatori:[3,8,129,202,203,217,218,221,316,385,492,522],explantori:[3,312],explic:445,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,317,324,325,360,381,393,394,397,402,404,414,416,428,438,481,489,492,496,499,517],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,305,306,308,316,319,320,338,339,345,353,359,361,362,364,365,368,370,385,391,392,393,395,398,399,400,401,402,403,404,405,406,407,408,410,411,413,414,415,417,418,419,420,421,422,423,424,428,429,430,431,432,433,434,435,436,437,438,442,444,446,447,448,449,450,451,453,458,459,466,467,468,469,470,471,472,474,475,476,477,478,479,480,481,483,485,486,487,495,497,498,504,505,507,508,514,516,517],explictli:[16,508],exploit:[15,17,299],explor:[130,177],expon:[3,307,309,317,414,418,420,423,437,445,459],exponenti:[96,418,454,475,483,487,509,522],expos:11,exposit:[215,411,413],express:[6,152,164,178,210,211,228,267,297,307,317,345,351,358,397,414,416,431,441,464,465,474,522],expression:358,expressiont:397,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,314,315,316,319,322,327,330,332,336,337,338,339,340,342,343,345,347,350,354,355,420,441,444,457,458,465,512,513,521],extensiv:[66,209,513],extent:[1,3,42,43,46,60,76,176,180,202,214,224,251,352,355,375,378,393,460,462,476,477,492,495,498],exterior:[3,6,176,354],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,304,305,306,316,333,384,385,388,389,410,421,424,427,441,446,492,493,495,498,507,516,522],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,309,386,407,417,441,465,493,500,512],extract_atom:11,extract_comput:[11,493],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,270,343,416,479,516],extrema:437,extreme:416,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,347],f_a:[478,479,480],f_ave:129,f_c:479,f_f:480,f_fix_id:306,f_foo:522,f_harm:343,f_i:[29,454],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,265,335,347,513,522],f_ij:454,f_indent:222,f_int:342,f_j:29,f_jj:100,f_k:454,f_langevin:345,f_max:[306,311],f_msst:268,f_r:[254,478,479,480],f_sigma:397,f_solid:343,f_ss:6,face:[3,6,60,62,76,166,176,180,214,350,352,353,354,355,378,420,441,458,495,498],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,302,333,343,421,456,464,507],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,299,303,307,315,317,320,323,325,333,337,341,348,349,350,354,365,376,378,385,391,393,394,397,398,400,402,407,408,409,411,412,416,421,424,428,429,441,444,446,448,449,450,451,457,459,466,475,481,492,495,498,499,504,507,509,510,513,516,521,522],factori:[3,493],factoriz:375,fail:[3,9,11,12,62,182,228,231,375,384,386,409,457,493],failur:[133,461,494,522],fairli:[11,446,504,509,517],faken:78,falcon:250,fall:[3,6,206,221,302,493,522],fals:[95,356,464,522],fame:8,famili:[483,492],familiar:[0,11,517],fan:454,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,270,297,315,316,333,350,361,365,382,386,387,482,493,495,500,513],farago:253,farrel:[478,480],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,305,306,308,316,322,326,332,335,343,345,349,350,351,353,355,386,424,438,498,507,522,526],fasolino:426,fast:[6,7,9,12,13,17,40,202,203,281,306,346,375,376,399,438,439,444,474,476,477,497,502,504,513,523,527],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,303,307,308,316,319,320,333,340,342,345,349,353,359,361,362,364,365,368,370,375,376,388,389,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,498,504,508,516],fastest:[1,6,14,17,166,345,346,391,492],fatal:[3,512],fault:[75,457],faulti:12,fava:420,favor:227,favorit:7,fbmc:340,fcc:[],fcm:[287,522],fcold:237,fdirect:234,fdotr:425,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:414,feedback:[7,250],feel:[7,250,251,259,297,354,356,386,446],felling:443,felt:354,femtosecond:521,fene:[],fennel:[407,429],fep:[],ferguson:[6,184,507],fermi:[1,9,10,12,15,164,391,480],fermion:416,fernando:440,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,254,270,302,305,307,320,347,375,384,385,386,393,464,492,495,500,504,506,514,525],fewer:[1,3,11,15,16,64,259,504],fewest:3,fextern:243,feynman:299,fff:493,ffield:[406,417,456,457,464],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,298,375,376,504],fft_inc:[12,376],fft_lib:12,fft_path:12,fftbench:[375,514],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:473,fictiti:[6,212,213,236,243,247,299,315,407,429,433,473],field1:[496,500],field2:496,field:[],fifth:[6,330,418,450],figur:[1,3,8,12,306,492,493,517],fij:410,file0:297,file1:[11,13,241,297,344,358,385,500,502,506],file2:[11,13,241,344,358,385,500,502,506],file:[],file_from:204,filen:385,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,301,304,307,308,309,312,313,316,317,318,344,345,372,373,374,385,386,392,393,397,407,414,415,417,418,426,441,442,443,448,449,450,454,455,456,457,464,465,475,476,477,478,479,480,483,491,492,493,496,497,502,506,513,522,525,526,527],filennam:502,filep:[3,202,203,206,497,502,527],filepo:313,fill:[7,9,178,205,302,345,378,387,397,444,457,498,517],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,409],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,242,245,269,297,302,303,311,315,382,384,386,387,407,424,429,433,441,448,449,464,474,476,477,516,517,522],find_custom:8,fine:[16,17,182,212,236,343,387,391,517,522],finer:[152,178,522],finest:375,finger:[178,201,267,498],finish:[6,11,42,224,358,372,374,375,388,390,391,482,500,522,523],finit:[],finni:[7,414,474],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,299,304,305,306,308,313,316,320,322,330,331,333,334,335,342,343,344,345,347,351,356,358,359,366,378,384,385,386,387,390,391,392,393,396,397,398,400,402,404,406,407,414,416,417,418,421,422,424,425,426,427,428,429,433,438,439,441,443,444,446,448,449,450,454,456,457,464,465,473,475,476,477,478,479,480,483,487,490,491,492,493,495,496,497,500,502,504,507,508,509,512,513,516,517,522,523,524,525,527],fischer:[6,9,19,20,184,402,507],fit:[3,6,9,12,38,57,198,240,315,333,393,397,426,441,446,448,449,469,476,477,479,503,517,522],five:[78,164,306,385,397,442,495,509],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,303,306],fix_manifoldforc:517,fix_modifi:[],fix_nh:8,fix_nv:517,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:320,fix_reax_bond:456,fix_saed_vtk:318,fix_setforc:8,fix_shak:320,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:410,flag1:[233,389],flag2:[233,389],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,298,305,316,330,332,333,340,344,353,356,371,373,376,385,389,390,391,393,423,428,441,444,473,488,490,492,493,495,496,497,499,500,501,505,517,522],flag_buck:401,flag_coul:[401,410,433],flag_lj:[410,433],flagfld:[399,438,439],flaghi:[3,399,438,439],flaglog:[399,438,439],flagn:233,flagvf:[399,438,439],flat:[6,345,350,351,355],flavor:[2,7,12],fld:[350,438,439],flen:394,flex_press:394,flexibl:[3,6,8,179,205,218,229,247,271,341,348,416,479,513],flip:[3,6,230,270,352,353],floor:522,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,228,245,246,253,256,270,275,297,298,303,321,343,345,368,412],fluid:[],fluid_veloc:260,flush:[3,206,512],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,316,320,346,397,444,513,516],fmackai:9,fmag:232,fmass:299,fmax:[384,513],fmomentum:234,fmsec:[2,206,253,254,267,270,303,316,336,337,504,515,521,523],fname:374,fno:[9,16],fnorm:[384,513],fnpt:234,fnve:237,fnvt:234,foce:424,fock:394,focu:320,fogarti:[9,309,457],foil:[152,297,465],fold:[331,504],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,298,299,301,304,305,306,307,309,311,313,315,316,317,318,320,335,336,337,338,341,342,343,344,345,347,348,356,357,361,362,363,364,365,368,370,373,378,381,384,385,386,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447,448,449,450,451,453,454,455,456,457,458,459,461,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483,485,486,487,488,490,492,493,495,496,498,500,502,503,504,507,509,510,511,516,517,522,523,526],foo:[4,8,11,12,202,205,243,317,493,506,522],foo_species:317,foot:6,footprint:[12,391],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[315,423],forcegroup:256,forcezero:382,ford:410,forestgreen:206,forev:76,forget:[254,516],forgiv:270,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,298,309,311,315,316,317,345,350,354,359,360,363,368,381,383,385,386,393,394,397,404,412,414,416,419,423,424,428,440,441,443,444,448,449,450,451,454,456,457,458,464,465,466,474,476,478,479,480,486,489,492,493,495,500,505,512,516,522],formal:[6,83,86,100,246,247,253,270,299,333,341,464],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,298,301,305,307,309,312,316,317,318,329,344,345,356,357,360,381,385,386,392,393,397,404,414,417,418,428,441,443,448,449,455,456,457,459,465,476,477,483,484,492,493,495,496,497,500,511,512,513,522,524,525],formation:241,former:[6,12,16,40,42,206,224,345,349,397,399,501,507,522],formerli:[7,13],formul:[1,6,9,41,67,153,212,236,253,270,293,307,309,315,320,344,375,393,397,414,416,420,441,453],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,304,313,319,327,331,333,336,337,338,347,350,353,355,356,358,359,360,362,369,378,385,393,394,396,397,402,403,404,405,410,411,414,415,420,421,422,423,425,428,429,431,432,433,435,436,438,439,441,445,446,447,458,459,466,474,475,476,478,479,480,483,485,486,491,495,498,505,512,513,521,522,523],forth:[1,6,11,12,13,14,15,390,493,498,502],fortran:[3,6,9,11,12,13,243,414,424,441,456,457],fortun:8,forward:[3,8,96,374,386,391],foster:[397,453,454],foul:181,found:[3,6,9,12,78,172,202,227,229,237,245,250,256,262,298,340,346,358,374,387,404,407,410,490,496,497,512],four:[6,11,55,88,114,115,152,174,268,345,368,385,386,444,490],fourier:[],fourth:[6,116,315,330,340,402,418,450,464],fox:[6,130,184,472,507],fphi:[38,57,476,477],fpic:12,fplo:[38,57,476,477],fprime:[476,477],fqdn:252,fqq:410,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,225,226,227,228,268,302,306,313,314,333,338,339,378,386,391,397,399,418,421,438,439,500,505],fragment:[43,250,313],fraig:43,frame:[92,152,206,215,268,306,352,420],framer:[205,206],framework:[5,247,392,465],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,297,333,342,343,344,345,383,386,394,416,437,444,447,454,486,492],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,316,320,336,337,338,343,384,410,513,516,523],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[6,237,245,343],freq:214,frequenc:[3,6,16,40,114,206,220,284,298,299,306,311,373,411,416,457,464,490,504,509,522,526],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,225,226,237,242,341,348,446,481,502],fri:[268,306],friction:[4,5,6,9,10,43,209,247,253,306,311,316,345,349,351,421,505],friedrich:323,from:[],front:[268,306,352],frontend:[205,310],frozen:[6,124,182,244,246,254,387,419],fs2:[6,100],fscale:250,fstr:522,fstring:493,ftol:[384,386,490,509],fuchsia:206,fuction:407,fudg:320,fugac:245,fugacity_coeff:245,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,100,205,219,220,229,237,256,297,317,375,376,391,397,414,416,417,420,481,495,497,502,503,507,509,514,516,526],full_energi:[3,245],fuller:384,fulli:[3,6,83,247,252,297,384,386,407,454,455,495,517,524,525],fulton:414,fumi:398,func:[493,522],funcfl:414,functionaliri:229,fund:[0,7],fundament:[333,521],funnel_flow:329,funrol:444,further:[3,4,6,8,12,13,64,66,68,73,76,84,95,102,116,119,128,205,206,209,218,221,222,225,231,235,256,260,299,307,318,321,323,333,345,347,356,376,382,384,385,386,387,392,396,406,444,464,490,509,510,522],furthermor:[27,187,237,317,412,416],furthest:64,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:454,g_p:345,ga3:177,gaa:397,gahler:383,gai:[3,420,474],gain:340,gainsboro:206,galindo:445,game:250,gamma0:29,gamma:[3,6,29,253,256,260,298,306,307,309,311,349,411,412,415,420,441,445,468,471,472,475,478,480,483,513],gamma_:[3,345,351],gamma_ijk:478,gamma_n:[351,421],gamma_p:[3,345],gamma_t:[351,421],gammaa: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1,335],input:[],input_doubl:3,inquir:323,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,245,251,302,375,465,473,493,499,516],insertion:[3,231,245,302],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,242,245,251,256,259,302,316,333,350,352,353,354,355,356,373,378,493,494,495,497,498,505,522],inside:[256,431,493,509],insight:[6,13],instabl:[256,410,463],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,376,386,401,402,425,429,433,437,444,490,496,497,502,510,517,527],install:[],instanc:[6,9,11,210,229,247,352,419,424,446,454,493,516],instantan:[6,66,227,228,246,247,270,275,298,303,306,311,313,316,340,501,513],instanti:[6,11,12,215,424,492],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,184,198,202,203,211,218,221,222,224,228,229,245,253,256,259,260,298,304,305,314,316,335,353,373,375,376,379,387,391,400,401,414,428,430,437,441,444,447,474,481,490,498,502,509,511,516,522],institut:[9,250,301],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,308,316,319,320,353,359,361,362,364,365,368,370,376,391,392,393,395,398,399,400,401,402,403,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,475,476,478,479,480,481,483,485,486,487,498,504,516],instruction:11,insuffici:[3,6,12],insult:270,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,231,236,238,242,243,245,248,253,266,304,305,314,316,333,345,350,354,355,356,358,374,385,387,391,405,420,424,452,458,476,488,492,493,495,496,500,503,504,512,513,522,523],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,243,245,246,247,250,253,254,255,256,298,301,302,305,306,311,316,333,335,337,340,344,345,364,375,378,399,411,412,413,427,441,456,457,461,463,465,490,492,493,494,495,503,504,505,509,512,522,523],integer:[3,495],integr:[],integral:[299,448,449],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,246,455,495],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,242,249,259,268,270,275,313,316,318,333,341,345,347,348,512,513,521],intensiv:[66,209,513],intepol:522,inter:[14,18,43,64,65,158,181,182,202,227,253,255,269,308,316,375,386,397,505,516,522,525,527],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,244,245,250,251,253,255,259,284,297,299,301,302,307,309,315,316,317,324,325,333,334,340,345,349,350,351,354,355,360,361,362,363,365,367,369,375,376,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,451,452,453,454,457,458,459,461,463,464,465,466,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,490,493,495,497,499,500,504,505,507,512,513,516,525],interatom:[3,4,7,9,10,178,202,269,342,343,392,397,414,416,425,441,444,464,479,522],intercept:130,interchang:6,interconnect:18,interconvert:416,intereract:40,interesect:354,interest:[1,5,7,8,9,11,13,76,177,299,340,343,376,415,439,456,457,493,522],interf:[391,517],interfac:[],interfer:[12,270,393],interg:[6,516],intergr:504,interi:439,interior:[3,6,42,354,498],interlac:441,interleav:[6,178,503],intermedi:[6,12,62,205,269,297,368,386,493,494,503,507],intermix:490,intermolecular:[154,393],intern:[],internal:[3,205,211,302,522],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:252,interpenetr:441,interpentr:[468,469,471],interpol:[6,15,38,57,111,198,205,206,215,240,241,256,297,375,376,386,397,446,448,449,457,470,476,477,478],interpret:[2,6,11,205,221,421,466,490,493,509,522],interrupt:306,intersect:[3,6,130,206,354,356,498],intersert:354,interspers:384,interstiti:[176,444],intertia:[3,104],interv:[3,6,100,204,219,253,270,306,311,312,325,464,470,490,509,522],intestieti:130,intial:[6,391,393],intiial:[42,500],intiti:[3,332],intra:316,intra_energi:245,intramolecular:[29,154,245],introduc:[6,9,101,118,205,237,270,306,311,316,368,375,392,407,416,429,433,437,475,509,522],introduct:[],intuit:378,inv:[130,177,318],invalid:[3,12,76,98,181,284,386,438,439,497],invari:[118,145,150,152],invent:320,invers:[],inverse:516,invert:[1,6,182,298],invis:354,invoc:[176,227,391,461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244,245,246,247,248,249,250,251,253,254,255,265,267,270,272,273,274,275,276,277,278,279,280,284,287,288,290,291,293,294,295,298,299,301,302,303,305,307,308,311,314,315,316,319,320,322,330,332,333,334,336,337,338,339,341,342,343,344,345,347,348,349,350,351,353,354,355,356,358,359,361,362,364,365,366,368,370,374,375,376,378,381,383,384,385,386,387,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,483,485,486,487,489,490,491,492,493,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,512,513,514,516,517,521,522,523,524,525,527],young:[421,460,462],your:[],yourself:[6,8,12,13,228,385,517],yplane:351,ypo:178,ysu:[3,202,203,335,496],yuan:9,yukawa:[],yukawa_1_1:484,yxz:492,yzx:492,z_i:[416,480,487],z_j:[480,487],z_meam:441,zachari:13,zannoni:420,zbl:[],zblcut:480,zblcutinn:465,zblcutout:465,zblexpscal:480,zblz:465,zcm:316,zcylind:351,zepeda:216,zero:[],zeta:[3,256,307,417],zfactor:205,zflag:[165,166,257,259,266,316,340],zhang:[316,341,421],zhi:[3,6,180,202,214,344,350,353,355,495,498,513],zhi_bound:[6,202],zhou:[13,397,417,454,478,480],zhu:472,ziegenhain:13,ziegler:[301,441,474,480,487],zimmerman2004:215,zimmerman2010:215,zimmerman:[9,75,215,397],zlat:[230,251,513],zlib:[9,202],zlim:464,zlo:[3,6,180,202,214,344,350,352,353,355,495,498,513],zlo_bound:[6,202],zmax:[214,256,522],zmin:[256,522],zn2:177,zone:[130,318],zoom:[3,202,205,206],zorig:76,zplane:351,zr4:177,zrest:332,zsu:[3,202,203,335,496],zwall:350,zwall_veloc:256,zxy:492,zybin:457,zyx:492},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,298,299,302,303,304,305,306,308,311,313,314,316,318,333,335,340,341,342,343,346,348,350,352,356,369,373,375,376,378,379,382,383,385,387,388,389,391,394,397,399,416,438,439,444,446,456,457,473,474,490,491,492,495,496,498,500,502,503,504,507,509,511,512,513,514,515,521,523,525,526],"function":522,"long":[220,398,400,401,402,403,407,409,410,429,433,437,451,459,481],"new":8,"static":12,acceler:1,account:517,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:517,addition:[12,13,517],addtorqu:213,adiabat:6,adjust_dt:323,adp:392,after:517,airebo:393,alloi:414,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,305,522],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,394],axel:517,balanc:[42,224],barostat:6,basal:71,beck:395,berendsen:[303,336],between:6,binary2txt:13,bodi:[6,8,43,72,157,273,277,282,291,396],body:9,bond:[8,13,73,74,225,226,227,312],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:397,born:[398,409],boundari:[7,60],box:[6,61,228],branch:517,brownian:399,buck:[400,401,409,440],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:517,change_box:62,charmm:[6,20,184,402,437],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,359,403],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,350,405,486],colvar:[13,229],colvars:9,com:[79,80,159],comb3:406,comb:[308,406],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,522],compute_modifi:113,condit:7,conduct:[6,341],constant:[6,522],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:361,coul:[398,400,401,402,403,407,408,409,422,429,433,437,451,459],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:337,csvr:337,cubic:431,cuda:14,custom:[8,202,203],cut:[50,394,400,403,407,410,416,419,429,430,437,445,451,481],cvff:362,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[407,429],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],diagnost:7,diel:408,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,410],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:363,distribut:[7,12],document:0,dpd:[9,89,90,411,412],drag:232,dreid:423,dreiding:6,drude:[6,9,163,233,234,254,516],dsf:[407,429],dsmc:413,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:307,eam:[13,414],echo:208,edip:415,eff:[9,13,107,108,162,164,169,255,271,283,294,339,416],efield:236,ehex:237,eim:417,elastic:6,emac:13,energi:[135,412],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:242,event:95,exampl:[4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],exp6:418,exp:[27,187],expand:[47,432],extend:[8,11],extern:243,fcc:297,fdt:412,featur:[7,8,517,522],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:307,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246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8,130,151,152,157,165,172,174,175,176,197,201,202,205,208,216,217,218,220,221,258,266,267,305,315,333,334,344,354,392,418,422,455,456,495,509,511,521],columnar:175,colvar:[],colvarmodul:12,com:[],comamnd:229,comand:226,comannd:390,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:407,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,155,156,170,201,204,214,220,236,244,249,258,261,269,285,291,298,304,320,336,345,353,356,358,374,375,377,382,390,404,406,407,411,415,416,417,423,435,436,464,474,477,479,480,482,485,497,502,507,515,521,523],come:[],comfort:[12,13],comit:516,comm:[0,3,11,12,63,77,203,249,251,252,375,385,390,410,445,452,475,476,496],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,183,197,201,239,240,253,315,316,344,384,385,391,413,414,416,417,427,440,447,448,449,456,463,464,474,475,476,477,478,479,482,491,492,494,515,516,521],commerci:7,commit:[9,516],commmand:[3,6,12,61,118,293,426,488,489,491,508,525],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,179,201,204,206,369,421,430,464,477,479,494,497,506],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,175,180,181,204,205,223,224,225,227,228,229,249,251,255,257,258,259,269,297,304,306,307,308,315,320,332,344,355,372,374,386,387,388,390,411,412,451,487,491,492,503,504,521,524,526],communc:374,comp:[7,203,251,252,285,291,319,375,385,415,445,452,457,471,475,476,478],compact:[65,208,403,473],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,129,160,176,185,196,205,233,306,355,357,374,375,383,385,440,463,489,508,509,515,520],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:379,compass:[7,9,20,21,36,43,44,55,184,185,196,358,359,368,402,473],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,130,188,201,206,210,216,217,218,220,221,223,236,297,309,336,339,346,349,352,374,390,424,443,445,475,491,492,521],compens:[6,224,225,313,386,415],compet:343,competit:375,compil:[3,7,8,9,12,13,14,15,16,17,18,175,201,203,204,206,249,343,375,390,443,494,495,499,515,521],compl:16,complain:[11,12,16],complement:440,complementari:[7,406,428],complet:[3,6,9,11,12,14,41,61,75,205,223,228,258,298,301,304,332,343,345,356,357,373,385,390,416,460,462,481,489,494,499,502,506,508,511,515,521],complex:[4,6,8,11,12,13,24,40,42,64,100,117,151,153,165,177,178,255,285,328,353,372,385,415,443,475,476,492,494,497,521],compli:[339,343],complic:[6,7,9,12,13,215,244,492],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,138,141,142,143,144,147,148,149,151,152,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,172,173,174,200,201,202,204,205,211,212,216,217,218,219,220,221,222,226,227,229,230,235,236,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,318,319,321,325,326,329,332,335,336,337,339,346,347,352,353,354,374,377,382,383,384,385,390,410,415,420,437,438,460,462,463,464,494,495,504,512,521,522],componenet:6,composit:[6,215,255,413],compound:[405,415,416,482],compres:[75,125,217],compress:[],compris:[40,353,417,457,481],compton:[129,176],comptu:3,compuat:375,comput:[],computation:[3,6,224,225,344,396],computational:515,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[129,317],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:176,concaten:[2,3,525],concav:353,concentr:[75,240,316,413,417,448,476],concept:[6,157,167,217,503],conceptu:[3,6,75,165,227,229,385,406,423,440,499],concern:[6,77,95,203,245],concetr:75,concis:[11,343],conclud:12,concret:8,concurr:[15,375,521],conden:[344,477,479],condens:[6,159,344,392,408,413,428,482],condit:[],conducit:6,conduct:[],cone:497,confer:443,confid:[3,508],config:[12,201,491],configfil:228,configur:[1,2,6,12,14,16,37,61,133,179,197,200,201,204,208,227,228,229,230,234,244,251,252,283,298,306,343,372,383,385,392,396,414,440,443,474,477,479,482,489,494,496,497,508,516],confin:[494,508],conflict:[3,12,40,202,445,492,516],conform:[3,6,13,61,226,227,268,314,321,343,367,385,415,506],confus:[3,482],conjuct:[9,410],conjug:[7,8,252,382,415,455,456],conjunct:[6,7,75,94,95,125,160,165,171,177,181,205,209,210,252,255,259,283,301,302,306,307,308,310,315,320,332,340,347,352,374,375,385,397,399,403,406,410,415,422,428,445,450,458,480,494,497,501,515,526],connect:[3,6,9,95,162,180,226,249,300,315,319,329,379,385,407,420,455,456,472,479,491,492,494,498,515],conner:392,connor:392,conput:3,consecut:[3,11,12,39,75,177,205,209,210,230,249,250,406,428,432,489,495,497],consequ:[1,6,215,344,427,508],conserv:[3,9,28,208,215,226,233,234,245,248,252,254,255,259,265,267,269,283,285,315,319,320,335,336,340,347,348,352,385,409,410,411,420,434,463,503,508],consid:[6,74,75,82,95,126,159,162,163,180,201,202,205,209,210,216,218,223,225,226,230,256,270,297,315,339,340,343,344,347,375,403,415,423,456,457,463,472,489,490,492,495,496,497,499,502,504,512,515,521],consider:[6,8,252,253,335,336,337,390,503],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,157,160,162,177,189,200,206,211,212,217,229,230,233,235,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,316,335,336,337,338,348,374,375,377,379,384,385,390,392,396,398,404,406,415,419,423,426,437,438,440,443,445,447,448,457,460,462,463,475,476,483,492,494,495,496,497,498,499,506,515,521],consistent_fe_initi:214,consit:315,constant:[],constantli:236,constitu:[3,6,258,315,349,353,404,457],constitut:[460,462],constrain:[3,6,8,9,154,155,156,157,158,160,163,164,165,166,167,169,170,208,217,230,236,244,245,250,258,261,263,285,291,300,301,313,315,319,330,340,347,383,384,415,499,506,515],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,129,151,176,227,269,297,314,316,353,386,390,409,443,445,472,474,475,476,497,498,513,521],constructor:[8,11],consult:456,consum:[1,310,451,521],consumpt:372,contact:[],contact_stiff:[459,461],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,129,151,153,157,165,175,176,177,179,183,185,196,197,201,202,204,205,206,208,209,210,214,216,217,218,220,221,223,228,230,235,239,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,317,322,332,339,343,344,353,354,357,373,375,384,385,388,389,391,392,393,396,405,406,409,413,414,415,417,423,424,440,443,447,448,449,453,454,455,456,464,474,475,476,477,478,479,480,482,489,490,491,492,494,495,496,497,499,501,503,506,508,509,511,512,515,516,521,524,526],content:[4,8,9,12,17,456,510,512],context:[3,6,8,12,16,127,128,205,224,225,230,300,312,348,382,485,494,501,510,520,521,522],contibut:74,contigu:491,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,173,205,208,209,210,215,217,218,219,220,221,223,226,227,228,229,230,236,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,317,321,331,332,334,341,342,344,350,353,357,373,389,390,396,410,412,430,433,455,456,457,460,462,478,489,492,494,496,497,502,508,509,511,512,521,524],continuum:[6,7,9,214,344,460,462],contour_integr:214,contract:[61,227,229,269,302,315],contradictori:3,contrain:319,contraint:283,contrari:[246,253],contrast:[1,6,42,55,66,159,162,202,229,355,460,462,485,525],contrib:344,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,210,215,216,217,218,220,221,227,244,252,255,258,259,264,270,292,293,300,301,309,312,315,317,319,346,374,383,385,393,410,412,413,415,423,437,438,443,445,455,456,463,506,512,515,516],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,133,151,186,201,202,204,208,214,215,223,227,228,229,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,316,323,324,335,336,337,344,348,372,374,387,415,419,443,455,456,459,461,474,479,489,491,503,509,510],control_typ:214,controlfil:456,convect:99,conveni:[6,12,28,201,206,221,317,377,464,480,516,521],convent:[3,8,28,188,195,196,202,205,314,329,356,413,415,521],converg:[3,6,41,96,201,202,204,206,211,223,226,227,235,242,274,285,291,305,307,310,314,319,381,382,383,385,405,406,428,463,489,501,508],convers:[3,8,151,204,205,215,218,302,374,406,407,408,415,428,432,436,450,492,508,520],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,177,184,201,204,205,218,221,267,301,304,355,358,360,364,367,377,385,391,413,443,477,479,486,492,494,495,496,501,511,515,520,521,524,526],convex:[42,353],convinc:[7,12],cook:9,cooki:7,cool:[7,167,236,248,313],cooordin:[201,202],cooper:[5,7],coord123:125,coord1:[3,125,217],coord2:[3,125,217],coord3:[3,125,217],coord:[],coordb:463,coordbb:463,coordiat:383,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,145,151,160,166,172,174,175,177,181,200,201,202,203,204,205,206,208,211,216,217,220,223,224,225,226,227,228,229,230,233,235,236,237,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,318,319,321,326,329,330,331,332,334,342,343,344,351,352,354,355,377,383,384,385,390,391,392,395,414,463,489,494,495,496,497,499,502,504,508,515,521,522],coordn:[125,217],coords:463,copi:[0,3,4,8,9,11,12,14,16,40,130,204,344,385,403,455,492,516],copper:486,coproccesor:15,coprocessor:[1,7,9,15,16,390,507],coproprocessor:16,copy_arrai:8,copyright:[7,8,300],coral:205,core:[],core_shel:159,cores:515,coreshel:[4,6,9],coreshell:[],cornel:[6,183,506],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,204,353,354,377,481,494,516],cornflowerblu:205,cornsilk:205,corp:9,corpor:15,corr:405,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,159,164,171,183,202,204,229,236,244,246,252,269,270,292,300,302,305,343,349,353,374,385,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,484,485,486,487,494,509,512,515,516],correction_max_iter:214,correctli:[3,8,11,16,75,87,112,113,114,154,155,156,158,160,162,163,164,165,166,169,170,173,201,205,211,230,235,242,253,263,269,270,308,315,319,329,331,350,353,385,386,390,408,438,443,491,492,494,504,516,520,522],correl:[],correpond:[239,240],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,138,141,142,143,144,145,147,148,149,151,154,155,164,171,175,176,183,184,185,186,187,188,189,191,192,194,195,197,200,201,202,204,205,209,210,211,217,219,220,222,225,227,229,236,237,240,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,316,318,319,339,349,350,352,353,354,356,358,359,360,361,363,364,367,369,375,380,382,384,385,391,392,394,397,398,399,400,401,402,403,404,405,406,409,410,413,414,415,416,417,418,419,420,421,422,423,426,428,429,430,431,432,433,434,435,436,437,440,441,443,445,446,448,449,450,452,453,455,456,457,458,463,464,465,474,475,476,477,478,479,480,482,484,485,486,489,491,492,494,495,497,507,508,509,511,512,515,521],correspondingli:[437,438,503],corrupt:3,cosin:[],cosineshift:26,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,129,152,176,204,205,217,223,224,225,241,269,307,344,374,375,388,406,428,432,443,445,474,491,503],costheta0:[474,477,479,482],costheta:453,costli:[11,96,246,386],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,157,167,172,174,190,201,202,204,205,209,210,217,218,223,229,242,251,304,305,306,310,313,315,318,332,333,339,343,344,345,349,353,355,357,365,371,373,381,383,386,390,392,393,418,422,423,426,455,456,490,491,492,494,496,498,501,502,509,510,515,521,522],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,152,178,182,306,308,345,374,375,383,390,397,399,400,401,402,405,406,407,408,409,415,420,421,423,428,432,436,439,445,450,455,456,458,463,473,479,480,482,485,499,506,512,515,520],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,165,175,181,183,211,212,215,217,220,222,223,230,235,241,244,250,269,283,301,319,335,336,353,375,383,384,385,387,390,418,422,445,512,521],counter:[3,350,489,500,502,508],counteract:244,counterbal:[236,248],counterbalanc:28,counterclockwis:183,counterpart:[201,315,489],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:322,cours:[3,8,137,139,171,201,209,210,245,314,329,343,349,351,352,354,355,375,437,465,491,494,507,515,521,524],courtesi:377,cov:463,coval:[6,9,28,415,440,463,515],covari:246,cover:[6,12,75,197,205,214,255,415,481],coverag:75,cpc:251,cpp:[1,3,6,8,9,11,12,13,95,201,209,210,242,319],cpu:[1,3,9,10,12,14,15,16,17,65,75,205,219,233,253,345,372,375,390,403,473,489,507,508,511,512,513,521],cpuremain:512,cpus:12,cr2:176,cr3:176,crack:[4,386],crada:[5,7],crai:[5,7,13,17,201],crash:[3,12,386,515],craympi:390,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:214,create_faceset:214,create_group:203,create_nodeset:214,createatom:[],creation:[],crimson:205,critchlei:300,criteria:[3,127,178,204,205,224,225,226,264,383,452,481,496,499,521],criterion:[12,41,132,177,180,215,223,226,244,283,307,322,350,355,383,385,405,415,420,463,499,508,509],criterioni:508,critic:[6,48,49,267,339,344,383],crmax:75,crmin:75,cross:[3,12,21,75,97,155,175,185,201,202,204,216,225,229,266,268,292,315,325,329,331,340,347,359,377,385,401,410,412,413,421,422,423,428,430,432,453,458,460,462,477,479,486,494,498,504,524],crossov:1,crossterm:494,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,77,117,296,297,342,377,386,494,498,512,515],crystallin:[6,113,297,377,478,515],crystallis:339,crystallogr:[129,176],crystallograph:[377,512],crystallographi:[129,176,377],cs1:176,cs_chunk:6,cs_im:[40,494],cs_re:[40,494],csanyi:[151,454,464],cscl:440,csequ:6,csh:[11,12,403],cshrc:[11,12],csic:[414,474,477,479,482],csinfo:6,csisi:[414,474,477,479,482],csld:[],cst:413,cstherm:6,cstyle:491,csvr:[],ctcm:[391,413],ctemp_core:233,cterm:321,ctr:9,ctype:11,cu1:176,cu2:176,cu3au:440,cube:[6,175,180,233,353,377,515],cubes:[41,223],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:396,cummul:[3,6,221,224,225,226,228,241,246,252,254,332,335,336,337,338,340,347,422,512],cumul:[6,215,217,220,234,244,252,267,269,274,283,315,317,385],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,141,152,157,165,167,173,175,178,181,200,201,202,203,204,205,206,209,210,214,217,221,223,224,225,226,227,228,229,230,234,235,236,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,316,319,320,321,322,323,324,325,326,328,330,331,332,335,336,337,343,344,347,348,349,350,351,352,354,355,357,372,373,374,375,378,379,380,382,383,384,385,390,396,403,405,409,413,415,416,420,423,424,427,437,438,440,441,442,445,453,455,456,459,460,461,462,465,477,479,480,483,489,490,491,492,494,495,496,497,498,500,501,502,504,506,508,509,511,512,516,521,522,523,524,525,526],curv:[6,177,244,285,291,297],curvatur:[419,457,486],custom:[],cut0:492,cut1:503,cut2:503,cut:[],cuthi:[296,308],cutinn:[398,437,438],cutlo:[296,308],cutmax:453,cutoff1:[402,409,428,432,436,439,450,458],cutoff2:[397,399,400,402,408,409,428,432,436,439,450,458,480],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,151,175,178,180,181,225,226,231,239,240,296,305,306,308,310,312,315,320,332,345,349,353,355,372,374,375,383,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,457,458,463,464,465,466,467,468,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,492,496,499,503,515,521],cutoffa:414,cutoffc:414,cuu3:413,cval:176,cvd:339,cvel:321,cvff:[],cwiggl:[3,266,349,352,354,521],cyan:[2,204,205],cycl:[3,244,267,269,270,274],cyclic:[3,183,197],cygwin:12,cylind:[3,4,75,204,217,250,291,301,350,353,379,497],cylinder_d:379,cylindr:[6,250,329,350],cypress:390,cyrot:396,cyrstal:297,d3q15:255,d3q19:255,d_double_double:14,d_e:344,d_flag2:304,d_flag:304,d_name:[124,201,304,334,504],d_single_double:14,d_single_single:14,d_sx:304,d_sy:304,d_sz:304,daan:342,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,208,213,252,253,254,259,269,270,274,291,302,305,306,310,315,335,336,348,350,351,382,383,385,397,399,401,406,409,415,420,428,436,450,458,473,480,508,515],damp_com:253,damp_drud:253,dampen:[315,515],dampflag:[350,420],dan:16,danger:[3,12,244,355,410,512],dangl:180,daniel:9,darden:[375,409],darkblu:205,darkcyan:205,darken:204,darkgoldenrod:205,darkgrai:205,darkgreen:205,darkkhaki:205,darkmagenta:205,darkolivegreen:205,darkorang:205,darkorchid:205,darkr:205,darksalmon:205,darkseagreen:205,darkslateblu:205,darkslategrai:205,darkturquois:205,darkviolet:205,dasgupta:306,dash:[420,511],dat:[6,99,197,214,490],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,317],dataset:317,datatyp:3,date:[0,4,6,12,13,200,455,456,521],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,201,218],davenport:439,davi:349,david:[9,18,374,375,477,479],daw:[413,453],dbg:[],dcd:[3,6,7,201,203,204,205,206,298,495,499],dcs:9,ddim:200,deactiv:436,dealt:251,debug:[6,7,11,12,13,16,57,129,133,176,177,298,303,372,374,424,445,483,492,493,501,504,511,521],deby:[],decai:[100,406,486],decid:[3,6,12,15,75,266,304,315,345,509,516],decipher:377,deck:304,declar:203,declin:332,decod:204,decompos:[95,464],decomposit:[3,5,7,17,64,214,298,320],decoupl:[6,515],decreas:[3,201,202,211,212,219,226,229,235,236,242,244,252,343,374],decrement:321,deepli:371,deeppink:205,deepskyblu:205,def:[12,13,492],defaul:63,defect:[6,74,175,443],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,183,184,185,186,187,188,189,191,192,194,195,196,197,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,233,234,235,238,240,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,319,322,326,330,332,334,335,336,337,338,340,341,342,344,346,347,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,372,374,375,377,380,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,406,407,409,410,411,412,414,415,417,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,438,439,443,444,445,446,447,448,449,450,452,453,455,456,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,494,495,497,498,499,500,503,504,505,506,508,509,511,512,515,517,518,519,520,521,522,523],definit:[2,3,6,8,12,13,82,85,127,151,205,217,218,219,220,221,229,238,250,274,317,334,346,349,352,354,356,368,372,384,393,396,404,411,415,426,453,460,462,464,481,492,494,496,503,505,520,521],defint:512,deform:[],deg2theta:176,deg:515,degener:[3,300],degrad:[8,17,297,375,503],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,176,177,183,184,187,188,195,197,200,204,217,226,233,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,319,335,336,337,342,358,360,364,367,369,383,409,413,422,504,512,515,522],degrees:197,degress:[157,217],del:508,delai:[3,6,12,386,412,512],deleg:423,delet:[2,3,7,8,12,54,59,62,65,175,180,181,208,217,218,220,221,224,226,241,244,269,317,335,336,355,357,373,384,386,389,445,472,494,495,496,497,505,506,511,516,517,519,521,522],delete_atom:[],delete_bond:[],delete_el:214,deli:200,delimit:[316,492,521],dellago:[6,236],deloc:[270,415,463],delr:440,delt_lo:508,delta:[],delta_1:396,delta_3:396,delta_7:396,delta_conf:3,delta_ij:[440,453],delta_pi:396,delta_r:453,delta_sigma:396,deltah_f:240,delx:200,delz:200,demand:310,demo:11,demon:295,demonstr:[305,440],den:301,dendrim:422,dendtrit:379,denniston:[9,255,257,258,259,297],denomin:[7,182],denot:[129,233,236,253,297,308,310,406,421,423,456,460,462],dens:[75,226,415],densiti:[3,6,7,9,17,40,41,61,110,127,137,151,163,175,177,209,210,214,217,223,229,242,255,258,262,263,297,301,302,304,306,344,349,377,380,384,391,392,396,413,440,441,442,447,448,453,457,463,467,469,470,471,494,503,504,512,520],density_continuity:462,density_summation:462,dent:379,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,130,151,153,154,160,164,165,171,177,178,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,204,205,208,209,210,211,212,215,217,219,220,221,222,223,225,227,229,235,237,240,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,316,318,319,320,326,332,335,336,337,339,341,343,344,346,349,352,353,354,355,357,358,359,360,361,363,364,367,369,375,377,383,384,386,387,388,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,440,441,443,444,446,447,448,449,450,452,453,455,456,457,458,463,464,465,473,474,475,477,478,479,480,482,484,485,486,489,491,494,496,497,500,504,506,508,511,512,514,521,522],dependend:6,depflags:12,dephas:[489,508],depos:230,deposit:[],deprec:[3,306,455],deprect:217,depth:[51,155,204,344,417,419,457],dequidt:9,der:[95,118,404,405,436,455,456,485],deriv:[6,7,8,9,37,56,65,95,151,171,197,218,227,229,236,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,341,342,344,349,350,353,382,384,392,396,404,409,415,416,421,430,434,435,440,443,455,456,473,475,476,485,515],derjagin:485,derlet:296,descend:205,descent:[7,382],descib:[40,204,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,129,141,151,152,155,156,157,161,162,165,168,170,171,175,176,177,179,180,189,194,197,201,202,203,208,209,210,217,218,219,220,221,223,226,227,228,229,230,232,233,239,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,316,321,329,332,333,334,335,336,337,338,339,340,341,342,347,349,350,352,357,374,375,377,381,382,383,384,385,389,392,393,395,397,398,399,401,402,403,404,405,406,409,413,415,416,417,419,420,421,423,426,428,429,430,431,432,433,434,435,436,437,438,439,440,443,444,447,448,452,453,454,455,456,457,458,463,464,465,472,473,474,475,476,477,478,479,480,482,484,485,486,487,489,491,492,494,495,496,497,498,504,507,508,511,516,521,522,524],descript:[],descriptor:[151,201,424],deserno:375,design:[0,3,6,7,8,11,13,14,16,129,159,162,176,214,226,232,233,269,270,296,297,317,339,344,393,394,395,398,401,406,408,415,436,437,438,441,442,453,456,475],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,152,159,177,190,200,217,221,227,229,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,319,332,335,336,337,338,343,350,365,371,374,375,377,381,383,384,385,410,413,422,437,438,474,477,479,490,491,492,494,498,503,508,509,511,512,521,522,524],desk:7,desktop:[4,6,7,10,12,204],despit:515,destabil:396,destre:367,destroi:[9,11,39,224,225],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,130,151,152,154,155,156,157,160,170,171,172,174,177,178,181,182,185,196,200,201,202,204,205,208,209,210,214,217,218,219,220,221,223,225,226,227,228,229,230,236,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,319,320,332,335,336,337,338,339,340,342,343,344,345,346,347,348,355,357,359,368,374,375,378,383,384,386,387,390,391,392,393,395,396,398,400,401,402,403,404,405,406,409,410,415,416,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,444,445,447,448,452,455,456,457,463,464,465,473,481,484,485,487,492,494,495,496,497,499,500,503,504,506,509,512,513,516,521,522,526],detect:[2,3,12,42,63,65,94,100,243,301,343,385,405,422,427,489,491,494,505,508,521],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,138,152,165,166,175,176,177,200,201,202,204,205,206,207,211,212,213,216,217,218,219,220,221,222,223,227,229,230,233,235,240,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,318,322,324,326,332,335,336,337,339,345,346,349,350,351,352,353,354,355,368,374,375,377,384,386,387,390,392,393,400,405,409,412,413,417,418,420,423,424,432,440,443,445,448,456,457,463,472,475,476,480,485,491,494,495,497,499,501,504,508,510,511,513,520,521,522],determinist:320,detil:119,devan:[9,458],devanathan:479,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,249,274,300,305,306,309,392,396,415,442,443,463,482,496],devemi:9,deviat:[267,274,296,418],deviator:9,devic:[1,3,12,14,16,249,390],device_typ:390,devin:[307,405],devis:442,dfactor:204,dff:515,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,375],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,443],dhi:[61,200,229,301],dhug:[267,305],dhugoniot:[267,305],dia:440,diagnost:[],diagon:[3,6,91,151,152,153,227,269,302,315,347,460,462],diagonalstyl:464,diagram:[41,129,176,196,223,298],diallo:422,diam:[204,205,301,384],diamet:[3,6,40,42,124,177,201,202,204,205,209,210,252,301,304,315,332,334,348,350,384,404,419,420,430,457,481,485,494,495,504],diamond:[377,415,440],diamter:[40,301],dick:6,dicsuss:266,dictat:[215,267],did:[3,12,383,410,412,413,420,445,477,479,502],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,173,346,374],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,131,151,153,154,155,156,157,158,160,163,164,165,166,167,169,170,171,177,178,180,185,196,197,200,201,204,205,208,210,213,215,217,220,223,224,225,226,227,228,229,233,236,239,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,319,321,329,330,332,335,336,337,340,341,342,344,347,348,349,350,353,357,358,368,371,373,374,375,377,378,381,382,384,385,387,388,389,390,391,392,396,400,401,403,404,405,410,411,413,415,417,419,420,421,423,426,428,429,431,432,439,440,441,442,444,445,446,447,448,449,453,455,456,457,458,459,460,462,463,464,465,473,474,475,476,477,479,481,482,485,488,489,491,492,494,496,497,498,499,502,503,504,506,508,509,511,512,513,515,520,521,522,524],differenti:[1,3,6,28,197,316,374,406,453,478],difficult:[227,298,390,422,503],difficulti:[100,117,319,455],diffract:[7,9,129,176,317],diffus:[],diffuse:[4,6],digit:[2,3,205,357,443,521],dih_table1:197,dih_table2:197,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,198],dihedraltyp:225,dihydrid:415,dij:319,dilat:[],dim1:3,dim2:3,dim:[3,61,75,154,158,159,160,163,164,165,166,167,169,177,200,229,250,350,377,440,497,520,521,522],dimdim:521,dimems:297,dimens:[],dimensinon:75,dimension:[3,39,100,123,129,151,154,157,158,159,160,163,164,165,166,167,169,176,199,217,268,297,344,377,381,385,453,494,504],dimensionless:[115,132,133,135,138,140,142,147,151,344,375,464,485],dimensions:317,diment:3,dimentionless:146,dimer:[6,315,440],dimgrai:205,dimstr:[41,223],dinola:[302,335],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,201,202,334,515],dir1:505,dir2:505,dir:[1,3,4,8,10,11,12,267,296,305,331,453,455,456,492,505,521],dirac:151,direc:453,direct:[],directli:[3,6,8,9,11,12,95,124,151,153,201,202,203,204,211,235,246,250,255,297,316,317,336,348,350,351,352,353,377,382,390,391,392,397,399,400,406,409,413,415,428,432,445,450,458,472,492,504,505,506,512,521],directoi:[],directori:[],disabl:[3,12,15,344,427,492,507,521],disadvantag:[6,223],disallow:[201,229,269],disappear:496,discard:[2,3,41,75,219,223,345,353,491,496,497],discontinu:[197,383,434],discourag:440,discov:[13,345],discret:[6,8,40,42,204,205,252,255,291],discuss:[],disk:[6,92,93,100,170,199,230,244,301,492],disloc:[74,443],disord:[39,74,443],disp:[],dispar:457,disperion:[409,432],dispers:[3,6,7,9,175,297,374,375,400,409,432,437,445,456,475,482],displac:[],displace_atom:[],displace_box:61,displacemet:497,displai:[11,13,21,36,44,55,185,196,201,204,359,368,403,473],dispters:3,disregard:443,dissip:[6,9,40,88,89,238,245,252,297,320,341,342,398,410,411,420,437,438,473],dissolut:224,dist:[6,73,99,119,128,201,298,314,412,472,489,522],distanc:[],distinct:[6,233,312,374,457],distinguish:[6,94,151,258,415,493,521],distort:[175,391],distrbut:391,distribut:[],distro:[122,403,452,453],ditto:[8,12,14,15,16,17,42,126,225,486,492],div:8,divd:128,diverg:[3,12,39,315,342,392,496,515,524],divid:[3,6,15,41,99,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60,63,70,123,153,201,202,203,204,205,218,219,227,229,233,246,269,298,300,301,310,315,319,332,374,375,381,386,390,396,404,406,423,428,432,443,447,448,457,475,501,526],efficient:[9,300],effort:[5,7,495],efftemp:[106,107,163],efi:[455,456],efield:[],eflux:248,eforc:202,eggebrecht:[406,463],ehb:[455,456],ehex:[],eigensolv:3,eigenvalu:[297,298,374],eigtol:3,eike:171,eim:[],eimp:512,eindhoven:9,einstein:[6,310,342],either:[1,2,3,6,8,9,10,11,12,14,15,16,21,32,41,44,50,61,65,75,113,118,124,127,129,151,152,157,159,160,175,176,177,180,185,190,197,201,202,203,204,205,208,216,218,220,221,223,226,227,228,229,230,236,244,250,251,255,259,266,267,269,270,274,292,296,304,312,315,316,318,319,321,329,332,339,346,350,353,357,359,372,374,375,377,382,383,387,390,396,398,404,413,417,423,424,426,437,438,440,443,445,448,451,453,472,476,477,479,481,489,492,494,496,497,498,501,503,506,509,511,521],ejtehadi:[404,419,457],elaplong:[209,210,250,497,512,521],elaps:[3,200,209,210,211,212,222,229,235,247,248,250,252,253,266,301,318,326,335,336,337,349,350,352,354,465,489,497,499,500,504,508,512,521],elast:[4,6,7,9,44,45,46,55,122,208,268,297,350,382,385,420,452,478],elastic:[],elastic_t:4,elba:28,electr:[6,208,214,235,253,374,375,416,455,456,486,515,520],electrolyt:[9,485],electron:[3,6,7,9,13,40,106,107,124,129,161,163,168,202,208,214,232,233,253,254,270,282,293,308,338,344,382,384,391,393,405,409,413,415,416,440,443,453,454,463,479,482,486,494,514,515,520],electron_integr:214,electron_temperatur:214,electron_unit:415,electroneg:[6,306,307,308,405,416,463],electroneg_compon:463,electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,15,17,215,244,306,308,309,345,374,375,404,409,415,428,436,438,456,463,485],eleftheri:315,elem1:[416,440,464],elem2:[416,440,464],elem:463,element1:[312,391,413,463],element2:[312,391,413,463],element:[3,6,7,8,9,12,13,42,65,87,97,113,115,123,128,130,145,151,152,153,154,155,156,157,158,159,160,164,165,166,167,169,170,173,201,202,203,204,205,206,208,209,214,218,220,221,297,312,339,346,391,392,396,405,413,414,415,416,423,424,425,440,441,442,443,449,453,454,455,456,463,464,474,477,478,479,482,512,515,521,525],elementn:[391,413],elementset:214,elev:508,elif:[151,357],elig:[3,215,224,225,241,244,422],elimin:[3,6,75,175,245,252,253,315,319,341,342,489],elj:409,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,75,90,155,199],ellipsoid:[3,4,6,7,9,13,40,42,75,90,124,141,155,177,199,200,201,202,252,266,271,275,279,280,285,289,315,332,379,380,383,419,438,457,473,494,504,524],ellipsoidflag:494,elong:[233,253,512],elp:[455,456],els:[3,7,8,12,75,118,127,128,130,204,216,217,218,220,221,244,269,315,332,344,345,346,355,357,374,423,493,505,521,525],elsewher:[8,266,332,440,454,455,456,506,512,521],elt:440,emac:[],email:[0,3,5,7,8,9,11,416],emb:[3,9,353],emb_lin_neg:440,embed:[3,4,5,7,9,11,12,13,28,96,153,175,344,391,413,416,436,440,441,442,453,473,483,492],embt:184,emi:[7,9],emile:9,emol:[455,456,512],emphas:420,empir:[9,214,336,415],empiric:392,emploi:[236,297,306,310,478],empti:[3,59,75,175,179,315,374,386,427,494,505,506,521],empty:3,enabl:[3,6,8,9,11,12,13,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,32,34,36,37,39,40,43,45,46,47,48,49,50,51,53,54,55,56,62,63,64,66,70,82,85,91,95,96,106,107,108,109,110,111,115,118,122,123,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,154,155,156,159,161,163,164,168,169,171,175,176,183,184,186,187,188,189,190,191,192,194,195,196,197,201,202,203,205,206,208,209,210,211,212,213,215,219,222,224,225,226,228,229,230,235,236,237,241,242,243,244,245,246,247,249,250,251,252,253,254,255,256,257,258,259,261,262,263,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,284,285,287,288,289,290,291,292,293,294,296,297,298,300,301,305,306,307,308,309,310,311,312,314,315,318,319,321,322,323,324,325,326,328,329,331,332,338,339,340,341,342,344,345,347,349,350,351,352,353,356,358,360,361,363,364,365,367,368,369,375,383,385,389,390,391,392,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,445,446,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,492,495,496,497,501,503,513,521,526],enclos:[2,6,12,179,201,303,357,440,463,490,492,502,521],encod:[13,39,42,201,204,205,304,423],encompass:[3,6,40,42,59,61,127,178,328,346,473,497],encount:[3,8,12,61,117,220,389,499,521],encourag:[7,8,309,330],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,180,181,184,200,201,202,204,205,206,209,210,218,220,221,226,229,236,245,250,252,254,268,269,270,283,291,302,314,315,321,332,335,336,337,338,340,343,344,347,351,354,355,373,374,384,385,389,390,410,413,419,426,439,443,457,460,462,464,465,483,489,492,494,495,496,497,499,501,502,506,510,512,515,521,526],end_of_step:8,endbondtors:[3,184,190,494],endif:8,energet:[226,392,456],energi:[],energy_compon:463,energy_update_freq:456,enforc:[6,9,59,60,114,200,201,202,203,204,206,208,215,226,229,269,295,297,307,315,319,357,374,428,491,521,522],enforce2d:[],eng:[11,68,73,119,201,242,355,357,405,442],eng_previ:357,engiliti:9,engilitycorp:9,engin:229,engineer:[214,300,321,341,413],enginer:441,enhanc:[210,214,236,489],enlarg:[61,204],enough:[3,40,63,94,177,178,180,181,223,253,301,305,310,315,345,349,350,353,386,390,406,451,494,498,499],enpub:413,ensembl:[],ensight:6,ensur:[3,6,151,201,202,215,219,227,244,245,269,322,343,375,396,412,436,474,482],enter:[59,167,416,443,482,508],enthalpi:[134,271,272,273,316,413,511,512,521],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,152,157,176,177,205,208,209,210,217,223,226,228,236,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,316,330,344,346,357,390,409,432,445,475,476,494,502,503],entireti:481,entiti:[6,8,40,42,201,315],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,138,141,142,143,144,145,147,148,149,175,197,202,205,209,220,228,239,240,305,355,384,396,414,440,447,448,449,456,464,474,475,476,477,478,479,482,521],entries:205,entropi:508,entry1:[37,56,205,403,447,448,475,476],entry2:205,entryn:205,enumer:[178,201,487],enumuer:6,env:390,environ:[1,3,6,11,12,15,16,17,204,246,251,296,390,391,396,403,405,414,415,453,477,491,505,521],eos:[9,239,240],epair:[118,205,392,418,422,455,456,512],epen:[455,456],epfl:[246,251],epp:409,epq:409,eps0:485,eps14:436,eps:[452,473],epsilon0:479,epsilon:[3,6,35,45,46,50,53,54,95,183,209,210,244,315,332,349,353,381,383,395,401,402,404,406,407,408,409,417,419,421,422,423,426,427,428,429,430,431,432,433,434,435,436,439,444,450,457,458,468,474,480,481,484,485,503,515,520],epsilon_0:486,epsilon_14:401,epsilon_:457,epsilon_d:407,epsilon_i:[419,445,457],epsilon_i_:457,epsilon_i_a:[419,457],epsilon_i_b:[419,457],epsilon_i_c:[419,457],epsilon_ij:445,epsilon_j:[419,445,457],epsilon_j_:457,epsilon_j_a:[419,457],epsilon_j_b:[419,457],epsilon_j_c:[419,457],epsilon_lj:457,epton:452,eqch:172,eqeq:[455,456],eqp:409,eqq:409,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,130,152,155,171,173,175,177,200,204,205,208,209,210,211,212,215,218,219,220,221,222,223,227,229,230,235,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,316,318,321,326,328,335,336,337,340,341,342,344,346,347,349,352,354,355,357,373,377,383,385,386,387,389,390,392,405,410,411,418,419,422,426,437,443,444,453,455,456,457,459,460,461,463,464,465,475,476,481,482,486,490,491,492,494,496,497,501,502,505,508,510,512,521,522],equat:[3,6,7,8,9,99,117,123,129,176,185,196,208,227,233,234,236,238,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,316,319,320,332,340,344,347,349,350,352,354,374,375,379,404,409,410,411,415,416,417,420,425,437,438,440,445,448,457,460,462,467,468,470,471,476,486,515],equation:[246,296,367],equi:270,equidist:268,equil:[3,306,378,501,526],equilater:504,equilibr:[3,4,5,6,7,9,61,99,177,208,215,218,226,227,244,267,269,270,292,293,302,305,306,307,308,340,341,342,347,405,406,455,456,490,504],equilibria:347,equilibribum:[224,225],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,160,161,184,186,227,229,244,245,246,253,255,269,274,292,305,306,310,314,319,321,329,332,339,340,342,347,358,360,364,367,405,440,449,463,515],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:214,equival:[6,12,13,28,61,63,135,136,144,149,175,179,205,220,221,227,229,244,252,269,292,302,314,315,352,392,410,415,463,477,479,480,494,497,502,503,512,515],equlibrium:6,equliibr:[306,308],er3:176,eradiu:[40,124,202,415,494],eras:[318,341],erat:[229,438],erc:406,erfc:[406,428,445],erforc:[124,202],erg:520,erhart:[215,413,477,479],ermscal:393,ernst:9,eror:3,eros:440,erose_form:440,erot:[],errata:[477,479],erratum:349,erron:3,error:[],erta:420,ervel:[124,202,494],escap:[230,515],especi:[8,15,165,177,208,215,223,244,305,310,313,314,390,491],espresso:[9,309],essenti:[11,12,26,96,139,158,159,160,163,164,165,166,167,169,186,218,297,348,375,392,406,428,479,499,512],essential:[8,274],essex:28,establish:[95,248],estim:[1,3,6,10,12,37,41,56,99,152,214,223,234,267,332,339,374,375,381,445,456,475,476,508,512],estimat:3,esu:520,esub:440,eta:[6,255,269,305,306,308,348,414,416,419,453,478,482,520],eta_dot:269,eta_ij:453,eta_ji:416,etag:[40,494],etail:512,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,152,154,157,158,159,160,161,163,164,165,166,167,169,171,177,179,180,181,190,201,202,204,205,208,209,214,215,216,217,220,221,224,225,229,230,242,244,245,252,269,301,312,317,344,345,353,357,373,374,383,384,385,386,388,413,414,423,436,438,443,451,455,456,474,477,479,482,489,492,494,495,496,501,503,504,508,509,510,511,512,513,515,520,521,524,526],ethernet:17,etol:[383,385,489,508],etot0:305,etot:[6,104,106,107,121,152,163,205,233,253,267,305,511,512],eu2:176,eu3:176,euler:[383,385],eulerian:214,euqat:466,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,130,151,153,157,167,175,177,183,200,201,202,204,205,209,210,211,212,214,216,217,218,219,220,221,222,229,235,245,247,248,250,251,252,253,297,303,306,318,322,326,335,336,337,346,349,352,354,355,357,381,383,443,445,447,448,453,459,461,463,475,476,489,490,492,496,497,499,501,502,503,504,508,510,512,521,522],evaluat:[374,375,521],evalut:[357,492],evan:[165,292],evanseck:[6,19,183,401,506],evapor:[],evaul:[8,383],evdwl:[118,153,455,456,512],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,130,175,178,179,193,197,201,202,205,208,209,210,215,216,217,220,221,223,224,225,227,229,230,233,236,250,253,267,269,270,297,301,310,312,315,317,328,332,340,344,347,349,353,355,366,374,381,383,385,390,395,415,416,420,423,426,445,457,482,483,487,494,495,497,499,500,501,503,504,506,509,511,512,513,515,526],evenli:[3,41,57,152,197,223,255,426,483],event:[],eventu:[3,6,12,14,179,508],eventual:306,ever:[9,54,56,251,332],everaer:[404,419,457,473],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,130,139,165,180,201,202,203,204,205,206,208,209,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,234,236,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,317,319,321,332,334,335,336,337,338,339,340,343,344,345,346,347,355,357,373,375,385,386,387,390,410,412,423,436,455,456,463,469,488,489,490,494,496,498,499,501,502,503,508,509,510,512,516,521,526],everyth:[8,118,516],everywher:[127,430],eviri:415,evolut:[236,246,255,298,489],evolv:[255,298,345],ewald:[2,3,5,6,7,8,9,12,96,121,129,152,345,374,375,383,397,399,400,406,409,415,428,432,450,458,473,475,480],ewald_disp:409,ewalddisp:3,exact:[21,41,44,75,133,171,180,185,223,226,245,246,252,253,254,301,310,311,332,344,359,374,403,496,501,508,521,524,526],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,155,161,168,177,197,209,210,220,223,229,234,239,245,252,253,254,270,282,283,293,297,304,305,332,337,338,351,390,403,410,413,420,423,437,445,447,448,475,476,496,497,504,508,521],exager:515,examin:[6,8,16,226,297],examp:[492,521],exampl:[],exce:[3,6,15,16,17,41,60,75,179,216,217,220,221,223,227,229,234,241,269,297,312,317,323,324,332,383,390,494,521],exceed:[3,41,61,223,229,269,332,502],excel:415,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,177,181,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,205,208,211,217,218,220,222,223,227,229,237,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,318,319,329,332,338,344,352,355,356,357,358,359,360,361,363,364,367,368,369,374,375,377,380,384,385,386,388,389,390,391,392,394,397,398,399,400,401,402,403,404,405,406,408,409,410,413,414,415,416,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,441,446,449,450,452,455,456,457,458,465,473,474,475,477,478,479,480,482,484,485,486,489,491,492,494,496,497,499,502,503,504,505,506,508,512,515,520,521,522,525],exception:492,excess:[219,415],exchang:[2,3,6,8,63,64,208,214,215,236,244,248,252,307,315,340,344,347,374,390,415,509],exchange:374,excit:415,excite:415,exclud:[3,6,9,12,15,16,65,75,112,123,151,157,164,165,181,201,217,224,225,256,265,300,313,315,339,350,355,383,384,386,398,420,423,426,437,438,445,472,506],exclude:386,exclus:[1,3,12,15,95,183,405,443,445,503,513],excurs:[269,489],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,178,204,249,309,357,373,376,389,490,492,502,505,508,521],exempl:463,exemplari:245,exemplifi:415,exert:[6,250,253,285,310,351,352,353,375],exhaust:[214,389,521],exhibit:[100,236,248,269,382,415,503],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,133,177,178,196,203,204,205,208,213,222,225,227,230,244,300,301,303,304,355,356,358,360,361,362,364,368,378,384,411,423,455,472,483,490,492,494,495,496,505,506,507,516,521,522,524],exit:[2,3,11,12,41,59,201,223,239,240,373,389,492,493,502,511,521],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,151,201,505,521],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,158,169,175,197,223,235,244,246,266,296,302,304,305,310,315,355,375,386,403,440,443,445,489,492,494,496,499,503,508,521],expens:[6,75,205,296,300,315,344,355,374,375,386,390,492],experi:[6,13,14,222,230,249,258,268,302,314,315,381,385,410,445,503,508],experienc:[6,12,257,258],experiment:[16,244,374,390,508],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,157,165,197,201,202,204,205,208,217,218,221,223,225,227,229,269,285,296,304,315,329,355,357,373,374,377,384,385,389,395,413,426,463,465,481,492,495,496,499,501,504,515,516,521,526],explan:[3,6,61,124,151,201,202,217,268,296,423,488,491,492,494,503],explanatori:[3,8,128,201,202,216,217,220,315,384,491,521],explantori:[3,311],explic:444,explicit:[6,9,11,21,44,81,95,124,127,171,185,209,210,229,316,323,324,359,380,392,393,396,401,403,413,415,427,437,480,488,491,495,498,516],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,154,164,167,175,177,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,229,237,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,318,319,337,338,344,352,358,360,361,363,364,367,369,384,390,391,392,394,397,398,399,400,401,402,403,404,405,406,407,409,410,412,413,414,416,417,418,419,420,421,422,423,427,428,429,430,431,432,433,434,435,436,437,441,443,445,446,447,448,449,450,452,457,458,465,466,467,468,469,470,471,473,474,475,476,477,478,479,480,482,484,485,486,494,496,497,503,504,506,507,513,515,516],explictli:[15,507],exploit:[14,16,298],explor:[129,176],expon:[3,306,308,316,413,417,419,422,436,444,458],exponenti:[95,417,453,474,482,486,508,521],expos:11,exposit:[214,410,412],express:[6,151,163,177,209,210,227,266,296,306,316,344,350,357,396,413,415,430,440,463,464,473,521],expression:357,expressiont:396,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,130,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,202,208,211,212,215,221,222,228,231,235,236,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,318,321,326,329,331,335,336,337,338,339,341,342,344,346,349,353,354,419,440,443,456,457,464,511,512,520],extensiv:[65,208,512],extent:[1,3,41,42,45,59,75,175,179,201,213,223,250,351,354,374,377,392,459,461,475,476,491,494,497],exterior:[3,6,175,353],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,129,152,154,155,156,158,160,163,164,165,166,167,169,170,176,177,178,179,205,220,223,225,269,303,304,305,315,332,383,384,387,388,409,420,423,426,440,445,491,492,494,497,506,515,521],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,130,209,210,308,385,406,416,440,464,492,499,511],extract_atom:11,extract_comput:[11,492],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,204,219,227,229,269,342,415,478,515],extrema:436,extreme:415,extrins:214,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[173,346],f_a:[477,478,479],f_ave:128,f_c:478,f_f:479,f_fix_id:305,f_foo:521,f_harm:342,f_i:[28,453],f_id:[6,75,128,130,201,202,208,216,217,218,219,220,221,264,334,346,512,521],f_ij:453,f_indent:221,f_int:341,f_j:28,f_jj:99,f_k:453,f_langevin:344,f_max:[305,310],f_msst:267,f_r:[253,477,478,479],f_sigma:396,f_solid:342,f_ss:6,face:[3,6,59,61,75,165,175,179,213,349,351,352,353,354,377,419,440,457,494,497],face_threshold:175,facet:175,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,246,301,332,342,420,455,463,506],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,129,151,171,176,179,183,194,200,201,204,205,209,210,218,223,227,229,230,236,244,249,252,254,255,267,269,270,274,298,302,306,314,316,319,322,324,332,336,340,347,348,349,353,364,375,377,384,390,392,393,396,397,399,401,406,407,408,410,411,415,420,423,427,428,440,443,445,447,448,449,450,456,458,465,474,480,491,494,497,498,503,506,508,509,512,515,520,521],factori:[3,492],factoriz:374,fail:[3,9,11,12,61,181,227,230,374,383,385,408,456,492],failur:[132,460,493,521],fairli:[11,445,503,508,516],faken:77,falcon:249,fall:[3,6,205,220,301,492,521],fals:[94,355,463,521],fame:8,famili:[482,491],familiar:[0,11,516],fan:453,far:[3,6,12,16,59,61,63,94,201,202,205,206,223,224,225,227,230,269,296,314,315,332,349,360,364,381,385,386,481,492,494,499,512],farago:252,farrel:[477,479],farther:201,fashion:[6,8,41,75,177,205,208,209,210,215,223,225,230,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,321,325,331,334,342,344,348,349,350,352,354,385,423,437,497,506,521,525],fasolino:425,fast:[6,7,9,12,13,16,39,201,202,280,305,345,374,375,398,437,438,443,473,475,476,496,501,503,512,522,526],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,154,164,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,223,229,237,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,318,319,332,339,341,344,348,352,358,360,361,363,364,367,369,374,375,387,388,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,409,410,413,414,416,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,441,446,449,450,452,457,458,465,473,474,475,477,478,479,480,482,484,485,486,489,497,503,507,515],fastest:[1,6,16,165,344,345,390,491],fatal:[3,511],fault:[74,456],faulti:12,fava:419,favor:226,favorit:7,fbmc:339,fcc:[],fcm:[286,521],fcold:236,fdirect:233,fdotr:424,fdt:[],fdti:95,fe2:176,fe3:176,fe_md_boundari:214,featu:8,featur:[],fecr:413,feedback:[7,249],feel:[7,249,250,258,296,353,355,385,445],felling:442,felt:353,femtosecond:520,fene:[],fennel:[406,428],fep:[],ferguson:[6,183,506],fermi:[1,9,10,12,14,163,390,479],fermion:415,fernando:439,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,206,216,217,218,220,221,236,253,269,301,304,306,319,346,374,383,384,385,392,463,491,494,499,503,505,513,524],fewer:[1,3,11,14,15,63,258,503],fewest:3,fextern:242,feynman:298,fff:492,ffield:[405,416,455,456,463],ffmpeg:[3,12,204],ffplai:204,fft:[1,3,7,9,11,12,14,96,120,121,152,297,374,375,503],fft_inc:[12,375],fft_lib:12,fft_path:12,fftbench:[374,513],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:236,ficiti:472,fictiti:[6,211,212,235,242,246,298,314,406,428,432,472],field1:[495,499],field2:495,field:[],fifth:[6,329,417,449],figur:[1,3,8,12,305,491,492,516],fij:409,file0:296,file1:[11,13,240,296,343,357,384,499,501,505],file2:[11,13,240,343,357,384,499,501,505],file:[],file_from:203,filen:384,filenam:[3,12,13,37,41,56,197,201,202,204,205,206,214,217,218,219,220,221,223,228,239,240,296,300,303,306,307,308,311,312,315,316,317,343,344,371,372,373,384,385,391,392,396,406,413,414,416,417,425,440,441,442,447,448,449,453,454,455,456,463,464,474,475,476,477,478,479,482,490,491,492,495,496,501,505,512,521,524,525,526],filennam:501,filep:[3,201,202,205,496,501,526],filepo:312,fill:[7,9,177,204,301,344,377,386,396,443,456,497,516],filter:[205,214],final_integr:8,final_integrate_respa:8,finchham:[6,159,408],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,180,197,206,215,226,227,239,240,241,244,268,296,301,302,310,314,381,383,385,386,406,423,428,432,440,447,448,463,473,475,476,515,516,521],find_custom:8,fine:[15,16,181,211,235,342,386,390,516,521],finer:[151,177,521],finest:374,finger:[177,200,266,497],finish:[6,11,41,223,357,371,373,374,387,389,390,481,499,521,522],finit:[],finni:[7,413,473],finverse:233,fiorin:[9,228],fire:[],firebrick:205,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,138,141,144,145,149,152,162,165,171,173,175,176,178,179,180,184,197,201,202,203,204,205,206,208,209,217,218,220,221,223,226,229,239,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,319,321,329,330,332,333,334,341,342,343,344,346,350,355,357,358,365,377,383,384,385,386,389,390,391,392,395,396,397,399,401,403,405,406,413,415,416,417,420,421,423,424,425,426,427,428,432,437,438,440,442,443,445,447,448,449,453,455,456,463,464,472,474,475,476,477,478,479,482,486,489,490,491,492,494,495,496,499,501,503,506,507,508,511,512,515,516,521,522,523,524,526],fischer:[6,9,18,19,183,401,506],fit:[3,6,9,12,37,56,197,239,314,332,392,396,425,440,445,447,448,468,475,476,478,502,516,521],five:[77,163,305,384,396,441,494,508],fix:[],fix_deposit:3,fix_ehex07:236,fix_flux:214,fix_heat:236,fix_id:[3,227,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:516,fix_modifi:[],fix_nh:8,fix_nv:516,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:319,fix_reax_bond:455,fix_saed_vtk:317,fix_setforc:8,fix_shak:319,fix_srd:3,fixedpoint:[227,269],fixextern:242,fixid:214,fji:409,flag1:[232,388],flag2:[232,388],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,172,176,180,198,201,202,204,205,206,221,226,228,232,249,252,256,258,265,266,297,304,315,329,331,332,339,343,352,355,370,372,375,384,388,389,390,392,422,427,440,443,472,487,489,491,492,494,495,496,498,499,500,504,516,521],flag_buck:400,flag_coul:[400,409,432],flag_lj:[409,432],flagfld:[398,437,438],flaghi:[3,398,437,438],flaglog:[398,437,438],flagn:232,flagvf:[398,437,438],flat:[6,344,349,350,354],flavor:[2,7,12],fld:[349,437,438],flen:393,flex_press:393,flexibl:[3,6,8,178,204,217,228,246,270,340,347,415,478,512],flip:[3,6,229,269,351,352],floor:521,flop:12,floralwhit:205,flow:[],fluctuat:[6,66,95,227,244,245,252,255,269,274,296,297,302,320,342,344,367,411],fluid:[],fluid_veloc:259,flush:[3,205,511],flux:[],flv:204,fly:[7,9,12,41,204,208,214,219,230,233,315,319,345,396,443,512,515],fmackai:9,fmag:231,fmass:298,fmax:[383,512],fmomentum:233,fmsec:[2,205,252,253,266,269,302,315,335,336,503,514,520,522],fname:373,fno:[9,15],fnorm:[383,512],fnpt:233,fnve:236,fnvt:233,foce:423,fock:393,focu:319,fogarti:[9,308,456],foil:[151,296,464],fold:[330,503],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,130,151,152,155,156,157,163,165,170,173,175,177,178,183,186,187,188,189,191,192,194,195,197,201,203,204,205,208,214,215,216,217,218,219,220,221,223,228,229,230,233,234,238,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,317,319,334,335,336,337,340,341,342,343,344,346,347,355,356,360,361,362,363,364,367,369,372,377,380,383,384,385,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,43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210],improv:[0,1,9,15,39,41,205,223,236,248,269,297,390,422,428,443,445,456,474,478],imrop:366,in3:176,inaccur:[1,3,6,180,267,374],inaccuraci:353,inact:422,inappropri:177,incid:[129,176,230],includ:[],include:[12,371],includelink:9,includig:[357,373],inclus:[],inclusion:12,incom:249,incompat:[3,11,261,285,291,424],incomplet:[3,11,494],incompress:[270,415],inconsist:[3,181,226,495],inconveni:377,incorpor:[305,396,407,516],incorrect:[3,160,252,440],incorrectli:[3,377,420,521],increas:[1,3,6,17,37,56,59,61,120,129,152,197,201,202,204,205,219,224,225,226,229,236,239,240,244,252,302,313,314,315,340,343,347,374,375,385,390,392,415,419,447,448,456,475,476,478,492,503,508,521],increasingli:415,increment:[3,11,139,211,212,222,223,230,235,241,269,301,321,322,355,373,389,426,463,489,492,506,508,521],incur:[16,217,241,344,491],inde:160,indefatig:7,indefinit:341,indent:[],independ:[4,6,9,11,12,15,16,41,61,65,86,99,128,130,163,177,200,208,216,217,218,220,221,223,226,227,228,229,230,245,247,252,253,255,258,269,297,302,306,310,315,317,321,331,342,344,377,420,443,489,492,511,522],indetermin:[201,202,205],index:[0,3,6,8,11,12,37,39,40,56,57,71,73,128,130,175,197,201,205,216,218,239,240,249,251,298,317,344,355,356,357,380,389,445,447,448,455,456,475,476,483,494,509,521],indianr:205,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,152,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,173,184,197,201,204,209,210,227,269,297,315,344,355,358,367,374,384,386,405,412,416,423,440,443,445,449,455,456,463,477,479,491,493,494,496,512,516,521],indigo:205,indirectli:[6,304,521],indistinguish:252,indium:464,individu:[],induc:[],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,151,165,204,229,269,297,374,387],inelig:215,inerti:438,inertia:[],inexpens:[246,503],inf:[2,3,12,347,497],infer:[3,104,106,107,171,211,212,223,224,225,235,249,300,332,340,347,377,403,416,494,506,512],infil:[3,13,315,491],infin:[3,383,499,512],infininti:204,infinit:[3,230,243,250,252,255,297,332,344,350,351,375,377,415,494,498,520],infinitesim:6,inflect:[407,430,473],influenc:[3,9,41,85,159,266,301,374,375,445,477,478,479],inform:[0,1,2,3,6,7,8,9,11,12,13,14,16,39,41,42,61,63,64,65,71,96,126,128,129,176,177,183,201,202,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,233,234,235,236,237,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,317,318,319,322,329,330,332,333,335,336,337,338,339,340,341,343,346,347,348,349,351,352,353,354,356,372,374,375,378,382,383,384,385,386,388,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,409,410,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,450,452,453,454,455,456,457,458,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,482,484,485,486,487,491,492,494,495,496,498,499,501,506,508,509,511,513,521,523,524,525,526],informat:[8,12,495],infrequ:[6,269,410,489,508],infti:[407,437,438],ingtegr:396,inher:[374,383,445],inherit:[6,480],inhomogen:[17,344,445],inidividu:383,init:[3,8,313,463],init_fil:344,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,141,173,178,179,197,200,201,202,204,205,206,209,210,213,214,218,223,225,226,227,229,237,239,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,318,320,331,332,334,339,341,342,343,344,345,346,349,350,351,352,354,355,357,374,378,382,383,385,392,393,409,410,412,443,447,448,454,455,456,463,475,476,489,491,492,494,496,497,499,501,502,504,508,509,512,515,521,522,524,526],initial:[2,3,6,87,113,179,521],initial_integr:8,initial_integrate_respa:8,initialis:454,initialt:344,inlclud:11,inlin:492,inner2:[401,421],inner:[3,8,15,57,201,250,357,373,381,382,383,385,389,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,409,410,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,452,454,455,456,457,458,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,503,508,521],inner_distance_cutoff:422,innergroup:258,innermost:[37,56,75,388,475,476,503],innernod:258,innner:434,inordin:345,inorgan:[6,482],inp:[228,357,464,482],input1:[68,71,73,84,102,119,124,125,126,128,130,334],input2:[68,71,73,84,102,119,124,125,126,128,130,334],input:[],input_doubl:3,inquir:322,insensit:12,insert:[3,5,7,8,9,12,61,177,208,230,244,250,301,374,464,472,492,498,515],insertion:[3,230,244,301],insid:[2,3,6,8,11,75,140,146,177,201,202,205,216,230,231,236,241,244,250,255,258,301,315,332,349,351,352,353,354,355,372,377,492,493,494,496,497,504,521],inside:[255,430,492,508],insight:[6,13],instabl:[255,409,462],instal:[1,3,6,8,9,11,12,14,15,16,175,201,203,204,206,375,385,400,401,424,428,432,436,443,489,495,496,501,509,516,526],install:[],instanc:[6,9,11,209,228,246,351,418,423,445,453,492,515],instantan:[6,65,226,227,245,246,269,274,297,302,305,310,312,315,339,500,512],instanti:[6,11,12,214,423,491],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,155,159,181,183,197,201,202,210,217,220,221,223,227,228,244,252,255,258,259,297,303,304,313,315,334,352,372,374,375,378,386,390,399,400,413,427,429,436,440,443,446,473,480,489,497,501,508,510,515,521],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,154,164,175,183,184,186,187,188,189,191,192,194,195,197,199,204,211,222,229,237,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,318,319,352,358,360,361,363,364,367,369,375,390,391,392,394,397,398,399,400,401,402,404,405,406,409,410,413,414,416,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,441,446,449,450,452,457,458,465,474,475,477,478,479,480,482,484,485,486,497,503,515],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,16,39,40,63,77,112,114,177,178,197,201,202,204,205,211,224,225,230,235,237,241,242,244,247,252,265,303,304,313,315,332,344,349,353,354,355,357,373,384,386,390,404,419,423,451,457,475,487,491,492,494,495,499,502,503,511,512,521,522],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,130,151,175,177,180,181,183,187,188,192,197,200,201,204,205,215,217,224,225,226,230,232,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,332,334,336,339,343,344,363,374,377,398,410,411,412,426,440,455,456,460,462,464,489,491,492,493,494,502,503,504,508,511,521,522],integer:[3,494],integr:[],integral:[298,447,448],integrate_ulsph:[],intel:[],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,219,245,454,494],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,129,130,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,172,173,174,176,208,217,218,220,221,223,224,225,226,234,241,248,258,267,269,274,312,315,317,332,340,344,346,347,511,512,520],intensiv:[65,208,512],intepol:521,inter:[17,42,63,64,157,180,181,201,226,252,254,268,307,315,374,385,396,504,515,521,524,526],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,133,134,135,136,138,139,140,141,142,143,144,146,147,148,149,151,152,153,155,156,170,171,175,178,179,180,181,182,183,185,189,190,193,196,201,202,208,209,210,224,225,226,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,316,323,324,332,333,339,344,348,349,350,353,354,359,360,361,362,364,366,368,374,375,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,450,451,452,453,456,457,458,460,462,463,464,465,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,489,492,494,496,498,499,503,504,506,511,512,515,524],interatom:[3,4,7,9,10,177,201,268,341,342,391,396,413,415,424,440,443,463,478,521],intercept:129,interchang:6,interconnect:17,interconvert:415,intereract:39,interesect:353,interest:[1,5,7,8,9,11,13,75,176,298,339,342,375,414,438,455,456,492,521],interf:[390,516],interfac:[],interfer:[12,269,392],interg:[6,515],intergr:503,interi:438,interior:[3,6,41,353,497],interlac:440,interleav:[6,177,502],intermedi:[6,12,61,204,268,296,367,385,492,493,502,506],intermix:489,intermolecular:[153,392],intern:[],internal:[3,204,210,301,521],internal_element_set:214,internal_quadratur:214,internat:[129,176,214],internet:251,interpenetr:440,interpentr:[467,468,470],interpol:[6,14,37,56,110,197,204,205,214,239,240,255,296,374,375,385,396,445,447,448,456,469,475,476,477],interpret:[2,6,11,204,220,420,465,489,492,508,521],interrupt:305,intersect:[3,6,129,205,353,355,497],intersert:353,interspers:383,interstiti:[175,443],intertia:[3,103],interv:[3,6,99,203,218,252,269,305,310,311,324,463,469,489,508,521],intestieti:129,intial:[6,390,392],intiial:[41,499],intiti:[3,331],intra:315,intra_energi:244,intramolecular:[28,153,244],introduc:[6,9,100,117,204,236,269,305,310,315,367,374,391,406,415,428,432,436,474,508,521],introduct:[],intuit:377,inv:[129,176,317],invalid:[3,12,75,97,180,283,385,437,438,496],invari:[117,144,149,151],invent:319,invers:[],inverse:515,invert:[1,6,181,297],invis:353,invoc:[175,226,390,460,462,492],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,130,154,164,171,172,175,177,178,180,181,183,184,186,187,188,189,191,192,194,195,197,201,202,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220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,508,509,511,512,513,515,516,520,521,522,523,524,526],young:[420,459,461],your:[],yourself:[6,8,12,13,227,384,516],yplane:350,ypo:177,ysu:[3,201,202,334,495],yuan:9,yukawa:[],yukawa_1_1:483,yxz:491,yzx:491,z_i:[415,479,486],z_j:[479,486],z_meam:440,zachari:13,zannoni:419,zbl:[],zblcut:479,zblcutinn:464,zblcutout:464,zblexpscal:479,zblz:464,zcm:315,zcylind:350,zepeda:215,zero:[],zeta:[3,255,306,416],zfactor:204,zflag:[164,165,256,258,265,315,339],zhang:[315,340,420],zhi:[3,6,179,201,213,343,349,352,354,494,497,512],zhi_bound:[6,201],zhou:[13,396,416,453,477,479],zhu:471,ziegenhain:13,ziegler:[300,440,473,479,486],zimmerman2004:214,zimmerman2010:214,zimmerman:[9,74,214,396],zlat:[229,250,512],zlib:[9,201],zlim:463,zlo:[3,6,179,201,213,343,349,351,352,354,494,497,512],zlo_bound:[6,201],zmax:[213,255,521],zmin:[255,521],zn2:176,zone:[129,317],zoom:[3,201,204,205],zorig:75,zplane:350,zr4:176,zrest:331,zsu:[3,201,202,334,495],zwall:349,zwall_veloc:255,zxy:491,zybin:456,zyx:491},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":224,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,129,133,134,151,157,165,166,170,176,177,180,182,196,199,200,201,202,204,205,206,207,209,210,211,213,214,215,217,221,224,225,227,228,229,230,234,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,317,332,334,339,340,341,342,345,347,349,351,355,368,372,374,375,377,378,381,382,384,386,387,388,390,393,396,398,415,437,438,443,445,455,456,472,473,489,490,491,494,495,497,499,501,502,503,506,508,510,511,512,513,514,520,522,524,525],"function":521,"long":[219,397,399,400,401,402,406,408,409,428,432,436,450,458,480],"new":8,"static":12,acceler:1,account:516,ackland:66,acknowledg:7,adapt:[209,210],addforc:211,adding:516,addition:[12,13,516],addtorqu:212,adiabat:6,adjust_dt:322,adp:391,after:516,airebo:392,alloi:413,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:213,arrai:6,aspher:[6,90,155,271,275,279,280,289],asphere:9,atc:[9,214],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,151,152,175,213,215,216,304,521],atom_modifi:39,atom_styl:40,attract:5,aveforc:222,awpmd:[9,393],axel:516,balanc:[41,223],barostat:6,basal:70,beck:394,berendsen:[302,335],between:6,binary2txt:13,bodi:[6,8,42,71,156,272,276,281,290,395],body:9,bond:[8,13,72,73,224,225,226,311],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:396,born:[397,408],boundari:[7,59],box:[6,60,227],branch:516,brownian:398,buck:[399,400,408,439],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:516,change_box:61,charmm:[6,19,183,401,436],chunk:[6,69,75,79,86,98,103,114,116,125,157,172,174,217],citat:7,class2:[9,20,43,184,358,402],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,349,404,485],colvar:[13,228],colvars:9,com:[78,79,158],comb3:405,comb:[307,405],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,517,518,519,520,521,522,523,524,525,526],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,521],compute_modifi:112,condit:7,conduct:[6,340],constant:[6,521],constraint:7,contact:[80,131],coord:81,core:6,coreshell:9,correl:[218,219],cosin:[22,23,24,25,26,27,186],cossq:360,coul:[397,399,400,401,402,406,407,408,421,428,432,436,450,458],coupl:6,creat:225,create_atom:177,create_bond:178,create_box:179,createatom:13,creation:7,csld:336,csvr:336,cubic:430,cuda:[],custom:[8,201,202],cut:[49,393,399,402,406,409,415,418,428,429,436,444,450,480],cvff:361,damag:[82,132],data2xmovi:13,data:6,databas:13,deby:[406,428],defgrad:138,deform:[160,161,229],delete_atom:180,delete_bond:181,delta:23,deposit:230,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,517,518,519,520,521,522,523,524,525,526],diagnost:7,diel:407,dielectr:182,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:185,dihedral_styl:[2,183,184,186,187,188,189,190,191,192,193,194,195,196,197,198],dilat:85,dimens:199,dipol:[6,28,86,409],dipole:9,direct:233,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:200,distanc:362,distribut:[7,12],document:0,dpd:[9,88,89,410,411],drag:231,dreid:422,dreiding:6,drude:[6,9,162,232,233,253,515],dsf:[406,428],dsmc:412,dump:[6,8,201,202,203,204,206],dump_modifi:205,dynam:306,eam:[13,413],echo:207,edip:414,eff:[9,13,106,107,161,163,168,254,270,282,293,338,415],efield:235,ehex:236,eim:416,elastic:6,emac:13,energi:[134,411],enforce2d:237,ensembl:7,erot:[90,91,92,93],error:[3,133],evapor:241,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,507,508,509,510,511,512,513,514,517,518,519,520,521,522,523,524,525,526],exp6:417,exp:[26,186],expand:[46,431],extend:[8,11],extern:242,fcc:296,fdt:411,featur:[7,8,516,521],fene:[45,46],fep:[9,13,95,210],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246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zw>y>)j?{6^w_s2K2d)#cEmD4)^YDJ*)Wt>}W{$}Tb;VZc}vwWy}H+Vt(b*_O=Li(=bf}NW8r??` z{-<_Bwi)x}kW!t8a3|Y1vrH$a5tvYxLa-G+uX(E}D>W!JXj3f}Hr6j+H&(tF5VVIY zLTQIRN|6>dL1hFscH!nc2m0dY)LR5|mzC_0gnY8k!-(s;-DCzT{iH`uuE_WMNuszKRk)8Jxpye|Sw1-TM^&GHq~T1TYOl=>>NY&fnBW;`;wQWq;nI-50UL%L%D~Q41^}=$3sk~wB+lKl6)$q${btpo zX@qS2xE}Z6mOCuTovXwRw@e?%(PB_Yg$=j>ZQVJ9M-@XrOPH_ui@O+xcFDRsi2xw@+8wq zV9EBy9Y#i>2F!#>$XVWv`v(TdWF@gKk6Olj{wvHDG zbQ)w&+=sr8;Jv&M)r+m2x@K&Q`&>gPl^tTab#145Wi89l%t@^BX7g1%trmK(BK)2! z@ab-Yry??d;$=SJ;PyrP>UpfN=ia#m<3xv&V1G$L@s%h&afL@?Rh>Cg@ful7T1APXKtA9y5x&z?n$q^rAKO>K{$>myQCO!Oe)_L%JQ=PN^3~d zpJ!m|dJpxs)+Xb6e7Wh3%vfVgohN_{5RB40==h+C55xUEYVdIrdXC&|Wtkg{9^1-L zpVz+L=;|x9Pox3>{p{=jAPKw`i+yO5QTVa=k8*U=OZo!*%7)uGeM ziwg&nsrxD`Pfu46i!wX{0ng#P!@*jcQ^Z++v!qLeqQ&Uw80E+fB`iWSWSLblqE(;f}&D~>FLDryBW6<33P(NdreHn$qPe> z%JY4Jec8|6+&-dp{51PtR+s+#Wb^Ld2*Y=KX}zq9bZ+SK4@+qa2U1&Z%Sp}LEyZ}{ z1(V&G4mEBkglhROD;w0d-UmaMxhg(!MQe@&`r!y20Bc^!uRE)lSzJL#C|v)d$-&5R^_&Jq4qo8G#kkxUsE5n#sAT3oCxT z9xF!f{aG0S^=1mQ80hUQxeiSXmQpeCHh7(H`7zrrzH@n1apG)erT6p;<%%@_ zWJrGSOp|>#fviMJs##|DsVZS+2IM#K`tz*v1pk8nL_Ta3S9#sWuEwFm z^pO7tN2*rS>=b%|POu-4LCnESSu>w_s>;urw$yw#)I_O!bvIB30cdM~OkC$?{Cr2~ ZFWS$e=5YJs@IRN}-=a(ZZAd>I`xivbY!Cnd From 78c0df7de2978de1a3f6eaa9813c8e05de80339c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:41:19 +0000 Subject: [PATCH 083/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15127 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/fix_eos_table_rx.html | 2 +- doc/html/fix_rx.html | 10 +++++----- doc/html/pair_exp6_rx.html | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/html/fix_eos_table_rx.html b/doc/html/fix_eos_table_rx.html index c9db07b19e..6ae5c9ea01 100644 --- a/doc/html/fix_eos_table_rx.html +++ b/doc/html/fix_eos_table_rx.html @@ -154,7 +154,7 @@ of state to relate the concentration-dependent particle internal energy (u_i) to the particle internal temperature (dpdTheta_i).

      The concentration-dependent particle internal energy (u_i) is computed according to the following relation:

      -Eqs/fix_eos_table_rx.jpg +_images/fix_eos_table_rx.jpg

      where m is the number of species, c_i,j is the concentration of species j in particle i, u_j is the internal energy of species j, DeltaH_f,j is the heat of formation of species j, N is the number of diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html index 752afbe7ef..cc3341ad21 100644 --- a/doc/html/fix_rx.html +++ b/doc/html/fix_rx.html @@ -153,9 +153,9 @@

      Fix rx solves the reaction kinetic ODEs for a given reaction set that is defined within the file associated with this command.

      For a general reaction such that

      -Eqs/fix_rx_reaction.jpg +_images/fix_rx_reaction.jpg

      the reaction rate equation is defined to be of the form

      -Eqs/fix_rx_reactionRate.jpg +_images/fix_rx_reactionRate.jpg

      In the current implementation, the exponents are defined to be equal to the stoichiometric coefficients. A given reaction set consisting of n reaction equations will contain a total of m species. A set of m ordinary @@ -180,7 +180,7 @@ coefficient. The only delimiters that are recognized between the species are either a + or = character. The = character corresponds to an irreversible reaction. After specifying the reaction, the reaction rate constant is determined through the temperature dependent Arrhenius equation:

      -Eqs/fix_rx.jpg +_images/fix_rx.jpg

      where A is the Arrhenius factor in time units or concentration/time units, n is the unitless exponent of the temperature dependence, and E_a is the activation energy in energy units. The temperature dependence can be removed @@ -190,9 +190,9 @@ reaction rate constants at every DPD timestep by specifying the keyword none Alternatively, the keyword lucy can be specified to compute a local-average particle internal temperature for use in the reaction rate constant expressions. The local-average particle internal temperature is defined as:

      -Eqs/fix_rx_localTemp.jpg +_images/fix_rx_localTemp.jpg

      where the Lucy function is expressed as:

      -Eqs/fix_rx_localTemp2.jpg +_images/fix_rx_localTemp2.jpg

      The self-particle interaction is included in the above equation.

      The format of a tabulated file is as follows (without the parenthesized comments):

      diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html index b6b354ed7b..cbbe26c5b3 100644 --- a/doc/html/pair_exp6_rx.html +++ b/doc/html/pair_exp6_rx.html @@ -152,7 +152,7 @@ from a set of n reaction rate equations through the       +_images/pair_exp6_rx.jpg

      where the epsilon parameter determines the depth of the potential minimum located at Rm, and alpha determines the softness of the repulsion.

      The coefficients must be defined for each species in a given particle type @@ -195,9 +195,9 @@ parameter (distance units). If a species tag of “1fluid” is listed pair coefficient, a one-fluid approximation is specified where a concentration-dependent combination of the parameters is computed through the following equations:

      -Eqs/pair_exp6_rx_oneFluid.jpg +_images/pair_exp6_rx_oneFluid.jpg

      where

      -Eqs/pair_exp6_rx_oneFluid2.jpg +_images/pair_exp6_rx_oneFluid2.jpg

      and xa and xb are the mole fractions of a and b, respectively, which comprise the gas mixture.

      From 0f5dcedee1062541026f2965dd60e5a16848be73 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:49:15 +0000 Subject: [PATCH 084/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15128 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/fix_eos_cv.txt | 8 +- doc/src/fix_eos_table.txt | 12 ++- doc/src/fix_eos_table_rx.txt | 12 ++- doc/src/fix_rx.txt | 106 +++++++++++----------- doc/src/fix_shardlow.txt | 8 +- doc/src/pair_dpd_fdt.txt | 5 +- doc/src/pair_exp6_rx.txt | 70 ++++++++------- doc/src/pair_multi_lucy.txt | 87 ++++++++++-------- doc/src/pair_multi_lucy_rx.txt | 155 ++++++++++++++++++--------------- doc/src/pair_table_rx.txt | 44 ++++++---- 10 files changed, 282 insertions(+), 225 deletions(-) diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt index 4d0f5306d9..49909f035b 100644 --- a/doc/src/fix_eos_cv.txt +++ b/doc/src/fix_eos_cv.txt @@ -38,8 +38,12 @@ possible. [Restrictions:] -The fix {eos/cv} is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This command also requires use of the "atom_style dpd"_atom_style.html +command. [Related commands:] diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 7dfeb173a6..b6b7daacad 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -98,13 +98,17 @@ one that matches the specified keyword. [Restrictions:] -The fix {eos/table} is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This command also requires use of the "atom_style dpd"_atom_style.html +command. The equation of state must be a monotonically increasing function. -An exit error will occur if the internal temperature or internal -energies are not within the table cutoffs. +An error will occur if the internal temperature or internal energies +are not within the table cutoffs. [Related commands:] diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index b2a0051889..9c97151202 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -120,13 +120,17 @@ the reactions with the "fix rx"_fix_rx.html command. [Restrictions:] -The fix {eos/table/rx} is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This command also requires use of the "atom_style dpd"_atom_style.html +command. The equation of state must be a monotonically increasing function. -An exit error will occur if the internal temperature or internal -energies are not within the table cutoffs. +An error will occur if the internal temperature or internal energies +are not within the table cutoffs. [Related commands:] diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index a32290d366..f9d1aa0d55 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -38,19 +38,20 @@ the reaction rate equation is defined to be of the form :c,image(Eqs/fix_rx_reactionRate.jpg) -In the current implementation, the exponents are defined to be equal to the -stoichiometric coefficients. A given reaction set consisting of {n} reaction -equations will contain a total of {m} species. A set of {m} ordinary -differential equations (ODEs) that describe the change in concentration of a -given species as a function of time are then constructed based on the {n} -reaction rate equations. +In the current implementation, the exponents are defined to be equal +to the stoichiometric coefficients. A given reaction set consisting +of {n} reaction equations will contain a total of {m} species. A set +of {m} ordinary differential equations (ODEs) that describe the change +in concentration of a given species as a function of time are then +constructed based on the {n} reaction rate equations. -The ODE systems are solved over the full DPD timestep {dt} using a 4th order -Runge-Kutta {rk4} method with a fixed step-size {h}, specified by the -{lammps_rk4} keyword. The number of ODE steps per DPD timestep for the rk4 method -is optionally specified immediately after the rk4 keyword. The ODE step-size is set as -{dt/num_steps}. Smaller step-sizes tend to yield more accurate results but there -is not control on the error. +The ODE systems are solved over the full DPD timestep {dt} using a 4th +order Runge-Kutta {rk4} method with a fixed step-size {h}, specified +by the {lammps_rk4} keyword. The number of ODE steps per DPD timestep +for the rk4 method is optionally specified immediately after the rk4 +keyword. The ODE step-size is set as {dt/num_steps}. Smaller +step-sizes tend to yield more accurate results but there is not +control on the error. :line @@ -58,27 +59,29 @@ The filename specifies a file that contains the entire set of reaction kinetic equations and corresponding Arrhenius parameters. The format of this file is described below. -There is no restriction on the total number or reaction equations that are -specified. The species names are arbitrary string names that are associated -with the species concentrations. -Each species in a given reaction must be preceded by it's stoichiometric -coefficient. The only delimiters that are recognized between the species are -either a {+} or {=} character. The {=} character corresponds to an -irreversible reaction. After specifying the reaction, the reaction rate -constant is determined through the temperature dependent Arrhenius equation: +There is no restriction on the total number or reaction equations that +are specified. The species names are arbitrary string names that are +associated with the species concentrations. Each species in a given +reaction must be preceded by it's stoichiometric coefficient. The +only delimiters that are recognized between the species are either a +{+} or {=} character. The {=} character corresponds to an +irreversible reaction. After specifying the reaction, the reaction +rate constant is determined through the temperature dependent +Arrhenius equation: :c,image(Eqs/fix_rx.jpg) -where {A} is the Arrhenius factor in time units or concentration/time units, -{n} is the unitless exponent of the temperature dependence, and {E_a} is the -activation energy in energy units. The temperature dependence can be removed -by specifying the exponent as zero. +where {A} is the Arrhenius factor in time units or concentration/time +units, {n} is the unitless exponent of the temperature dependence, and +{E_a} is the activation energy in energy units. The temperature +dependence can be removed by specifying the exponent as zero. -The internal temperature of the coarse-grained particles can be used in constructing the -reaction rate constants at every DPD timestep by specifying the keyword {none}. -Alternatively, the keyword {lucy} can be specified to compute a local-average particle -internal temperature for use in the reaction rate constant expressions. -The local-average particle internal temperature is defined as: +The internal temperature of the coarse-grained particles can be used +in constructing the reaction rate constants at every DPD timestep by +specifying the keyword {none}. Alternatively, the keyword {lucy} can +be specified to compute a local-average particle internal temperature +for use in the reaction rate constant expressions. The local-average +particle internal temperature is defined as: :c,image(Eqs/fix_rx_localTemp.jpg) @@ -90,7 +93,8 @@ The self-particle interaction is included in the above equation. :line -The format of a tabulated file is as follows (without the parenthesized comments): +The format of a tabulated file is as follows (without the +parenthesized comments): # Rxn equations and parameters (one or more comment or blank lines) :pre 1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49E+01 0.0 1.34 (rxn equation, A, n, Ea) @@ -102,21 +106,23 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. -Following a blank line, the next N lines list the N reaction equations. -Each species within the reaction equation is specified through its -stoichiometric coefficient and a species tag. Reactant species are specified -on the left-hand side of the equation and product species are specified on the -right-hand side of the equation. After specifying the reactant and product -species, the final three arguments of each line represent the Arrhenius -parameter {A}, the temperature exponent {n}, and the activation energy {Ea}. +Following a blank line, the next N lines list the N reaction +equations. Each species within the reaction equation is specified +through its stoichiometric coefficient and a species tag. Reactant +species are specified on the left-hand side of the equation and +product species are specified on the right-hand side of the equation. +After specifying the reactant and product species, the final three +arguments of each line represent the Arrhenius parameter {A}, the +temperature exponent {n}, and the activation energy {Ea}. -Note that the species tags that are defined in the reaction equations are -used by the "fix eos/table/rx"_fix_eos_table_rx.html command to define the -thermodynamic properties of each species. Furthermore, the number of species -molecules (i.e., concentration) can be specified either with the "set"_set.html -command using the "d_" prefix or by reading directly the concentrations from a -data file. For the latter case, the "read_data"_read_data.html command with the -fix keyword should be specified, where the fix-ID will be the "fix rx" ID with a +Note that the species tags that are defined in the reaction equations +are used by the "fix eos/table/rx"_fix_eos_table_rx.html command to +define the thermodynamic properties of each species. Furthermore, the +number of species molecules (i.e., concentration) can be specified +either with the "set"_set.html command using the "d_" prefix or by +reading directly the concentrations from a data file. For the latter +case, the "read_data"_read_data.html command with the fix keyword +should be specified, where the fix-ID will be the "fix rx" ID with a "_SPECIES" suffix, e.g. fix foo all rx reaction.file ... @@ -126,11 +132,15 @@ read_data data.dpd fix foo_SPECIES NULL Species [Restrictions:] -The fix {rx} is only available if LAMMPS is built with the USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -The fix {rx} must be used with the "atom_style dpd"_atom_style.html command. +This command also requires use of the "atom_style dpd"_atom_style.html +command. -The fix {rx} can only be used with a constant energy or constant enthalpy DPD simulation. +This command can only be used with a constant energy or constant +enthalpy DPD simulation. [Related commands:] @@ -139,5 +149,3 @@ The fix {rx} can only be used with a constant energy or constant enthalpy DPD si "pair dpd/fdt/energy"_dpd_fdt_energy.html [Default:] none - -:line diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 2cb102f8fe..485f0a4b6f 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -54,9 +54,9 @@ examples/USER/dpd directory. [Restrictions:] -This fix is only available if LAMMPS is built with the USER-DPD -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This fix is currently limited to orthogonal simulation cell geometries. @@ -66,7 +66,7 @@ integration, e.g. "fix nve"_fix_nve.html or "fix nph"_fix_nh.html. The Shardlow splitting algorithm requires the sizes of the sub-domain lengths to be larger than twice the cutoff+skin. Generally, the -domain decomposition is dependant on the number of processors +domain decomposition is dependent on the number of processors requested. [Related commands:] diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index ac31e82e30..07d5f3d5bb 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -110,8 +110,9 @@ specified. [Restrictions:] -Pair styles {dpd/fdt} and {dpd/fdt/energy} are only available if -LAMMPS is built with the USER-DPD package. +These commands are part of the USER-DPD package. They are only +enabled if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the "communicate vel yes"_communicate.html option so that velocites are diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 5e65fee84c..d9e91cd97b 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -23,34 +23,37 @@ pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre [Description:] -Style {exp6/rx} is used in reaction DPD simulations, where the coarse-grained (CG) -particles are composed of {m} species whose reaction rate kinetics are determined -from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. -The species of one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. The {exp6/rx} style -computes an exponential-6 potential given by +Style {exp6/rx} is used in reaction DPD simulations, where the +coarse-grained (CG) particles are composed of {m} species whose +reaction rate kinetics are determined from a set of {n} reaction rate +equations through the "fix rx"_fix_rx.html command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. The +{exp6/rx} style computes an exponential-6 potential given by :c,image(Eqs/pair_exp6_rx.jpg) where the {epsilon} parameter determines the depth of the potential minimum located at {Rm}, and {alpha} determines the softness of the repulsion. -The coefficients must be defined for each species in a given particle type -via the "pair_coeff"_pair_coeff.html command as in the examples above, where -the first argument is the filename that includes the exponential-6 parameters -for each species. The file includes the species tag followed by the {alpha}, -{epsilon} and {Rm} parameters. The format of the file is described below. +The coefficients must be defined for each species in a given particle +type via the "pair_coeff"_pair_coeff.html command as in the examples +above, where the first argument is the filename that includes the +exponential-6 parameters for each species. The file includes the +species tag followed by the {alpha}, {epsilon} and {Rm} +parameters. The format of the file is described below. -The second and third arguments specify the site-site interaction -potential between two species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the "fix rx"_fix_rx.html command -or they must correspond to the tag "1fluid", signifying interaction -with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential is -stored before and after the reaction kinetics solver is applied, where the -difference is defined to be the internal chemical energy (uChem). +The second and third arguments specify the site-site interaction +potential between two species contained within two different +particles. The species tags must either correspond to the species +defined in the reaction kinetics files specified with the "fix +rx"_fix_rx.html command or they must correspond to the tag "1fluid", +signifying interaction with a product species mixture determined +through a one-fluid approximation. The interaction potential is +weighted by the geometric average of the concentrations of the two +species. The coarse-grained potential is stored before and after the +reaction kinetics solver is applied, where the difference is defined +to be the internal chemical energy (uChem). The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents. @@ -58,7 +61,8 @@ The final argument specifies the interaction cutoff. :line -The format of a tabulated file is as follows (without the parenthesized comments): +The format of a tabulated file is as follows (without the +parenthesized comments): # exponential-6 parameters for various species (one or more comment or blank lines) :pre h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon) @@ -68,16 +72,16 @@ co2 exp6 13.00 0.03 3.20 :pre A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments -between sections. +between sections. -Following a blank line, the next N lines list the species and their -corresponding parameters. The first argument is the species tag, -the second argument is the exp6 tag, the 3rd argument is the {alpha} -parameter (energy units), the 4th argument is the {epsilon} parameter -(energy-distance^6 units), and the 5th argument is the {Rm} -parameter (distance units). If a species tag of "1fluid" is listed as a -pair coefficient, a one-fluid approximation is specified where a -concentration-dependent combination of the parameters is computed +Following a blank line, the next N lines list the species and their +corresponding parameters. The first argument is the species tag, the +second argument is the exp6 tag, the 3rd argument is the {alpha} +parameter (energy units), the 4th argument is the {epsilon} parameter +(energy-distance^6 units), and the 5th argument is the {Rm} parameter +(distance units). If a species tag of "1fluid" is listed as a pair +coefficient, a one-fluid approximation is specified where a +concentration-dependent combination of the parameters is computed through the following equations: :c,image(Eqs/pair_exp6_rx_oneFluid.jpg) @@ -105,7 +109,9 @@ pair interaction. [Restrictions:] -None +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt index 48dad8be29..2d0852e79c 100644 --- a/doc/src/pair_multi_lucy.txt +++ b/doc/src/pair_multi_lucy.txt @@ -22,14 +22,15 @@ pair_coeff * * multibody.table ENTRY1 7.0 :pre [Description:] -Style {multi/lucy} computes a density-dependent force following from the many-body -form described in "(Moore)"_#Moore and "(Warren)"_#Warren as +Style {multi/lucy} computes a density-dependent force following from +the many-body form described in "(Moore)"_#Moore and +"(Warren)"_#Warren as :c,image(Eqs/pair_multi_lucy.jpg) -which consists of a density-dependent function, A(rho), and a radial-dependent weight -function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken -as the Lucy function: +which consists of a density-dependent function, A(rho), and a +radial-dependent weight function, omegaDD(rij). The radial-dependent +weight function, omegaDD(rij), is taken as the Lucy function: :c,image(Eqs/pair_multi_lucy2.jpg) @@ -37,24 +38,29 @@ The density-dependent energy for a given particle is given by: :c,image(Eqs/pair_multi_lucy_energy.jpg) -See the supporting information of "(Brennan)"_#Brennan or the publication by "(Moore)"_#Moore -for more details on the functional form. +See the supporting information of "(Brennan)"_#Brennan or the +publication by "(Moore)"_#Moore for more details on the functional +form. -An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). -Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will -have units of energy / length^4. +An interpolation table is used to evaluate the density-dependent +energy (Integral(A(rho)drho) and force (A(rho)). Note that the +pre-factor to the energy is computed after the interpolation, thus the +Integral(A(rho)drho will have units of energy / length^4. -The interpolation table is created as a pre-computation by fitting cubic splines to -the file values and interpolating the density-dependent energy and force at each of {N} densities. -During a simulation, the tables are used to interpolate the density-dependent energy and force as -needed for each pair of particles separated by a distance {R}. The interpolation is done in -one of 2 styles: {lookup} and {linear}. +The interpolation table is created as a pre-computation by fitting +cubic splines to the file values and interpolating the +density-dependent energy and force at each of {N} densities. During a +simulation, the tables are used to interpolate the density-dependent +energy and force as needed for each pair of particles separated by a +distance {R}. The interpolation is done in one of 2 styles: {lookup} +and {linear}. -For the {lookup} style, the density is used to find the nearest table entry, which is the -density-dependent energy and force. +For the {lookup} style, the density is used to find the nearest table +entry, which is the density-dependent energy and force. -For the {linear} style, the density is used to find the 2 surrounding table values from -which the density-dependent energy and force are computed by linear interpolation. +For the {linear} style, the density is used to find the 2 surrounding +table values from which the density-dependent energy and force are +computed by linear interpolation. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples @@ -64,13 +70,14 @@ filename keyword cutoff (distance units) :ul -The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. +The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below. :line @@ -98,19 +105,19 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the {N} -specified in the "pair_style multi/lucy"_pair_multi_lucy.html command. Let -Ntable = {N} in the pair_style command, and Nfile = "N" in the +specified in the "pair_style multi/lucy"_pair_multi_lucy.html command. +Let Ntable = {N} in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the "RSQ" parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup. +uses these to interpolate the density-dependent energy and force at +Ntable different points. The resulting tables of length Ntable are +then used as described above, when computing the density-dependent +energy and force. This means that if you want the interpolation +tables of length Ntable to match exactly what is in the tabulated file +(with effectively no preliminary interpolation), you should set Ntable += Nfile, and use the "RSQ" parameter. This is because the internal +table abscissa is always RSQ (separation distance squared), for +efficient lookup. All other parameters are optional. If "R" or "RSQ" does not appear, then the distances in each line of the table are used @@ -167,7 +174,11 @@ This pair style can only be used via the {pair} keyword of the :line -[Restrictions:] none +[Restrictions:] + +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index f1c33e9711..5df2995a75 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -23,19 +23,21 @@ pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre [Description:] -Style {multi/lucy/rx} is used in reaction DPD simulations, where the coarse-grained -(CG) particles are composed of {m} species whose reaction rate kinetics are determined -from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. -The species of one CG particle can interact with a species in a neighboring CG particle -through a site-site interaction potential model. Style {multi/lucy/rx} computes the -site-site density-dependent force following from the many-body form described in -"(Moore)"_#Moore and "(Warren)"_#Warren as +Style {multi/lucy/rx} is used in reaction DPD simulations, where the +coarse-grained (CG) particles are composed of {m} species whose +reaction rate kinetics are determined from a set of {n} reaction rate +equations through the "fix rx"_fix_rx.html command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +{multi/lucy/rx} computes the site-site density-dependent force +following from the many-body form described in "(Moore)"_#Moore and +"(Warren)"_#Warren as :c,image(Eqs/pair_multi_lucy.jpg) -which consists of a density-dependent function, A(rho), and a radial-dependent weight -function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken -as the Lucy function: +which consists of a density-dependent function, A(rho), and a +radial-dependent weight function, omegaDD(rij). The radial-dependent +weight function, omegaDD(rij), is taken as the Lucy function: :c,image(Eqs/pair_multi_lucy2.jpg) @@ -43,24 +45,29 @@ The density-dependent energy for a given particle is given by: :c,image(Eqs/pair_multi_lucy_energy.jpg) -See the supporting information of "(Brennan)"_#Brennan or the publication by "(Moore)"_#Moore -for more details on the functional form. +See the supporting information of "(Brennan)"_#Brennan or the +publication by "(Moore)"_#Moore for more details on the functional +form. -An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). -Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will -have units of energy / length^4. +An interpolation table is used to evaluate the density-dependent +energy (Integral(A(rho)drho) and force (A(rho)). Note that the +pre-factor to the energy is computed after the interpolation, thus the +Integral(A(rho)drho will have units of energy / length^4. -The interpolation table is created as a pre-computation by fitting cubic splines to -the file values and interpolating the density-dependent energy and force at each of {N} densities. -During a simulation, the tables are used to interpolate the density-dependent energy and force as -needed for each pair of particles separated by a distance {R}. The interpolation is done in -one of 2 styles: {lookup} and {linear}. +The interpolation table is created as a pre-computation by fitting +cubic splines to the file values and interpolating the +density-dependent energy and force at each of {N} densities. During a +simulation, the tables are used to interpolate the density-dependent +energy and force as needed for each pair of particles separated by a +distance {R}. The interpolation is done in one of 2 styles: {lookup} +and {linear}. -For the {lookup} style, the density is used to find the nearest table entry, which is the -density-dependent energy and force. +For the {lookup} style, the density is used to find the nearest table +entry, which is the density-dependent energy and force. -For the {linear} style, the density is used to find the 2 surrounding table values from -which the density-dependent energy and force are computed by linear interpolation. +For the {linear} style, the density is used to find the 2 surrounding +table values from which the density-dependent energy and force are +computed by linear interpolation. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples @@ -72,23 +79,24 @@ species1 species2 cutoff (distance units) :ul -The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. +The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below. -The species tags define the site-site interaction potential between two -species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the "fix rx"_fix_rx.html command -or they must correspond to the tag "1fluid", signifying interaction -with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential -is stored before and after the reaction kinetics solver is applied, where +The species tags define the site-site interaction potential between +two species contained within two different particles. The species +tags must either correspond to the species defined in the reaction +kinetics files specified with the "fix rx"_fix_rx.html command or they +must correspond to the tag "1fluid", signifying interaction with a +product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). :line @@ -117,47 +125,48 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the {N} -specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html command. Let -Ntable = {N} in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the "RSQ" parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup. +specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html +command. Let Ntable = {N} in the pair_style command, and Nfile = "N" +in the tabulated file. What LAMMPS does is a preliminary +interpolation by creating splines using the Nfile tabulated values as +nodal points. It uses these to interpolate the density-dependent +energy and force at Ntable different points. The resulting tables of +length Ntable are then used as described above, when computing the +density-dependent energy and force. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile, and use the "RSQ" parameter. This is +because the internal table abscissa is always RSQ (separation distance +squared), for efficient lookup. -All other parameters are optional. If "R" or "RSQ" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in {density} uniformly or however you wish to position table -values in regions of large gradients. +All other parameters are optional. If "R" or "RSQ" does not appear, +then the distances in each line of the table are used as-is to perform +spline interpolation. In this case, the table values can be spaced in +{density} uniformly or however you wish to position table values in +regions of large gradients. If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} -and {rhi}. If specified, the density associated with each density-dependent -energy and force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The density values in the table file are ignored in this case. -For "R", distances uniformly spaced between {rlo} and {rhi} are -computed; for "RSQ", squared distances uniformly spaced between -{rlo*rlo} and {rhi*rhi} are computed. +and {rhi}. If specified, the density associated with each +density-dependent energy and force value is computed from these 2 +values (at high accuracy), rather than using the (low-accuracy) value +listed in each line of the table. The density values in the table +file are ignored in this case. For "R", distances uniformly spaced +between {rlo} and {rhi} are computed; for "RSQ", squared distances +uniformly spaced between {rlo*rlo} and {rhi*rhi} are computed. NOTE: If you use "R" or "RSQ", the tabulated distance values in the file are effectively ignored, and replaced by new values as described in the previous paragraph. If the density value in the table is not very close to the new value (i.e. round-off difference), then you will -be assigning density-dependent energy and force values to a different density, -which is probably not what you want. LAMMPS will warn if this is occurring. +be assigning density-dependent energy and force values to a different +density, which is probably not what you want. LAMMPS will warn if +this is occurring. Following a blank line, the next N lines list the tabulated values. On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in density units), the 3rd value is the density-dependent function value -(in energy units / length^4), and the 4th is the force (in force units). The -density values must increase from one line to the next. +r (in density units), the 3rd value is the density-dependent function +value (in energy units / length^4), and the 4th is the force (in force +units). The density values must increase from one line to the next. Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds @@ -186,7 +195,11 @@ This pair style can only be used via the {pair} keyword of the :line -[Restrictions:] none +[Restrictions:] + +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index b33ef1196d..6c765d2093 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -26,14 +26,16 @@ pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre [Description:] -Style {table/rx} is used in reaction DPD simulations,where the coarse-grained (CG) -particles are composed of {m} species whose reaction rate kinetics are determined -from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command. -The species of one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. Style {table/rx} creates -interpolation tables of length {N} from pair potential and force values listed in a -file(s) as a function of distance. The files are read by the -"pair_coeff"_pair_coeff.html command. +Style {table/rx} is used in reaction DPD simulations,where the +coarse-grained (CG) particles are composed of {m} species whose +reaction rate kinetics are determined from a set of {n} reaction rate +equations through the "fix rx"_fix_rx.html command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +{table/rx} creates interpolation tables of length {N} from pair +potential and force values listed in a file(s) as a function of +distance. The files are read by the "pair_coeff"_pair_coeff.html +command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of {N} @@ -54,7 +56,7 @@ used to find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or force. For the {bitmap} style, the N means to create interpolation tables -that are 2^N in length. Date: Tue, 7 Jun 2016 15:49:45 +0000 Subject: [PATCH 085/111] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15129 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/fix_eos_cv.txt | 7 +- doc/html/_sources/fix_eos_table.txt | 11 +- doc/html/_sources/fix_eos_table_rx.txt | 11 +- doc/html/_sources/fix_rx.txt | 107 ++++++++-------- doc/html/_sources/fix_shardlow.txt | 7 +- doc/html/_sources/pair_dpd_fdt.txt | 4 +- doc/html/_sources/pair_exp6_rx.txt | 66 +++++----- doc/html/_sources/pair_multi_lucy.txt | 86 +++++++------ doc/html/_sources/pair_multi_lucy_rx.txt | 154 ++++++++++++----------- doc/html/_sources/pair_table_rx.txt | 43 ++++--- doc/html/fix_eos_cv.html | 6 +- doc/html/fix_eos_table.html | 10 +- doc/html/fix_eos_table_rx.html | 10 +- doc/html/fix_rx.html | 104 ++++++++------- doc/html/fix_shardlow.html | 7 +- doc/html/pair_dpd_fdt.html | 4 +- doc/html/pair_exp6_rx.html | 58 +++++---- doc/html/pair_multi_lucy.html | 85 +++++++------ doc/html/pair_multi_lucy_rx.html | 151 +++++++++++----------- doc/html/pair_table_rx.html | 40 +++--- doc/html/searchindex.js | 2 +- 21 files changed, 526 insertions(+), 447 deletions(-) diff --git a/doc/html/_sources/fix_eos_cv.txt b/doc/html/_sources/fix_eos_cv.txt index 70e1d21e94..d1b1fc559d 100644 --- a/doc/html/_sources/fix_eos_cv.txt +++ b/doc/html/_sources/fix_eos_cv.txt @@ -45,8 +45,11 @@ Restrictions """""""""""" -The fix *eos/cv* is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. Related commands """""""""""""""" diff --git a/doc/html/_sources/fix_eos_table.txt b/doc/html/_sources/fix_eos_table.txt index 854409302c..c6fc225105 100644 --- a/doc/html/_sources/fix_eos_table.txt +++ b/doc/html/_sources/fix_eos_table.txt @@ -109,13 +109,16 @@ Restrictions """""""""""" -The fix *eos/table* is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. The equation of state must be a monotonically increasing function. -An exit error will occur if the internal temperature or internal -energies are not within the table cutoffs. +An error will occur if the internal temperature or internal energies +are not within the table cutoffs. Related commands """""""""""""""" diff --git a/doc/html/_sources/fix_eos_table_rx.txt b/doc/html/_sources/fix_eos_table_rx.txt index 0e6f6854c7..9a46afd956 100644 --- a/doc/html/_sources/fix_eos_table_rx.txt +++ b/doc/html/_sources/fix_eos_table_rx.txt @@ -140,13 +140,16 @@ Restrictions """""""""""" -The fix *eos/table/rx* is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. The equation of state must be a monotonically increasing function. -An exit error will occur if the internal temperature or internal -energies are not within the table cutoffs. +An error will occur if the internal temperature or internal energies +are not within the table cutoffs. Related commands """""""""""""""" diff --git a/doc/html/_sources/fix_rx.txt b/doc/html/_sources/fix_rx.txt index 8ad193cd02..a15c187e7c 100644 --- a/doc/html/_sources/fix_rx.txt +++ b/doc/html/_sources/fix_rx.txt @@ -42,19 +42,20 @@ the reaction rate equation is defined to be of the form .. image:: Eqs/fix_rx_reactionRate.jpg :align: center -In the current implementation, the exponents are defined to be equal to the -stoichiometric coefficients. A given reaction set consisting of *n* reaction -equations will contain a total of *m* species. A set of *m* ordinary -differential equations (ODEs) that describe the change in concentration of a -given species as a function of time are then constructed based on the *n* -reaction rate equations. +In the current implementation, the exponents are defined to be equal +to the stoichiometric coefficients. A given reaction set consisting +of *n* reaction equations will contain a total of *m* species. A set +of *m* ordinary differential equations (ODEs) that describe the change +in concentration of a given species as a function of time are then +constructed based on the *n* reaction rate equations. -The ODE systems are solved over the full DPD timestep *dt* using a 4th order -Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified by the -*lammps_rk4* keyword. The number of ODE steps per DPD timestep for the rk4 method -is optionally specified immediately after the rk4 keyword. The ODE step-size is set as -*dt/num_steps*\ . Smaller step-sizes tend to yield more accurate results but there -is not control on the error. +The ODE systems are solved over the full DPD timestep *dt* using a 4th +order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified +by the *lammps_rk4* keyword. The number of ODE steps per DPD timestep +for the rk4 method is optionally specified immediately after the rk4 +keyword. The ODE step-size is set as *dt/num_steps*\ . Smaller +step-sizes tend to yield more accurate results but there is not +control on the error. ---------- @@ -64,28 +65,30 @@ The filename specifies a file that contains the entire set of reaction kinetic equations and corresponding Arrhenius parameters. The format of this file is described below. -There is no restriction on the total number or reaction equations that are -specified. The species names are arbitrary string names that are associated -with the species concentrations. -Each species in a given reaction must be preceded by it's stoichiometric -coefficient. The only delimiters that are recognized between the species are -either a *+* or *=* character. The *=* character corresponds to an -irreversible reaction. After specifying the reaction, the reaction rate -constant is determined through the temperature dependent Arrhenius equation: +There is no restriction on the total number or reaction equations that +are specified. The species names are arbitrary string names that are +associated with the species concentrations. Each species in a given +reaction must be preceded by it's stoichiometric coefficient. The +only delimiters that are recognized between the species are either a +*+* or *=* character. The *=* character corresponds to an +irreversible reaction. After specifying the reaction, the reaction +rate constant is determined through the temperature dependent +Arrhenius equation: .. image:: Eqs/fix_rx.jpg :align: center -where *A* is the Arrhenius factor in time units or concentration/time units, -*n* is the unitless exponent of the temperature dependence, and *E_a* is the -activation energy in energy units. The temperature dependence can be removed -by specifying the exponent as zero. +where *A* is the Arrhenius factor in time units or concentration/time +units, *n* is the unitless exponent of the temperature dependence, and +*E_a* is the activation energy in energy units. The temperature +dependence can be removed by specifying the exponent as zero. -The internal temperature of the coarse-grained particles can be used in constructing the -reaction rate constants at every DPD timestep by specifying the keyword *none*\ . -Alternatively, the keyword *lucy* can be specified to compute a local-average particle -internal temperature for use in the reaction rate constant expressions. -The local-average particle internal temperature is defined as: +The internal temperature of the coarse-grained particles can be used +in constructing the reaction rate constants at every DPD timestep by +specifying the keyword *none*\ . Alternatively, the keyword *lucy* can +be specified to compute a local-average particle internal temperature +for use in the reaction rate constant expressions. The local-average +particle internal temperature is defined as: .. image:: Eqs/fix_rx_localTemp.jpg :align: center @@ -101,7 +104,8 @@ The self-particle interaction is included in the above equation. ---------- -The format of a tabulated file is as follows (without the parenthesized comments): +The format of a tabulated file is as follows (without the +parenthesized comments): .. parsed-literal:: @@ -118,21 +122,23 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. -Following a blank line, the next N lines list the N reaction equations. -Each species within the reaction equation is specified through its -stoichiometric coefficient and a species tag. Reactant species are specified -on the left-hand side of the equation and product species are specified on the -right-hand side of the equation. After specifying the reactant and product -species, the final three arguments of each line represent the Arrhenius -parameter *A*\ , the temperature exponent *n*\ , and the activation energy *Ea*\ . +Following a blank line, the next N lines list the N reaction +equations. Each species within the reaction equation is specified +through its stoichiometric coefficient and a species tag. Reactant +species are specified on the left-hand side of the equation and +product species are specified on the right-hand side of the equation. +After specifying the reactant and product species, the final three +arguments of each line represent the Arrhenius parameter *A*\ , the +temperature exponent *n*\ , and the activation energy *Ea*\ . -Note that the species tags that are defined in the reaction equations are -used by the :doc:`fix eos/table/rx ` command to define the -thermodynamic properties of each species. Furthermore, the number of species -molecules (i.e., concentration) can be specified either with the :doc:`set ` -command using the "d_" prefix or by reading directly the concentrations from a -data file. For the latter case, the :doc:`read_data ` command with the -fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. +Note that the species tags that are defined in the reaction equations +are used by the :doc:`fix eos/table/rx ` command to +define the thermodynamic properties of each species. Furthermore, the +number of species molecules (i.e., concentration) can be specified +either with the :doc:`set ` command using the "d_" prefix or by +reading directly the concentrations from a data file. For the latter +case, the :doc:`read_data ` command with the fix keyword +should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. fix foo all rx reaction.file ... read_data data.dpd fix foo_SPECIES NULL Species @@ -145,11 +151,14 @@ Restrictions """""""""""" -The fix *rx* is only available if LAMMPS is built with the USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. -The fix *rx* must be used with the :doc:`atom_style dpd ` command. +This command also requires use of the :doc:`atom_style dpd ` +command. -The fix *rx* can only be used with a constant energy or constant enthalpy DPD simulation. +This command can only be used with a constant energy or constant +enthalpy DPD simulation. Related commands """""""""""""""" @@ -161,10 +170,6 @@ Related commands **Default:** none ----------- - - - .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/fix_shardlow.txt b/doc/html/_sources/fix_shardlow.txt index c52e32630e..623c7621a2 100644 --- a/doc/html/_sources/fix_shardlow.txt +++ b/doc/html/_sources/fix_shardlow.txt @@ -56,9 +56,8 @@ Restrictions """""""""""" -This fix is only available if LAMMPS is built with the USER-DPD -package. See the :ref:`Making LAMMPS ` section -for more info. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This fix is currently limited to orthogonal simulation cell geometries. @@ -68,7 +67,7 @@ integration, e.g. :doc:`fix nve ` or :doc:`fix nph `. The Shardlow splitting algorithm requires the sizes of the sub-domain lengths to be larger than twice the cutoff+skin. Generally, the -domain decomposition is dependant on the number of processors +domain decomposition is dependent on the number of processors requested. Related commands diff --git a/doc/html/_sources/pair_dpd_fdt.txt b/doc/html/_sources/pair_dpd_fdt.txt index 602da2752b..1c35614fa6 100644 --- a/doc/html/_sources/pair_dpd_fdt.txt +++ b/doc/html/_sources/pair_dpd_fdt.txt @@ -124,8 +124,8 @@ Restrictions """""""""""" -Pair styles *dpd/fdt* and *dpd/fdt/energy* are only available if -LAMMPS is built with the USER-DPD package. +These commands are part of the USER-DPD package. They are only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the :doc:`communicate vel yes ` option so that velocites are diff --git a/doc/html/_sources/pair_exp6_rx.txt b/doc/html/_sources/pair_exp6_rx.txt index 0a5576911c..99aec901b7 100644 --- a/doc/html/_sources/pair_exp6_rx.txt +++ b/doc/html/_sources/pair_exp6_rx.txt @@ -25,12 +25,13 @@ Examples Description """"""""""" -Style *exp6/rx* is used in reaction DPD simulations, where the coarse-grained (CG) -particles are composed of *m* species whose reaction rate kinetics are determined -from a set of *n* reaction rate equations through the :doc:`fix rx ` command. -The species of one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. The *exp6/rx* style -computes an exponential-6 potential given by +Style *exp6/rx* is used in reaction DPD simulations, where the +coarse-grained (CG) particles are composed of *m* species whose +reaction rate kinetics are determined from a set of *n* reaction rate +equations through the :doc:`fix rx ` command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. The +*exp6/rx* style computes an exponential-6 potential given by .. image:: Eqs/pair_exp6_rx.jpg :align: center @@ -38,22 +39,23 @@ computes an exponential-6 potential given by where the *epsilon* parameter determines the depth of the potential minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion. -The coefficients must be defined for each species in a given particle type -via the :doc:`pair_coeff ` command as in the examples above, where -the first argument is the filename that includes the exponential-6 parameters -for each species. The file includes the species tag followed by the *alpha*\ , -*epsilon* and *Rm* parameters. The format of the file is described below. +The coefficients must be defined for each species in a given particle +type via the :doc:`pair_coeff ` command as in the examples +above, where the first argument is the filename that includes the +exponential-6 parameters for each species. The file includes the +species tag followed by the *alpha*\ , *epsilon* and *Rm* +parameters. The format of the file is described below. -The second and third arguments specify the site-site interaction -potential between two species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the :doc:`fix rx ` command -or they must correspond to the tag "1fluid", signifying interaction -with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential is -stored before and after the reaction kinetics solver is applied, where the -difference is defined to be the internal chemical energy (uChem). +The second and third arguments specify the site-site interaction +potential between two species contained within two different +particles. The species tags must either correspond to the species +defined in the reaction kinetics files specified with the :doc:`fix rx ` command or they must correspond to the tag "1fluid", +signifying interaction with a product species mixture determined +through a one-fluid approximation. The interaction potential is +weighted by the geometric average of the concentrations of the two +species. The coarse-grained potential is stored before and after the +reaction kinetics solver is applied, where the difference is defined +to be the internal chemical energy (uChem). The fourth and fifth arguments specify the *Rm* and *epsilon* scaling exponents. @@ -63,7 +65,8 @@ The final argument specifies the interaction cutoff. ---------- -The format of a tabulated file is as follows (without the parenthesized comments): +The format of a tabulated file is as follows (without the +parenthesized comments): .. parsed-literal:: @@ -80,14 +83,14 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. -Following a blank line, the next N lines list the species and their -corresponding parameters. The first argument is the species tag, -the second argument is the exp6 tag, the 3rd argument is the *alpha* -parameter (energy units), the 4th argument is the *epsilon* parameter -(energy-distance^6 units), and the 5th argument is the *Rm* -parameter (distance units). If a species tag of "1fluid" is listed as a -pair coefficient, a one-fluid approximation is specified where a -concentration-dependent combination of the parameters is computed +Following a blank line, the next N lines list the species and their +corresponding parameters. The first argument is the species tag, the +second argument is the exp6 tag, the 3rd argument is the *alpha* +parameter (energy units), the 4th argument is the *epsilon* parameter +(energy-distance^6 units), and the 5th argument is the *Rm* parameter +(distance units). If a species tag of "1fluid" is listed as a pair +coefficient, a one-fluid approximation is specified where a +concentration-dependent combination of the parameters is computed through the following equations: .. image:: Eqs/pair_exp6_rx_oneFluid.jpg @@ -121,7 +124,8 @@ Restrictions """""""""""" -None +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_multi_lucy.txt b/doc/html/_sources/pair_multi_lucy.txt index 00db4c15df..c4132d4f1c 100644 --- a/doc/html/_sources/pair_multi_lucy.txt +++ b/doc/html/_sources/pair_multi_lucy.txt @@ -24,15 +24,16 @@ Examples Description """"""""""" -Style *multi/lucy* computes a density-dependent force following from the many-body -form described in :ref:`(Moore) ` and :ref:`(Warren) ` as +Style *multi/lucy* computes a density-dependent force following from +the many-body form described in :ref:`(Moore) ` and +:ref:`(Warren) ` as .. image:: Eqs/pair_multi_lucy.jpg :align: center -which consists of a density-dependent function, A(rho), and a radial-dependent weight -function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken -as the Lucy function: +which consists of a density-dependent function, A(rho), and a +radial-dependent weight function, omegaDD(rij). The radial-dependent +weight function, omegaDD(rij), is taken as the Lucy function: .. image:: Eqs/pair_multi_lucy2.jpg :align: center @@ -42,24 +43,29 @@ The density-dependent energy for a given particle is given by: .. image:: Eqs/pair_multi_lucy_energy.jpg :align: center -See the supporting information of :ref:`(Brennan) ` or the publication by :ref:`(Moore) ` -for more details on the functional form. +See the supporting information of :ref:`(Brennan) ` or the +publication by :ref:`(Moore) ` for more details on the functional +form. -An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). -Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will -have units of energy / length^4. +An interpolation table is used to evaluate the density-dependent +energy (Integral(A(rho)drho) and force (A(rho)). Note that the +pre-factor to the energy is computed after the interpolation, thus the +Integral(A(rho)drho will have units of energy / length^4. -The interpolation table is created as a pre-computation by fitting cubic splines to -the file values and interpolating the density-dependent energy and force at each of *N* densities. -During a simulation, the tables are used to interpolate the density-dependent energy and force as -needed for each pair of particles separated by a distance *R*\ . The interpolation is done in -one of 2 styles: *lookup* and *linear*\ . +The interpolation table is created as a pre-computation by fitting +cubic splines to the file values and interpolating the +density-dependent energy and force at each of *N* densities. During a +simulation, the tables are used to interpolate the density-dependent +energy and force as needed for each pair of particles separated by a +distance *R*\ . The interpolation is done in one of 2 styles: *lookup* +and *linear*\ . -For the *lookup* style, the density is used to find the nearest table entry, which is the -density-dependent energy and force. +For the *lookup* style, the density is used to find the nearest table +entry, which is the density-dependent energy and force. -For the *linear* style, the density is used to find the 2 surrounding table values from -which the density-dependent energy and force are computed by linear interpolation. +For the *linear* style, the density is used to find the 2 surrounding +table values from which the density-dependent energy and force are +computed by linear interpolation. The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples @@ -69,13 +75,14 @@ above. * keyword * cutoff (distance units) -The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. +The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below. ---------- @@ -109,19 +116,19 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair_style multi/lucy ` command. Let -Ntable = *N* in the pair_style command, and Nfile = "N" in the +specified in the :doc:`pair_style multi/lucy ` command. +Let Ntable = *N* in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the "RSQ" parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup. +uses these to interpolate the density-dependent energy and force at +Ntable different points. The resulting tables of length Ntable are +then used as described above, when computing the density-dependent +energy and force. This means that if you want the interpolation +tables of length Ntable to match exactly what is in the tabulated file +(with effectively no preliminary interpolation), you should set Ntable += Nfile, and use the "RSQ" parameter. This is because the internal +table abscissa is always RSQ (separation distance squared), for +efficient lookup. All other parameters are optional. If "R" or "RSQ" does not appear, then the distances in each line of the table are used @@ -186,7 +193,10 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none + + +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_multi_lucy_rx.txt b/doc/html/_sources/pair_multi_lucy_rx.txt index b134a14b4d..23f67d0bc5 100644 --- a/doc/html/_sources/pair_multi_lucy_rx.txt +++ b/doc/html/_sources/pair_multi_lucy_rx.txt @@ -25,20 +25,22 @@ Examples Description """"""""""" -Style *multi/lucy/rx* is used in reaction DPD simulations, where the coarse-grained -(CG) particles are composed of *m* species whose reaction rate kinetics are determined -from a set of *n* reaction rate equations through the :doc:`fix rx ` command. -The species of one CG particle can interact with a species in a neighboring CG particle -through a site-site interaction potential model. Style *multi/lucy/rx* computes the -site-site density-dependent force following from the many-body form described in -:ref:`(Moore) ` and :ref:`(Warren) ` as +Style *multi/lucy/rx* is used in reaction DPD simulations, where the +coarse-grained (CG) particles are composed of *m* species whose +reaction rate kinetics are determined from a set of *n* reaction rate +equations through the :doc:`fix rx ` command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +*multi/lucy/rx* computes the site-site density-dependent force +following from the many-body form described in :ref:`(Moore) ` and +:ref:`(Warren) ` as .. image:: Eqs/pair_multi_lucy.jpg :align: center -which consists of a density-dependent function, A(rho), and a radial-dependent weight -function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken -as the Lucy function: +which consists of a density-dependent function, A(rho), and a +radial-dependent weight function, omegaDD(rij). The radial-dependent +weight function, omegaDD(rij), is taken as the Lucy function: .. image:: Eqs/pair_multi_lucy2.jpg :align: center @@ -48,24 +50,29 @@ The density-dependent energy for a given particle is given by: .. image:: Eqs/pair_multi_lucy_energy.jpg :align: center -See the supporting information of :ref:`(Brennan) ` or the publication by :ref:`(Moore) ` -for more details on the functional form. +See the supporting information of :ref:`(Brennan) ` or the +publication by :ref:`(Moore) ` for more details on the functional +form. -An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). -Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will -have units of energy / length^4. +An interpolation table is used to evaluate the density-dependent +energy (Integral(A(rho)drho) and force (A(rho)). Note that the +pre-factor to the energy is computed after the interpolation, thus the +Integral(A(rho)drho will have units of energy / length^4. -The interpolation table is created as a pre-computation by fitting cubic splines to -the file values and interpolating the density-dependent energy and force at each of *N* densities. -During a simulation, the tables are used to interpolate the density-dependent energy and force as -needed for each pair of particles separated by a distance *R*\ . The interpolation is done in -one of 2 styles: *lookup* and *linear*\ . +The interpolation table is created as a pre-computation by fitting +cubic splines to the file values and interpolating the +density-dependent energy and force at each of *N* densities. During a +simulation, the tables are used to interpolate the density-dependent +energy and force as needed for each pair of particles separated by a +distance *R*\ . The interpolation is done in one of 2 styles: *lookup* +and *linear*\ . -For the *lookup* style, the density is used to find the nearest table entry, which is the -density-dependent energy and force. +For the *lookup* style, the density is used to find the nearest table +entry, which is the density-dependent energy and force. -For the *linear* style, the density is used to find the 2 surrounding table values from -which the density-dependent energy and force are computed by linear interpolation. +For the *linear* style, the density is used to find the 2 surrounding +table values from which the density-dependent energy and force are +computed by linear interpolation. The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples @@ -77,23 +84,24 @@ above. * species2 * cutoff (distance units) -The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. +The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below. -The species tags define the site-site interaction potential between two -species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the :doc:`fix rx ` command -or they must correspond to the tag "1fluid", signifying interaction -with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential -is stored before and after the reaction kinetics solver is applied, where +The species tags define the site-site interaction potential between +two species contained within two different particles. The species +tags must either correspond to the species defined in the reaction +kinetics files specified with the :doc:`fix rx ` command or they +must correspond to the tag "1fluid", signifying interaction with a +product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). @@ -128,34 +136,34 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair_style multi/lucy/rx ` command. Let -Ntable = *N* in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the "RSQ" parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup. +specified in the :doc:`pair_style multi/lucy/rx ` +command. Let Ntable = *N* in the pair_style command, and Nfile = "N" +in the tabulated file. What LAMMPS does is a preliminary +interpolation by creating splines using the Nfile tabulated values as +nodal points. It uses these to interpolate the density-dependent +energy and force at Ntable different points. The resulting tables of +length Ntable are then used as described above, when computing the +density-dependent energy and force. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile, and use the "RSQ" parameter. This is +because the internal table abscissa is always RSQ (separation distance +squared), for efficient lookup. -All other parameters are optional. If "R" or "RSQ" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in *density* uniformly or however you wish to position table -values in regions of large gradients. +All other parameters are optional. If "R" or "RSQ" does not appear, +then the distances in each line of the table are used as-is to perform +spline interpolation. In this case, the table values can be spaced in +*density* uniformly or however you wish to position table values in +regions of large gradients. If used, the parameters "R" or "RSQ" are followed by 2 values *rlo* -and *rhi*\ . If specified, the density associated with each density-dependent -energy and force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The density values in the table file are ignored in this case. -For "R", distances uniformly spaced between *rlo* and *rhi* are -computed; for "RSQ", squared distances uniformly spaced between -*rlo*rlo* and *rhi*rhi* are computed. +and *rhi*\ . If specified, the density associated with each +density-dependent energy and force value is computed from these 2 +values (at high accuracy), rather than using the (low-accuracy) value +listed in each line of the table. The density values in the table +file are ignored in this case. For "R", distances uniformly spaced +between *rlo* and *rhi* are computed; for "RSQ", squared distances +uniformly spaced between *rlo*rlo* and *rhi*rhi* are computed. .. note:: @@ -163,14 +171,15 @@ computed; for "RSQ", squared distances uniformly spaced between file are effectively ignored, and replaced by new values as described in the previous paragraph. If the density value in the table is not very close to the new value (i.e. round-off difference), then you will - be assigning density-dependent energy and force values to a different density, - which is probably not what you want. LAMMPS will warn if this is occurring. + be assigning density-dependent energy and force values to a different + density, which is probably not what you want. LAMMPS will warn if + this is occurring. Following a blank line, the next N lines list the tabulated values. On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in density units), the 3rd value is the density-dependent function value -(in energy units / length^4), and the 4th is the force (in force units). The -density values must increase from one line to the next. +r (in density units), the 3rd value is the density-dependent function +value (in energy units / length^4), and the 4th is the force (in force +units). The density values must increase from one line to the next. Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds @@ -205,7 +214,10 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none + + +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_table_rx.txt b/doc/html/_sources/pair_table_rx.txt index e1af9b0ea4..1c5a57b038 100644 --- a/doc/html/_sources/pair_table_rx.txt +++ b/doc/html/_sources/pair_table_rx.txt @@ -28,14 +28,16 @@ Examples Description """"""""""" -Style *table/rx* is used in reaction DPD simulations,where the coarse-grained (CG) -particles are composed of *m* species whose reaction rate kinetics are determined -from a set of *n* reaction rate equations through the :doc:`fix rx ` command. -The species of one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. Style *table/rx* creates -interpolation tables of length *N* from pair potential and force values listed in a -file(s) as a function of distance. The files are read by the -:doc:`pair_coeff ` command. +Style *table/rx* is used in reaction DPD simulations,where the +coarse-grained (CG) particles are composed of *m* species whose +reaction rate kinetics are determined from a set of *n* reaction rate +equations through the :doc:`fix rx ` command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +*table/rx* creates interpolation tables of length *N* from pair +potential and force values listed in a file(s) as a function of +distance. The files are read by the :doc:`pair_coeff ` +command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of *N* @@ -56,7 +58,7 @@ used to find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or force. For the *bitmap* style, the N means to create interpolation tables -that are 2^N in length. ` and a linear interpolation is performed between adjacent table values. @@ -78,15 +80,15 @@ that extend to the largest tabulated distance. If specified, only file values up to the cutoff are used to create the interpolation table. The format of this file is described below. -The species tags define the site-site interaction potential between two -species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the :doc:`fix rx ` command -or they must correspond to the tag "1fluid", signifying interaction -with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential -is stored before and after the reaction kinetics solver is applied, where +The species tags define the site-site interaction potential between +two species contained within two different particles. The species +tags must either correspond to the species defined in the reaction +kinetics files specified with the :doc:`fix rx ` command or they +must correspond to the tag "1fluid", signifying interaction with a +product species mixture determined through a one-fluid approximation. +The interaction potential is weighted by the geometric average of the +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). @@ -227,7 +229,10 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none + + +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/fix_eos_cv.html b/doc/html/fix_eos_cv.html index 6248d4586f..ccc917df54 100644 --- a/doc/html/fix_eos_cv.html +++ b/doc/html/fix_eos_cv.html @@ -158,8 +158,10 @@ possible.
    4. keyword
    5. cutoff (distance units)
      6. -

      The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below.

      +

      The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below.

      The format of a tabulated file is a series of one or more sections, defined as follows (without the parenthesized comments):

      @@ -208,19 +215,19 @@ for the table. Each parameter is a keyword followed by one or more numeric values.

      The parameter “N” is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the pair_style multi/lucy command. Let -Ntable = N in the pair_style command, and Nfile = “N” in the +specified in the pair_style multi/lucy command. +Let Ntable = N in the pair_style command, and Nfile = “N” in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the “RSQ” parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup.

      +uses these to interpolate the density-dependent energy and force at +Ntable different points. The resulting tables of length Ntable are +then used as described above, when computing the density-dependent +energy and force. This means that if you want the interpolation +tables of length Ntable to match exactly what is in the tabulated file +(with effectively no preliminary interpolation), you should set Ntable += Nfile, and use the “RSQ” parameter. This is because the internal +table abscissa is always RSQ (separation distance squared), for +efficient lookup.

      All other parameters are optional. If “R” or “RSQ” does not appear, then the distances in each line of the table are used as-is to perform spline interpolation. In this case, the table values @@ -270,8 +277,8 @@ commands do need to be specified in the restart input script.

      Restrictions

      -
      -
      none
      +

      This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

      Description

      -

      Style multi/lucy/rx is used in reaction DPD simulations, where the coarse-grained -(CG) particles are composed of m species whose reaction rate kinetics are determined -from a set of n reaction rate equations through the fix rx command. -The species of one CG particle can interact with a species in a neighboring CG particle -through a site-site interaction potential model. Style multi/lucy/rx computes the -site-site density-dependent force following from the many-body form described in -(Moore) and (Warren) as

      +

      Style multi/lucy/rx is used in reaction DPD simulations, where the +coarse-grained (CG) particles are composed of m species whose +reaction rate kinetics are determined from a set of n reaction rate +equations through the fix rx command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +multi/lucy/rx computes the site-site density-dependent force +following from the many-body form described in (Moore) and +(Warren) as

      _images/pair_multi_lucy.jpg -

      which consists of a density-dependent function, A(rho), and a radial-dependent weight -function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken -as the Lucy function:

      +

      which consists of a density-dependent function, A(rho), and a +radial-dependent weight function, omegaDD(rij). The radial-dependent +weight function, omegaDD(rij), is taken as the Lucy function:

      _images/pair_multi_lucy2.jpg

      The density-dependent energy for a given particle is given by:

      _images/pair_multi_lucy_energy.jpg -

      See the supporting information of (Brennan) or the publication by (Moore) -for more details on the functional form.

      -

      An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)). -Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will -have units of energy / length^4.

      -

      The interpolation table is created as a pre-computation by fitting cubic splines to -the file values and interpolating the density-dependent energy and force at each of N densities. -During a simulation, the tables are used to interpolate the density-dependent energy and force as -needed for each pair of particles separated by a distance R. The interpolation is done in -one of 2 styles: lookup and linear.

      -

      For the lookup style, the density is used to find the nearest table entry, which is the -density-dependent energy and force.

      -

      For the linear style, the density is used to find the 2 surrounding table values from -which the density-dependent energy and force are computed by linear interpolation.

      +

      See the supporting information of (Brennan) or the +publication by (Moore) for more details on the functional +form.

      +

      An interpolation table is used to evaluate the density-dependent +energy (Integral(A(rho)drho) and force (A(rho)). Note that the +pre-factor to the energy is computed after the interpolation, thus the +Integral(A(rho)drho will have units of energy / length^4.

      +

      The interpolation table is created as a pre-computation by fitting +cubic splines to the file values and interpolating the +density-dependent energy and force at each of N densities. During a +simulation, the tables are used to interpolate the density-dependent +energy and force as needed for each pair of particles separated by a +distance R. The interpolation is done in one of 2 styles: lookup +and linear.

      +

      For the lookup style, the density is used to find the nearest table +entry, which is the density-dependent energy and force.

      +

      For the linear style, the density is used to find the 2 surrounding +table values from which the density-dependent energy and force are +computed by linear interpolation.

      The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above.

      @@ -184,22 +191,23 @@ above.

    6. species2
    7. cutoff (distance units)
      8. -

      The filename specifies a file containing the tabulated density-dependent -energy and force. The keyword specifies a section of the file. -The cutoff is an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below.

      -

      The species tags define the site-site interaction potential between two -species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the fix rx command -or they must correspond to the tag “1fluid”, signifying interaction -with a product species mixture determined through a one-fluid approximation. +

      The filename specifies a file containing the tabulated +density-dependent energy and force. The keyword specifies a section +of the file. The cutoff is an optional coefficient. If not +specified, the outer cutoff in the table itself (see below) will be +used to build an interpolation table that extend to the largest +tabulated distance. If specified, only file values up to the cutoff +are used to create the interpolation table. The format of this file +is described below.

      +

      The species tags define the site-site interaction potential between +two species contained within two different particles. The species +tags must either correspond to the species defined in the reaction +kinetics files specified with the fix rx command or they +must correspond to the tag “1fluid”, signifying interaction with a +product species mixture determined through a one-fluid approximation. The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential -is stored before and after the reaction kinetics solver is applied, where +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem).

      The format of a tabulated file is a series of one or more sections, @@ -226,46 +234,47 @@ for the table. Each parameter is a keyword followed by one or more numeric values.

      The parameter “N” is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the pair_style multi/lucy/rx command. Let -Ntable = N in the pair_style command, and Nfile = “N” in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing the density-dependent energy and force. -This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the “RSQ” parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup.

      -

      All other parameters are optional. If “R” or “RSQ” does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in density uniformly or however you wish to position table -values in regions of large gradients.

      +specified in the pair_style multi/lucy/rx +command. Let Ntable = N in the pair_style command, and Nfile = “N” +in the tabulated file. What LAMMPS does is a preliminary +interpolation by creating splines using the Nfile tabulated values as +nodal points. It uses these to interpolate the density-dependent +energy and force at Ntable different points. The resulting tables of +length Ntable are then used as described above, when computing the +density-dependent energy and force. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile, and use the “RSQ” parameter. This is +because the internal table abscissa is always RSQ (separation distance +squared), for efficient lookup.

      +

      All other parameters are optional. If “R” or “RSQ” does not appear, +then the distances in each line of the table are used as-is to perform +spline interpolation. In this case, the table values can be spaced in +density uniformly or however you wish to position table values in +regions of large gradients.

      If used, the parameters “R” or “RSQ” are followed by 2 values rlo -and rhi. If specified, the density associated with each density-dependent -energy and force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The density values in the table file are ignored in this case. -For “R”, distances uniformly spaced between rlo and rhi are -computed; for “RSQ”, squared distances uniformly spaced between -rlo*rlo and rhi*rhi are computed.

      +and rhi. If specified, the density associated with each +density-dependent energy and force value is computed from these 2 +values (at high accuracy), rather than using the (low-accuracy) value +listed in each line of the table. The density values in the table +file are ignored in this case. For “R”, distances uniformly spaced +between rlo and rhi are computed; for “RSQ”, squared distances +uniformly spaced between rlo*rlo and rhi*rhi are computed.

      Note

      If you use “R” or “RSQ”, the tabulated distance values in the file are effectively ignored, and replaced by new values as described in the previous paragraph. If the density value in the table is not very close to the new value (i.e. round-off difference), then you will -be assigning density-dependent energy and force values to a different density, -which is probably not what you want. LAMMPS will warn if this is occurring.

      +be assigning density-dependent energy and force values to a different +density, which is probably not what you want. LAMMPS will warn if +this is occurring.

      Following a blank line, the next N lines list the tabulated values. On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in density units), the 3rd value is the density-dependent function value -(in energy units / length^4), and the 4th is the force (in force units). The -density values must increase from one line to the next.

      +r (in density units), the 3rd value is the density-dependent function +value (in energy units / length^4), and the 4th is the force (in force +units). The density values must increase from one line to the next.

      Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword.

      @@ -288,8 +297,8 @@ commands do need to be specified in the restart input script.

      Restrictions

      -
      -
      none
      +

      This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

      Description

      -

      Style table/rx is used in reaction DPD simulations,where the coarse-grained (CG) -particles are composed of m species whose reaction rate kinetics are determined -from a set of n reaction rate equations through the fix rx command. -The species of one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. Style table/rx creates -interpolation tables of length N from pair potential and force values listed in a -file(s) as a function of distance. The files are read by the -pair_coeff command.

      +

      Style table/rx is used in reaction DPD simulations,where the +coarse-grained (CG) particles are composed of m species whose +reaction rate kinetics are determined from a set of n reaction rate +equations through the fix rx command. The species of +one CG particle can interact with a species in a neighboring CG +particle through a site-site interaction potential model. Style +table/rx creates interpolation tables of length N from pair +potential and force values listed in a file(s) as a function of +distance. The files are read by the pair_coeff +command.

      The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of N distances. During a simulation, these tables are used to interpolate @@ -170,7 +172,7 @@ stored at each of the N values in the table. The pair distance is used to find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or force.

      For the bitmap style, the N means to create interpolation tables -that are 2^N in length. <The pair distance is used to index into the +that are 2^N in length. The pair distance is used to index into the table via a fast bit-mapping technique (Wolff) and a linear interpolation is performed between adjacent table values.

      The following coefficients must be defined for each pair of atoms @@ -190,15 +192,15 @@ table itself (see below) will be used to build an interpolation table that extend to the largest tabulated distance. If specified, only file values up to the cutoff are used to create the interpolation table. The format of this file is described below.

      -

      The species tags define the site-site interaction potential between two -species contained within two different particles. -The species tags must either correspond to the species defined in the reaction -kinetics files specified with the fix rx command -or they must correspond to the tag “1fluid”, signifying interaction -with a product species mixture determined through a one-fluid approximation. +

      The species tags define the site-site interaction potential between +two species contained within two different particles. The species +tags must either correspond to the species defined in the reaction +kinetics files specified with the fix rx command or they +must correspond to the tag “1fluid”, signifying interaction with a +product species mixture determined through a one-fluid approximation. The interaction potential is weighted by the geometric average of the -concentrations of the two species. The coarse-grained potential -is stored before and after the reaction kinetics solver is applied, where +concentrations of the two species. The coarse-grained potential is +stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem).

      Here are some guidelines for using the pair_style table/rx command to @@ -312,8 +314,8 @@ commands do need to be specified in the restart input script.

      Restrictions

      -
      -
      none
      +

      This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.