diff --git a/bench/FERMI/README b/bench/FERMI/README index f8772483d1..db3f527bdc 100644 --- a/bench/FERMI/README +++ b/bench/FERMI/README @@ -14,7 +14,7 @@ lmp_linux_mixed lmp_linux_double The precision (single, mixed, double) refers to the GPU and USER-CUDA -pacakge precision. See the README files in the lib/gpu and lib/cuda +package precision. See the README files in the lib/gpu and lib/cuda directories for instructions on how to build the packages with different precisions. The GPU and USER-CUDA sub-sections of the doc/Section_accelerate.html file also describes this process. diff --git a/doc/.gitignore b/doc/.gitignore index bcd8f6db71..7d30949237 100644 --- a/doc/.gitignore +++ b/doc/.gitignore @@ -1,4 +1,5 @@ /html +/spelling /LAMMPS.epub /LAMMPS.mobi /Manual.pdf diff --git a/doc/Makefile b/doc/Makefile index e05715522b..79558674d7 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -22,7 +22,7 @@ endif SOURCES=$(wildcard src/*.txt) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) -.PHONY: help clean-all clean epub html pdf old venv +.PHONY: help clean-all clean epub html pdf old venv spelling # ------------------------------------------ @@ -44,6 +44,10 @@ clean-all: clean: rm -rf $(RSTDIR) html + rm -rf spelling + +clean-spelling: + rm -rf spelling html: $(OBJECTS) @(\ @@ -64,6 +68,17 @@ html: $(OBJECTS) @rm -rf html/USER/*/*.[sg]* @echo "Build finished. The HTML pages are in doc/html." +spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt + @(\ + . $(VENV)/bin/activate ;\ + pip install sphinxcontrib-spelling ;\ + cp -r src/* $(RSTDIR)/ ;\ + cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ + sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\ + deactivate ;\ + ) + @echo "Spell check finished." + epub: $(OBJECTS) @mkdir -p epub @rm -f LAMMPS.epub diff --git a/doc/src/2001/input_commands.html b/doc/src/2001/input_commands.html index 6f7266f2ca..797d6bec4e 100644 --- a/doc/src/2001/input_commands.html +++ b/doc/src/2001/input_commands.html @@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake", entirely rigid (e.g. water) the angletype option enables an additional check when SHAKE constraints are computed: if a cluster is of size 3 and both bonds in - the cluster are of a bondtype specified by the 2nd paramter of + the cluster are of a bondtype specified by the 2nd parameter of angletype, then the cluster is SHAKEn with an additional angle constraint that makes it rigid, using the equilibrium angle appropriate to the specified angletype @@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely since they will not be SHAKEn but neither will the angle force by computed for style region, a coeff of INF means + or - infinity (all the way to the boundary) -an atom can be assigned to multiple constraints, the contraints will be +an atom can be assigned to multiple constraints, the constraints will be applied in the reverse order they are assigned to that atom (e.g. each timestep, the last fix assigned to an atom will be applied to it first, then the next-to-last applied second, etc) @@ -689,7 +689,7 @@ coeffs: types remainder no other parameters required -used with "create temp" commmand to initialize velocities of atoms +used with "create temp" command to initialize velocities of atoms by default, the "create temp" command initializes the velocities of all atoms, this command limits the initialization to a group of atoms this command is only in force for the next "create temp" command, any @@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are applied when atoms move except for the following fixes associated with temperature control are not allowed (rescale, hoover/drag, langevin) -the minimizer does not invoke the "fix style shake" contraints on +the minimizer does not invoke the "fix style shake" constraints on bond lengths the minimizer does not invoke pressure control or volume control settings for good convergence, should specify use of smooth nonbond force fields @@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes can be used that are supported by native machine libraries this command is optional - if not used, a default mesh size will be chosen to satisfy accuracy criterion - if used, the - specifed mesh size will override the default + specified mesh size will override the default

@@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files when the minimizer is invoked this command means create a restart file at the end of the minimization with the filename filename.timestep.min a restart file stores atom and force-field information in binary form -allows program to restart from where it left off (see "read restart" commmand) +allows program to restart from where it left off (see "read restart" command) Default = 0 diff --git a/doc/src/99/basics.html b/doc/src/99/basics.html index a9a9cb4a8d..b6236f4bf9 100644 --- a/doc/src/99/basics.html +++ b/doc/src/99/basics.html @@ -167,7 +167,7 @@ tool on the small-system data file.

(6) flow

-2-d flow of Lennard-Jones atoms in a channel using various contraint +2-d flow of Lennard-Jones atoms in a channel using various constraint options.

(7) polymer

@@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f (compile and link with print.c) which can be used to generate random initial polymer configurations for bead-spring models like those used in examples/polymer. It uses an input polymer definition file (see -examples/polymer for two sample def files) that specfies how many +examples/polymer for two sample def files) that specifies how many chains of what length, a random number seed, etc.

diff --git a/doc/src/99/crib.html b/doc/src/99/crib.html index 0944980b17..80d64d3703 100755 --- a/doc/src/99/crib.html +++ b/doc/src/99/crib.html @@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.

  • maxtype = max # of atom types
  • - maxbond = max # of bonds to compute on one procesor + maxbond = max # of bonds to compute on one processor
  • maxangle = max # of angles to compute on one processor
  • diff --git a/doc/src/99/input_commands.html b/doc/src/99/input_commands.html index b904027153..baea02b5c2 100644 --- a/doc/src/99/input_commands.html +++ b/doc/src/99/input_commands.html @@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint use appropriate number of coeffs for a particular style the constraint itself is defined by the "fix style" command multiple groups of atoms can be assigned to the same constraint -an atom can be assigned to multiple constraints, the contraints will be +an atom can be assigned to multiple constraints, the constraints will be applied in the reverse order they are assigned to that atom (e.g. each timestep, the last fix assigned to an atom will be applied to it first, then the next-to-last applied second, etc) @@ -477,7 +477,7 @@ coeffs: types remainder no other parameters required -used with "create temp" commmand to initialize velocities of atoms +used with "create temp" command to initialize velocities of atoms by default, the "create temp" command initializes the velocities of all atoms, this command limits the initialization to a group of atoms this command is only in force for the next "create temp" command, any @@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size can be used that are supported by native machine libraries this command is optional - if not used, a default mesh size will be chosen to satisfy accuracy criterion - if used, the - specifed mesh size will override the default + specified mesh size will override the default Default = none @@ -1343,7 +1343,7 @@ value of 0 means never create one program will toggle between 2 filenames as the run progresses so always have at least one good file even if the program dies in mid-write restart file stores atom positions and velocities in binary form -allows program to restart from where it left off (see "read restart" commmand) +allows program to restart from where it left off (see "read restart" command) Default = 0 diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg b/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg new file mode 100644 index 0000000000..3d37ff25be Binary files /dev/null and b/doc/src/Eqs/pair_kolmogorov_crespi_z.jpg differ diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_z.tex b/doc/src/Eqs/pair_kolmogorov_crespi_z.tex new file mode 100644 index 0000000000..fb7ebf8dc4 --- /dev/null +++ b/doc/src/Eqs/pair_kolmogorov_crespi_z.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} +\thispagestyle{empty} + +\begin{document} + +\begin{eqnarray*} + E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ + V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\ + \rho_{ij}^2 = \rho_{ji}^2 & = & x_{ij}^2 + y_{ij}^2 ~\hspace{2cm} (\mathbf{n_i}\equiv\hat \mathbf{z})\\ + f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right) ^{2n} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 1da854c483..bb7a1452bc 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 -21 Feb 2017 version :c,h4 +10 Mar 2017 version :c,h4 Version info: :h4 diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 5b776defca..37201275fe 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index c36c961de3..6e526dcb51 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -281,12 +281,12 @@ the "minimize"_minimize.html command. A parallel tempering 3.4 Commands listed by category :link(cmd_4),h4 -This section lists all LAMMPS commands, grouped by category. The -"next section"_#cmd_5 lists the same commands alphabetically. The +This section lists core LAMMPS commands, grouped by category. +The "next section"_#cmd_5 lists all commands alphabetically. The next section also includes (long) lists of style options for entries that appear in the following categories as a single command (fix, compute, pair, etc). Commands that are added by user packages are not -included in these categories, but they are in the next section. +included in the categories here, but they are in the next section. Initialization: @@ -361,7 +361,7 @@ Settings: "timer"_timer.html, "timestep"_timestep.html -Operations within timestepping (fixes) and diagnositics (computes): +Operations within timestepping (fixes) and diagnostics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, @@ -1016,6 +1016,7 @@ package"_Section_start.html#start_3. "eff/cut"_pair_eff.html, "exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "lennard/mdf"_pair_mdf.html, "list"_pair_list.html, "lj/charmm/coul/long/soft (o)"_pair_charmm.html, @@ -1091,7 +1092,7 @@ package"_Section_start.html#start_3. "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, -"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c) +"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c) :line diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index f2ef986394..832c5718ab 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -574,11 +574,11 @@ group of atoms correctly. :dd {Bad quadratic solve for particle/line collision} :dt -This is an internal error. It should nornally not occur. :dd +This is an internal error. It should normally not occur. :dd {Bad quadratic solve for particle/tri collision} :dt -This is an internal error. It should nornally not occur. :dd +This is an internal error. It should normally not occur. :dd {Bad real space Coulomb cutoff in fix tune/kspace} :dt @@ -912,7 +912,7 @@ Atoms can not be added afterwards to this fix option. :dd {Cannot append atoms to a triclinic box} :dt -The simulation box must be defined with edges alligned with the +The simulation box must be defined with edges aligned with the Cartesian axes. :dd {Cannot balance in z dimension for 2d simulation} :dt @@ -992,7 +992,7 @@ file. :dd LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 factor that partitions the computation between real space and k-space -for Disptersion interactions. :dd +for Dispersion interactions. :dd {Cannot create an atom map unless atoms have IDs} :dt @@ -1327,7 +1327,7 @@ Self-explanatory. :dd This file is created when you use some LAMMPS features, to indicate what paper you should cite on behalf of those who implemented -the feature. Check that you have write priveleges into the directory +the feature. Check that you have write privileges into the directory you are running in. :dd {Cannot open log.lammps for writing} :dt @@ -2005,7 +2005,7 @@ Self-explanatory. :dd {Cannot use fix reax/bonds without pair_style reax} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt @@ -2088,7 +2088,7 @@ Self-explanatory. :dd {Cannot use lines with fix srd unless overlap is set} :dt -This is because line segements are connected to each other. :dd +This is because line segments are connected to each other. :dd {Cannot use multiple fix wall commands with pair brownian} :dt @@ -2131,7 +2131,7 @@ Self-explanatory. :dd {Cannot use newton pair with born/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use newton pair with buck/coul/cut/gpu pair style} :dt @@ -2291,7 +2291,7 @@ Self-explanatory. :dd {Cannot use newton pair with zbl/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use non-zero forces in an energy minimization} :dt @@ -2641,11 +2641,11 @@ uses a pairwise neighbor list. :dd {Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd +Radius cannot be bigger than 1/2 of a non-axis periodic dimension. :dd {Compute chunk/atom bin/sphere radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of any periodic dimention. :dd +Radius cannot be bigger than 1/2 of any periodic dimension. :dd {Compute chunk/atom compute array is accessed out-of-range} :dt @@ -2706,15 +2706,15 @@ It will only store IDs if its compress option is enabled. :dd {Compute chunk/atom stores no coord1 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord2 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord3 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom variable is not atom-style variable} :dt @@ -2735,11 +2735,11 @@ is used to find clusters. :dd {Compute cna/atom cutoff is longer than pairwise cutoff} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute cna/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute com/chunk does not use chunk/atom compute} :dt @@ -2747,7 +2747,7 @@ The style of the specified compute is not chunk/atom. :dd {Compute contact/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute contact/atom requires atom style sphere} :dt @@ -2760,7 +2760,7 @@ since those atoms are not in the neighbor list. :dd {Compute coord/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute damage/atom requires peridynamic potential} :dt @@ -2790,7 +2790,7 @@ Self-explanatory. :dd {Compute erotate/asphere requires extended particles} :dt -This compute cannot be used with point paritlces. :dd +This compute cannot be used with point particles. :dd {Compute erotate/rigid with non-rigid fix-ID} :dt @@ -2835,7 +2835,7 @@ Cannot compute order parameter beyond cutoff. :dd {Compute hexorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute improper/local used when impropers are not allowed} :dt @@ -2881,11 +2881,11 @@ Cannot compute order parameter beyond cutoff. :dd {Compute orientorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute pair must use group all} :dt -Pair styles accumlate energy on all atoms. :dd +Pair styles accumulate energy on all atoms. :dd {Compute pe must use group all} :dt @@ -2935,7 +2935,7 @@ The style of the specified compute is not chunk/atom. :dd {Compute property/local cannot use these inputs together} :dt Only inputs that generate the same number of datums can be used -togther. E.g. bond and angle quantities cannot be mixed. :dd +together. E.g. bond and angle quantities cannot be mixed. :dd {Compute property/local does not (yet) work with atom_style template} :dt @@ -3079,7 +3079,7 @@ Self-explanatory. :dd {Compute temp/asphere requires extended particles} :dt -This compute cannot be used with point paritlces. :dd +This compute cannot be used with point particles. :dd {Compute temp/body requires atom style body} :dt @@ -3524,12 +3524,12 @@ path and name are correct. :dd {Could not process Python file} :dt -The Python code in the specified file was not run sucessfully by +The Python code in the specified file was not run successfully by Python, probably due to errors in the Python code. :dd {Could not process Python string} :dt -The Python code in the here string was not run sucessfully by Python, +The Python code in the here string was not run successfully by Python, probably due to errors in the Python code. :dd {Coulomb PPPMDisp order has been reduced below minorder} :dt @@ -3638,7 +3638,7 @@ Self-explanatory. :dd {Cutoffs missing in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Cutoffs missing in pair_style lj/long/coul/long} :dt @@ -4385,7 +4385,7 @@ Self-explanatory. :dd {Fix ave/chunk does not use chunk/atom compute} :dt -The specified conpute is not for a compute chunk/atom command. :dd +The specified compute is not for a compute chunk/atom command. :dd {Fix ave/chunk fix does not calculate a per-atom array} :dt @@ -4617,11 +4617,11 @@ An index for the array is out of bounds. :dd {Fix ave/time compute does not calculate a scalar} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate a vector} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate an array} :dt @@ -4970,7 +4970,7 @@ Self-explanatory. :dd {Fix langevin angmom requires extended particles} :dt -This fix option cannot be used with point paritlces. :dd +This fix option cannot be used with point particles. :dd {Fix langevin omega is not yet implemented with kokkos} :dt @@ -6171,7 +6171,7 @@ map command will force an atom map to be created. :dd {Initial temperatures not all set in fix ttm} :dt -Self-explantory. :dd +Self-explanatory. :dd {Input line quote not followed by whitespace} :dt @@ -6199,7 +6199,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd {Insufficient Jacobi rotations for triangle} :dt -The calculation of the intertia tensor of the triangle failed. This +The calculation of the inertia tensor of the triangle failed. This should not happen if it is a reasonably shaped triangle. :dd {Insufficient memory on accelerator} :dt @@ -6463,15 +6463,15 @@ Self-explanatory. :dd {Invalid attribute in dump custom command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump local command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump modify command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid basis setting in create_atoms command} :dt @@ -6737,7 +6737,7 @@ or cause multiple files to be written. :dd Filenames used with the dump xyz style cannot be binary or cause files to be written by each processor. :dd -{Invalid dump_modify threshhold operator} :dt +{Invalid dump_modify threshold operator} :dt Operator keyword used for threshold specification in not recognized. :dd @@ -6751,7 +6751,7 @@ The fix is not recognized. :dd {Invalid fix ave/time off column} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid fix box/relax command for a 2d simulation} :dt @@ -7313,7 +7313,7 @@ Self-explanatory. Check the input script or data file. :dd {LJ6 off not supported in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Label wasn't found in input script} :dt @@ -7361,7 +7361,7 @@ This should not occur. Report the problem to the developers. :dd Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. :dd {MEAM library error %d} :dt @@ -7526,7 +7526,7 @@ Self-explanatory. :dd {Molecule template ID for create_atoms does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Molecule template ID for fix deposit does not exist} :dt @@ -7552,7 +7552,7 @@ Self-explanatory. :dd Self-explanatory. :dd -{Molecule toplogy/atom exceeds system topology/atom} :dt +{Molecule topology/atom exceeds system topology/atom} :dt The number of bonds, angles, etc per-atom in the molecule exceeds the system setting. See the create_box command for how to specify these @@ -7792,7 +7792,7 @@ Self-explanatory. :dd {Must use variable energy with fix addforce} :dt -Must define an energy vartiable when applyting a dynamic +Must define an energy variable when applying a dynamic force during minimization. :dd {Must use variable energy with fix efield} :dt @@ -8042,7 +8042,7 @@ Self-explanatory. :dd {Non digit character between brackets in variable} :dt -Self-explantory. :dd +Self-explanatory. :dd {Non integer # of swaps in temper command} :dt @@ -8663,7 +8663,7 @@ not be invoked by bond_style quartic. :dd {Pair style does not support compute group/group} :dt The pair_style does not have a single() function, so it cannot be -invokded by the compute group/group command. :dd +invoked by the compute group/group command. :dd {Pair style does not support compute pair/local} :dt @@ -8948,11 +8948,11 @@ Self-explanatory. :dd {Pair yukawa/colloid requires atom style sphere} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid requires atoms with same type have same radius} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid/gpu requires atom style sphere} :dt @@ -9166,7 +9166,7 @@ Self-explanatory. :dd {Python function evaluation failed} :dt -The Python function did not run succesfully and/or did not return a +The Python function did not run successfully and/or did not return a value (if it is supposed to return a value). This is probably due to some error condition in the function. :dd @@ -10025,7 +10025,7 @@ make sense in between runs. :dd {Threshhold for an atom property that isn't allocated} :dt -A dump threshhold has been requested on a quantity that is +A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. :dd {Timestep must be >= 0} :dt @@ -10087,7 +10087,7 @@ to a large size. :dd {Too many atom triplets for pair bop} :dt The number of three atom groups for angle determinations exceeds the -expected number. Check your atomic structrure to ensure that it is +expected number. Check your atomic structure to ensure that it is realistic. :dd {Too many atoms for dump dcd} :dt @@ -10155,7 +10155,7 @@ to a large size. :dd {Too many timesteps} :dt -The cummulative timesteps must fit in a 64-bit integer. :dd +The cumulative timesteps must fit in a 64-bit integer. :dd {Too many timesteps for NEB} :dt @@ -10654,7 +10654,7 @@ Only atom-style variables can be used. :dd {Variable for region cylinder is invalid style} :dt -Only equal-style varaibles are allowed. :dd +Only equal-style variables are allowed. :dd {Variable for region is invalid style} :dt @@ -10666,7 +10666,7 @@ Self-explanatory. :dd {Variable for region sphere is invalid style} :dt -Only equal-style varaibles are allowed. :dd +Only equal-style variables are allowed. :dd {Variable for restart is invalid style} :dt @@ -10707,7 +10707,7 @@ Self-explanatory. :dd {Variable has circular dependency} :dt A circular dependency is when variable "a" in used by variable "b" and -variable "b" is also used by varaible "a". Circular dependencies with +variable "b" is also used by variable "a". Circular dependencies with longer chains of dependence are also not allowed. :dd {Variable name between brackets must be alphanumeric or underscore characters} :dt @@ -10796,7 +10796,7 @@ Self-explanatory. :dd {Variable name for fix deform does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Variable name for fix efield does not exist} :dt @@ -11083,7 +11083,7 @@ for a dihedral) and adding a small amount of stretch. :dd {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt -Self-explantory. :dd +Self-explanatory. :dd {Calling write_dump before a full system init.} :dt @@ -11414,7 +11414,7 @@ The command options you have used caused atoms to be lost. :dd Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. :dd {MSM mesh too small, increasing to 2 points in each direction} :dt @@ -11452,7 +11452,7 @@ i.e. the first molecule in the template. :dd {Molecule template for fix shake has multiple molecules} :dt -The fix shake command will only recoginze molecules of a single +The fix shake command will only recognize molecules of a single type, i.e. the first molecule in the template. :dd {More than one compute centro/atom} :dt @@ -11537,7 +11537,7 @@ neigh_modify exclude command. :dd If a thermo_style command is used after a thermo_modify command, the settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify commmand acts on +default values. This is because the thermo_modify command acts on the currently defined thermo style, and a thermo_style command creates a new style. :dd @@ -11589,7 +11589,7 @@ This may not be what you intended. :dd {One or more dynamic groups may not be updated at correct point in timestep} :dt -If there are other fixes that act immediately after the intitial stage +If there are other fixes that act immediately after the initial stage of time integration within a timestep (i.e. after atoms move), then the command that sets up the dynamic group should appear after those fixes. This will insure that dynamic group assignments are made @@ -11886,7 +11886,7 @@ Self-explanatory. :dd {Using largest cutoff for buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Using largest cutoff for lj/long/coul/long} :dt diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt index 438284c9da..93e9947506 100644 --- a/doc/src/Section_history.txt +++ b/doc/src/Section_history.txt @@ -37,7 +37,7 @@ pitfalls or alternatives. Please see some of the closed issues for examples of how to suggest code enhancements, submit proposed changes, or report -possible bugs and how they are resoved. +possible bugs and how they are resolved. As an alternative to using GitHub, you may e-mail the "core developers"_http://lammps.sandia.gov/authors.html or send diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index b69d69614a..8cfbe1c46c 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -573,7 +573,7 @@ LJ epsilon of O-O = 0.16275 LJ sigma of O-O = 3.16435 LJ epsilon, sigma of OH, HH = 0.0 :all(b),p -Note that the when using the TIP4P pair style, the neighobr list +Note that the when using the TIP4P pair style, the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2 * (OM distance), to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is @@ -618,7 +618,7 @@ any of the parameters above, though it becomes a different model in that mode of usage. The SPC/E (extended) water model is the same, except -the partial charge assignemnts change: +the partial charge assignments change: O charge = -0.8476 H charge = 0.4238 :all(b),p @@ -863,7 +863,7 @@ boundary conditions in specific dimensions. See the command doc pages for details. The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simluation box is created. This happens in one of 3 ways. +time the simulation box is created. This happens in one of 3 ways. If the "create_box"_create_box.html command is used with a region of style {prism}, then a triclinic box is setup. See the "region"_region.html command for details. If the @@ -982,10 +982,10 @@ used with non-orthogonal basis vectors to define a lattice that will tile a triclinic simulation box via the "create_atoms"_create_atoms.html command. -A second use is to run Parinello-Rahman dyanamics via the "fix +A second use is to run Parinello-Rahman dynamics via the "fix npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure -tensor. The analalog for an "energy minimization"_minimize.html is +tensor. The analog for an "energy minimization"_minimize.html is the "fix box/relax"_fix_box_relax.html command. A third use is to shear a bulk solid to study the response of the @@ -1392,7 +1392,7 @@ custom"_dump.html command. There is also a "dump local"_dump.html format where the user specifies what local values to output. A pre-defined index keyword can be -specified to enumuerate the local values. Two additional kinds of +specified to enumerate the local values. Two additional kinds of keywords can also be specified (c_ID, f_ID), where a "compute"_compute.html or "fix"_fix.html or "variable"_variable.html provides the values to be output. In each case, the compute or fix @@ -1525,7 +1525,7 @@ Variables that generate values to output :h5,link(variable) "Variables"_variable.html defined in an input script can store one or more strings. But equal-style, vector-style, and atom-style or atomfile-style variables generate a global scalar value, global vector -or values, or a per-atom vector, resepctively, when accessed. The +or values, or a per-atom vector, respectively, when accessed. The formulas used to define these variables can contain references to the thermodynamic keywords and to global and per-atom data generated by computes, fixes, and other variables. The values generated by @@ -1585,7 +1585,7 @@ Temperature is computed as kinetic energy divided by some number of degrees of freedom (and the Boltzmann constant). Since kinetic energy is a function of particle velocity, there is often a need to distinguish between a particle's advection velocity (due to some -aggregate motiion of particles) and its thermal velocity. The sum of +aggregate motion of particles) and its thermal velocity. The sum of the two is the particle's total velocity, but the latter is often what is wanted to compute a temperature. @@ -1640,14 +1640,14 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. -DPD thermostatting alters pairwise interactions in a manner analagous +DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix langevin"_fix_langevin.html. Any of the thermostatting fixes can use temperature computes that remove bias which has two effects. First, the current calculated temperature, which is compared to the requested target temperature, is -caluclated with the velocity bias removed. Second, the thermostat +calculated with the velocity bias removed. Second, the thermostat adjusts only the thermal temperature component of the particle's velocities, which are the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the @@ -1888,7 +1888,7 @@ instances of LAMMPS to perform different calculations. The lammps_open_no_mpi() function is similar except that no MPI communicator is passed from the caller. Instead, MPI_COMM_WORLD is -used to instantiate LAMMPS, and MPI is initialzed if necessary. +used to instantiate LAMMPS, and MPI is initialized if necessary. The lammps_close() function is used to shut down an instance of LAMMPS and free all its memory. @@ -1976,7 +1976,7 @@ The lammps_get_natoms() function returns the total number of atoms in the system and can be used by the caller to allocate space for the lammps_gather_atoms() and lammps_scatter_atoms() functions. The gather function collects atom info of the requested type (atom coords, -types, forces, etc) from all procsesors, orders them by atom ID, and +types, forces, etc) from all processors, orders them by atom ID, and returns a full list to each calling processor. The scatter function does the inverse. It distributes the same kinds of values, passed by the caller, to each atom owned by individual processors. @@ -2013,7 +2013,7 @@ a simple Lennard-Jones fluid model. Also, see "this section"_Section_howto.html#howto_21 of the manual for an analogous discussion for viscosity. -The thermal conducitivity tensor kappa is a measure of the propensity +The thermal conductivity tensor kappa is a measure of the propensity of a material to transmit heat energy in a diffusive manner as given by Fourier's law @@ -2099,7 +2099,7 @@ and grad(Vstream) is the spatial gradient of the velocity of the fluid moving in another direction, normal to the area through which the momentum flows. Viscosity thus has units of pressure-time. -The first method is to perform a non-equlibrium MD (NEMD) simulation +The first method is to perform a non-equilibrium MD (NEMD) simulation by shearing the simulation box via the "fix deform"_fix_deform.html command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to thermostat the fluid via the SLLOD equations of motion. @@ -2125,7 +2125,7 @@ the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is swapped between atoms in two different layers of the simulation box in a different dimension. This induces a velocity gradient which can be monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cummulative momentum transfer that it performs. +The fix tallies the cumulative momentum transfer that it performs. See the "fix viscosity"_fix_viscosity.html command for details. The fourth method is based on the Green-Kubo (GK) formula which @@ -2268,7 +2268,7 @@ atoms with same local defect structure | chunk ID = output of "compute centro/at Note that chunk IDs are integer values, so for atom properties or computes that produce a floating point value, they will be truncated to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple intergers. +scales the floating point value to spread it across multiple integers. Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins. @@ -2353,7 +2353,7 @@ largest cluster or fastest diffusing molecule. :l Example calculations with chunks :h5 -Here are eaxmples using chunk commands to calculate various +Here are examples using chunk commands to calculate various properties: (1) Average velocity in each of 1000 2d spatial bins: @@ -2424,7 +2424,7 @@ which both have their up- and downsides. The first approach is to set desired real-space an kspace accuracies via the {kspace_modify force/disp/real} and {kspace_modify force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependend on the chosen unit +specified in force units and are thus dependent on the chosen unit settings. For real units, 0.0001 and 0.002 seem to provide reasonable accurate and efficient computations for the real-space and kspace accuracies. 0.002 and 0.05 work well for most systems using lj @@ -2444,7 +2444,7 @@ performance. This approach provides a fast initialization of the simulation. However, it is sensitive to errors: A combination of parameters that will perform well for one system might result in far-from-optimal conditions for other simulations. For example, -parametes that provide accurate and fast computations for +parameters that provide accurate and fast computations for all-atomistic force fields can provide insufficient accuracy or united-atomistic force fields (which is related to that the latter typically have larger dispersion coefficients). @@ -2478,7 +2478,7 @@ arithmetic mixing rule substantially increases the computational cost. The computational overhead can be reduced using the {kspace_modify mix/disp geom} and {kspace_modify splittol} commands. The first command simply enforces geometric mixing of the dispersion -coeffiecients in kspace computations. This introduces some error in +coefficients in kspace computations. This introduces some error in the computations but will also significantly speed-up the simulations. The second keyword sets the accuracy with which the dispersion coefficients are approximated using a matrix factorization @@ -2497,7 +2497,7 @@ to specify this command explicitly. 6.25 Polarizable models :link(howto_25),h4 In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environements. Polarizable +materials respond to their electrostatic environments. Polarizable systems can be simulated in LAMMPS using three methods: the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html @@ -2551,7 +2551,7 @@ this is done by "fix qeq/dynamic"_fix_qeq.html, and for the charge-on-spring models by the methods outlined in the next two sections. The assignment of masses to the additional degrees of freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the poarizable models and the simulation +choosing the parameters of the polarizable models and the simulation conditions. In the core-shell model the vibration of the shells is kept faster @@ -2727,18 +2727,18 @@ If "compute temp/cs"_compute_temp_cs.html is used, the decoupled relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small momentum to the system, which is noticable over long trajectories. -Therefore it is recomendable to use the "fix +Therefore it is recommendable to use the "fix momentum"_fix_momentum.html command in combination with "compute temp/cs"_compute_temp_cs.html when equilibrating the system to prevent any drift. -When intializing the velocities of a system with core/shell pairs, it +When initializing the velocities of a system with core/shell pairs, it is also desirable to not introduce energy into the relative motion of the core/shell particles, but only assign a center-of-mass velocity to the pairs. This can be done by using the {bias} keyword of the "velocity create"_velocity.html command and assigning the "compute temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html commmand, e.g. +"velocity"_velocity.html command, e.g. velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre @@ -2808,7 +2808,7 @@ CS-Info # header of additional section :pre 6.27 Drude induced dipoles :link(howto_27),h4 The thermalized Drude model, similarly to the "core-shell"_#howto_26 -model, representes induced dipoles by a pair of charges (the core atom +model, represents induced dipoles by a pair of charges (the core atom and the Drude particle) connected by a harmonic spring. The Drude model has a number of features aimed at its use in molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt index 228c7199fd..7d1fe03d01 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -159,17 +159,17 @@ pack_comm_vel: add velocity info to communication buffer (required) pack_comm_hybrid: store extra info unique to this atom style (optional) unpack_comm: retrieve an atom's info from the buffer (required) unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retreive extra info unique to this atom style (optional) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) pack_reverse: store an atom's info in a buffer communicating partial forces (required) pack_reverse_hybrid: store extra info unique to this atom style (optional) unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retreive extra info unique to this atom style (optional) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) pack_border_vel: add velocity info to buffer (required) pack_border_hybrid: store extra info unique to this atom style (optional) unpack_border: retrieve an atom's info from the buffer (required) unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retreive extra info unique to this atom style (optional) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) pack_exchange: store all an atom's info to migrate to another processor (required) unpack_exchange: retrieve an atom's info from the buffer (required) size_restart: number of restart quantities associated with proc's atoms (required) @@ -369,7 +369,7 @@ pre_force_respa: same as pre_force, but for rRESPA (optional) post_force_respa: same as post_force, but for rRESPA (optional) final_integrate_respa: same as final_integrate, but for rRESPA (optional) min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional) +min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) min_store: store extra data for linesearch based minimization on a LIFO stack (optional) min_pushstore: push the minimization LIFO stack one element down (optional) min_popstore: pop the minimization LIFO stack one element up (optional) @@ -517,7 +517,7 @@ class. See region.h for details. inside: determine whether a point is in the region surface_interior: determine if a point is within a cutoff distance inside of surc surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-depedent variable :tb(s=:) +shape_update : change region shape if set by time-dependent variable :tb(s=:) :line @@ -601,16 +601,16 @@ Adding keywords for the "thermo_style custom"_thermo_style.html command "here"_Section_modify.html#mod_13 on this page. Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaulate() method. Search for +editing one section of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding a new group function can be done by editing one section of the -Variable::evaulate() method. Search for the word "customize" to find +Variable::evaluate() method. Search for the word "customize" to find the appropriate location. You may need to add a new method to the Group class as well (see the group.cpp file). Accessing a new atom-based vector can be done by editing one section -of the Variable::evaulate() method. Search for the word "customize" +of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding new "compute styles"_compute.html (whose calculated values can @@ -740,7 +740,7 @@ entry to add to the USER-MISC/README file in that dir, along with the contribute several individual features. :l If you want your contribution to be added as a user-contribution and -it is several related featues, it is probably best to make it a user +it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief @@ -785,10 +785,10 @@ file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The -prerequiste for building the HTML format files are Python 3.x and +prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resuling HTML format +"make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code. :l For a new package (or even a single command) you should include one or diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index b9b96d66ad..e6a0132e2c 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -94,7 +94,7 @@ Package, Description, Author(s), Doc page, Example, Library :tb(ea=c) The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. +responsible for creating and maintaining the package. (1) The COLLOID package includes Fast Lubrication Dynamics pair styles which were created by Amit Kumar and Michael Bybee from Jonathan @@ -462,7 +462,7 @@ options you are optimizing for: CPU acceleration via OpenMP, GPU acceleration, or Intel Xeon Phi. (You can build multiple times to create LAMMPS executables for different hardware.) It also requires a C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is -used, and an appopriate KOKKOS_ARCH setting should be made in your +used, and an appropriate KOKKOS_ARCH setting should be made in your Makefile.machine for your GPU hardware and NVIDIA software. The simplest way to do this is to use Makefile.kokkos_cuda or @@ -955,8 +955,8 @@ multi-replica simulations in LAMMPS. Multi-replica methods included in the package are nudged elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated dynamics (TAD), parallel tempering, and a verlet/split algorithm for performing long-range -Coulombics on one set of processors, and the remainded of the force -field calcalation on another set. +Coulombics on one set of processors, and the remainder of the force +field calculation on another set. To install via make or Make.py: @@ -1176,7 +1176,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library :link(VMD,http://www.ks.uiuc.edu/Research/vmd) The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. +responsible for creating and maintaining the package. (1) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia). @@ -1295,13 +1295,13 @@ integrators with improved stability. See these doc pages to get started: -"bond_style oxdna_fene"_bond_oxdna_fene.html -"pair_style oxdna_excv"_pair_oxdna_excv.html +"bond_style oxdna/fene"_bond_oxdna.html +"pair_style oxdna/..."_pair_oxdna.html "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul Supporting info: /src/USER-CGDNA/README, "bond_style -oxdna_fene"_bond_oxdna_fene.html, "pair_style -oxdna_excv"_pair_oxdna_excv.html, "fix +oxdna/fene"_bond_oxdna.html, "pair_style +oxdna/..."_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich @@ -1778,7 +1778,7 @@ particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. -For technical details about this implemention of ReaxFF, see +For technical details about this implementation of ReaxFF, see this paper: Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods @@ -1848,7 +1848,7 @@ See this doc page to get started: The persons who created the USER-SMTBQ package are Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at -these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact them directly if you have any questions. Examples: examples/USER/smtbq diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt index 39fe734cce..0cc79b0943 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Section_perf.txt @@ -69,7 +69,7 @@ bench/in.lj input script. For all the benchmarks, a useful metric is the CPU cost per atom per timestep. Since performance scales roughly linearly with problem size -and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained +and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained potentials), the run time of any problem using the same model (atom style, force field, cutoff, etc) can then be estimated. diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index bd4dfcf538..50807e2d95 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python. Section 11.8 gives some examples of coupling LAMMPS to other tools via Python. For example, LAMMPS can easily be coupled to a GUI or other visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are inlcluded in the python +LAMMPS runs. Examples of such scripts are included in the python directory. Two advantages of using Python to run LAMMPS are how concise the @@ -177,7 +177,7 @@ of Python and your machine to successfully build LAMMPS. See the lib/python/README file for more info. If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceeding section (11.1) +must also follow the steps overviewed in the preceding section (11.1) for running LAMMPS from Python. I.e. you must build LAMMPS as a shared library and insure that Python can find the python/lammps.py file and the shared library. @@ -325,7 +325,7 @@ sudo python setup.py install :pre Again, the "sudo" is only needed if required to copy PyPar files into your Python distribution's site-packages directory. -If you have successully installed PyPar, you should be able to run +If you have successfully installed PyPar, you should be able to run Python and type import pypar :pre @@ -369,7 +369,7 @@ user privilege into the user local directory type python setup.py install --user :pre -If you have successully installed mpi4py, you should be able to run +If you have successfully installed mpi4py, you should be able to run Python and type from mpi4py import MPI :pre @@ -610,7 +610,7 @@ lmp = lammps() :pre create an instance of LAMMPS, wrapped in a Python class by the lammps Python module, and return an instance of the Python class as lmp. It -is used to make all subequent calls to the LAMMPS library. +is used to make all subsequent calls to the LAMMPS library. Additional arguments to lammps() can be used to tell Python the name of the shared library to load or to pass arguments to the LAMMPS @@ -662,7 +662,7 @@ or integers (int **) is returned. You need to specify the appropriate data type via the type argument. For extract_compute() and extract_fix(), the global, per-atom, or -local data calulated by the compute or fix can be accessed. What is +local data calculated by the compute or fix can be accessed. What is returned depends on whether the compute or fix calculates a scalar or vector or array. For a scalar, a single double value is returned. If the compute or fix calculates a vector or array, a pointer to the @@ -774,7 +774,7 @@ demo.py, invoke various LAMMPS library interface routines, simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, split.py, same as simple.py but running in parallel on a subset of procs, gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temeperature plot with GnuPlot via Pizza.py, +plot.py, real-time temperature plot with GnuPlot via Pizza.py, viz_tool.py, real-time viz via some viz package, vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 2146830753..47643569e6 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -80,7 +80,7 @@ This section has the following sub-sections: Read this first :h5,link(start_2_1) -If you want to avoid building LAMMPS yourself, read the preceeding +If you want to avoid building LAMMPS yourself, read the preceding section about options available for downloading and installing executables. Details are discussed on the "download"_download page. @@ -251,7 +251,7 @@ re-compile, after typing "make clean" (which will describe different clean options). The LMP_INC variable is used to include options that turn on ifdefs -within the LAMMPS code. The options that are currently recogized are: +within the LAMMPS code. The options that are currently recognized are: -DLAMMPS_GZIP -DLAMMPS_JPEG @@ -362,7 +362,7 @@ installed on your platform. If MPI is installed on your system in the usual place (under /usr/local), you also may not need to specify these 3 variables, assuming /usr/local is in your path. On some large parallel machines which use "modules" for their compile/link -environements, you may simply need to include the correct module in +environments, you may simply need to include the correct module in your build environment, before building LAMMPS. Or the parallel machine may have a vendor-provided MPI which the compiler has no trouble finding. @@ -430,7 +430,7 @@ use the KISS library described above. You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, so the compiler and linker can find the needed FFT header and library files. Note that on some large parallel machines which use "modules" -for their compile/link environements, you may simply need to include +for their compile/link environments, you may simply need to include the correct module in your build environment. Or the parallel machine may have a vendor-provided FFT library which the compiler has no trouble finding. @@ -450,7 +450,7 @@ you must also manually specify the correct library, namely -lsfftw or The FFT_INC variable also allows for a -DFFT_SINGLE setting that will use single-precision FFTs with PPPM, which can speed-up long-range -calulations, particularly in parallel or on GPUs. Fourier transform +calculations, particularly in parallel or on GPUs. Fourier transform and related PPPM operations are somewhat insensitive to floating point truncation errors and thus do not always need to be performed in double precision. Using the -DFFT_SINGLE setting trades off a little @@ -682,7 +682,7 @@ various make commands that can be used to manipulate packages. If you use a command in a LAMMPS input script that is part of a package, you must have built LAMMPS with that package, else you will get an error that the style is invalid or the command is unknown. -Every command's doc page specfies if it is part of a package. You can +Every command's doc page specifies if it is part of a package. You can also type lmp_machine -h :pre @@ -1008,7 +1008,7 @@ Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or rename if desired. Likewise it creates an executable named src/lmp_auto, which you can rename using the -o switch if desired. -The most recently executed Make.py commmand is saved in +The most recently executed Make.py command is saved in src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke the last command, or you can save a sequence of one or more Make.py commands to a file and invoke the file of commands using "-r". You @@ -1064,7 +1064,7 @@ src/MAKE/Makefile.foo and perform the build in the directory Obj_shared_foo. This is so that each file can be compiled with the -fPIC flag which is required for inclusion in a shared library. The build will create the file liblammps_foo.so which another application -can link to dyamically. It will also create a soft link liblammps.so, +can link to dynamically. It will also create a soft link liblammps.so, which will point to the most recently built shared library. This is the file the Python wrapper loads by default. @@ -1416,8 +1416,8 @@ LAMMPS is compiled with CUDA=yes. numa Nm :pre This option is only relevant when using pthreads with hwloc support. -In this case Nm defines the number of NUMA regions (typicaly sockets) -on a node which will be utilizied by a single MPI rank. By default Nm +In this case Nm defines the number of NUMA regions (typically sockets) +on a node which will be utilized by a single MPI rank. By default Nm = 1. If this option is used the total number of worker-threads per MPI rank is threads*numa. Currently it is always almost better to assign at least one MPI rank per NUMA region, and leave numa set to @@ -1481,7 +1481,7 @@ replica runs on on one or a few processors. Note that with MPI installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. -To run multiple independent simulatoins from one input script, using +To run multiple independent simulations from one input script, using multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 of the manual. World- and universe-style "variables"_variable.html are useful in this context. @@ -1760,7 +1760,7 @@ The first section provides a global loop timing summary. The {loop time} is the total wall time for the section. The {Performance} line is provided for convenience to help predicting the number of loop continuations required and for comparing performance with other, -similar MD codes. The {CPU use} line provides the CPU utilzation per +similar MD codes. The {CPU use} line provides the CPU utilization per MPI task; it should be close to 100% times the number of OpenMP threads (or 1 of no OpenMP). Lower numbers correspond to delays due to file I/O or insufficient thread utilization. diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index f469390ced..83fb7a6bce 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -471,7 +471,7 @@ These tools were written by Aidan Thompson at Sandia. restart2data tool :h4,link(restart) NOTE: This tool is now obsolete and is not included in the current -LAMMPS distribution. This is becaues there is now a +LAMMPS distribution. This is because there is now a "write_data"_write_data.html command, which can create a data file from within an input script. Running LAMMPS with the "-r" "command-line switch"_Section_start.html#start_7 as follows: diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index 2f3bf4a6cf..f4c33f5076 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -27,7 +27,7 @@ syntax

    • fix_modify AtC consistent_fe_initialization <on | off>

    examples

    diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index 088e6db113..f7f655a639 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -20,7 +20,7 @@ coprocessors via offloading neighbor list and non-bonded force calculations to the Phi. The same C++ code is used in both cases. When offloading to a coprocessor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows -LAMMPS to run on the CPU cores and coprocessor cores simulataneously. +LAMMPS to run on the CPU cores and coprocessor cores simultaneously. [Currently Available USER-INTEL Styles:] @@ -115,7 +115,7 @@ coprocessor and an Intel compiler are required. For this, the recommended version of the Intel compiler is 14.0.1.106 or versions 15.0.2.044 and higher. -Although any compiler can be used with the USER-INTEL pacakge, +Although any compiler can be used with the USER-INTEL package, currently, vectorization directives are disabled by default when not using Intel compilers due to lack of standard support and observations of decreased performance. The OpenMP standard now @@ -428,7 +428,7 @@ to the card. This allows for overlap of MPI communication of forces with computation on the coprocessor when the "newton"_newton.html setting is "on". The default is dependent on the style being used, however, better performance may be achieved by setting this option -explictly. +explicitly. When using offload with CPU Hyper-Threading disabled, it may help performance to use fewer MPI tasks and OpenMP threads than available diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index 3d31344c24..3bfd4bf379 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -217,7 +217,7 @@ best performance its CCFLAGS setting should use -O3 and have a KOKKOS_ARCH setting that matches the compute capability of your NVIDIA hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note the minimal required compute capability is 2.0, but this will give -signicantly reduced performance compared to Kepler generation GPUs +significantly reduced performance compared to Kepler generation GPUs with compute capability 3.x. For the LINK setting, "nvcc" should not be used; instead use g++ or another compiler suitable for linking C++ applications. Often you will want to use your MPI compiler wrapper @@ -234,7 +234,7 @@ provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is given in "Section 5.3"_Section_accelerate.html#acc_3. -KOKKOS_ARCH=KNC enables compiler switches needed when compling for an +KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an Intel Phi processor. KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism @@ -272,7 +272,7 @@ coprocessor support you need to insure there are one or more MPI tasks per coprocessor, and choose the number of coprocessor threads to use per MPI task (via the "-k" command-line switch discussed below). The product of MPI tasks * coprocessor threads/task should not exceed the -maximum number of threads the coproprocessor is designed to run, +maximum number of threads the coprocessor is designed to run, otherwise performance will suffer. This value is 240 for current generation Xeon Phi(TM) chips, which is 60 physical cores * 4 threads/core. Note that with the KOKKOS package you do not need to @@ -333,7 +333,7 @@ device=CUDA are the same. You must still use the "-k on" "command-line switch"_Section_start.html#start_7 to enable the KOKKOS package, and -specify its additional arguments for hardware options appopriate to +specify its additional arguments for hardware options appropriate to your system, as documented above. Use the "suffix kk"_suffix.html command, or you can explicitly add a diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt index 8c90e1fd3a..bdd3707ccb 100644 --- a/doc/src/angle_hybrid.txt +++ b/doc/src/angle_hybrid.txt @@ -81,7 +81,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. Unlike other angle styles, the hybrid angle style does not store angle coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when retarting a simulation from a restart +files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify angle_coeff commands. [Related commands:] diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 89572c0c72..d5c82f16ac 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -103,7 +103,7 @@ turns off the {first} option. It is OK to use the {first} keyword with a group that has not yet been defined, e.g. to use the atom_modify first command at the beginning of -your input script. LAMMPS does not use the group until a simullation +your input script. LAMMPS does not use the group until a simulation is run. The {sort} keyword turns on a spatial sorting or reordering of atoms @@ -116,7 +116,7 @@ various other factors. As a general rule, sorting is typically more effective at speeding up simulations of liquids as opposed to solids. In tests we have done, the speed-up can range from zero to 3-4x. -Reordering is peformed every {Nfreq} timesteps during a dynamics run +Reordering is performed every {Nfreq} timesteps during a dynamics run or iterations during a minimization. More precisely, reordering occurs at the first reneighboring that occurs after the target timestep. The reordering is performed locally by each processor, @@ -130,7 +130,7 @@ the processor's 1d list of atoms. The goal of this procedure is for atoms to put atoms close to each other in the processor's one-dimensional list of atoms that are also near to each other spatially. This can improve cache performance when -pairwise intereractions and neighbor lists are computed. Note that if +pairwise interactions and neighbor lists are computed. Note that if bins are too small, there will be few atoms/bin. Likewise if bins are too large, there will be many atoms/bin. In both cases, the goal of cache locality will be undermined. @@ -138,7 +138,7 @@ cache locality will be undermined. NOTE: Running a simulation with sorting on versus off should not change the simulation results in a statistical sense. However, a different ordering will induce round-off differences, which will lead -to diverging trajectories over time when comparing two simluations. +to diverging trajectories over time when comparing two simulations. Various commands, particularly those which use random numbers (e.g. "velocity create"_velocity.html, and "fix langevin"_fix_langevin.html), may generate (statistically identical) diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 9ba817a663..3d5c0a4f3d 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -115,7 +115,7 @@ particle. For the {ellipsoid} style, the particles are ellipsoids and each stores a flag which indicates whether it is a finite-size ellipsoid or a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diamters of the ellipsoid and a quaternion 4-vector +vector with the 3 diameters of the ellipsoid and a quaternion 4-vector with its orientation. For the {dipole} style, a point dipole is defined for each point @@ -149,7 +149,7 @@ Hydrodynamics. Both fluids and solids can be modeled. Particles store the mass and volume of an integration point, a kernel diameter used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent -individual physical bodies from penetretating each other. +individual physical bodies from penetrating each other. The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients @@ -165,7 +165,7 @@ For the {tri} style, the particles are planar triangles and each stores a per-particle mass and size and orientation (i.e. the corner points of the triangle). -The {template} style allows molecular topolgy (bonds,angles,etc) to be +The {template} style allows molecular topology (bonds,angles,etc) to be defined via a molecule template using the "molecule"_molecule.html command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms @@ -195,7 +195,7 @@ the {bstyle} argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its orientation @@ -280,7 +280,7 @@ The {dpd} style is part of the USER-DPD package for dissipative particle dynamics (DPD). The {meso} style is part of the USER-SPH package for smoothed particle -hydrodyanmics (SPH). See "this PDF +hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for the diff --git a/doc/src/balance.txt b/doc/src/balance.txt index b9d36452a6..79728d6569 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -12,7 +12,7 @@ balance command :h3 balance thresh style args ... keyword args ... :pre -thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l +thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l one style/arg pair can be used (or multiple for {x},{y},{z}) :l style = {x} or {y} or {z} or {shift} or {rcb} :l {x} args = {uniform} or Px-1 numbers between 0 and 1 @@ -30,7 +30,7 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l {shift} args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -76,13 +76,13 @@ sub-domain sizes and shapes on-the-fly during a "run"_run.html. Load-balancing is typically most useful if the particles in the simulation box have a spatially-varying density distribution or when -the computational cost varies signficantly between different +the computational cost varies significantly between different particles. E.g. a model of a vapor/liquid interface, or a solid with an irregular-shaped geometry containing void regions, or "hybrid pair style simulations"_pair_hybrid.html which combine pair styles with different computational cost. In these cases, the LAMMPS default of dividing the simulation box volume into a regular-spaced grid of 3d -bricks, with one equal-volume sub-domain per procesor, may assign +bricks, with one equal-volume sub-domain per processor, may assign numbers of particles per processor in a way that the computational effort varies significantly. This can lead to poor performance when the simulation is run in parallel. @@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting. With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically induces a different number of atoms assigned to each processor. Details on the various weighting options and examples for how they can be used are "given below"_#weighted_balance. @@ -222,7 +222,7 @@ listed in ascending order. They represent the fractional position of the cutting place. The left (or lower) edge of the box is 0.0, and the right (or upper) edge is 1.0. Neither of these values is specified. Only the interior Ps-1 positions are specified. Thus is -there are 2 procesors in the x dimension, you specify a single value +there are 2 processors in the x dimension, you specify a single value such as 0.75, which would make the left processor's sub-domain 3x larger than the right processor's sub-domain. @@ -266,7 +266,7 @@ assigned, particles are migrated to their new owning processor, and the balance procedure ends. NOTE: At each rebalance operation, the bisectioning for each cutting -plane (line in 2d) typcially starts with low and high bounds separated +plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks by 1/2 every iteration. Thus if {Niter} is specified as 10, the cutting plane will typically be @@ -286,24 +286,32 @@ above. It performs a recursive coordinate bisectioning (RCB) of the simulation domain. The basic idea is as follows. The simulation domain is cut into 2 boxes by an axis-aligned cut in -the longest dimension, leaving one new box on either side of the cut. -All the processors are also partitioned into 2 groups, half assigned -to the box on the lower side of the cut, and half to the box on the -upper side. (If the processor count is odd, one side gets an extra -processor.) The cut is positioned so that the number of particles in -the lower box is exactly the number that the processors assigned to -that box should own for load balance to be perfect. This also makes -load balance for the upper box perfect. The positioning is done -iteratively, by a bisectioning method. Note that counting particles -on either side of the cut requires communication between all -processors at each iteration. +one of the dimensions, leaving one new sub-box on either side of the +cut. Which dimension is chosen for the cut depends on the particle +(weight) distribution within the parent box. Normally the longest +dimension of the box is cut, but if all (or most) of the particles are +at one end of the box, a cut may be performed in another dimension to +induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in +shape. + +After the cut is made, all the processors are also partitioned into 2 +groups, half assigned to the box on the lower side of the cut, and +half to the box on the upper side. (If the processor count is odd, +one side gets an extra processor.) The cut is positioned so that the +number of (weighted) particles in the lower box is exactly the number +that the processors assigned to that box should own for load balance +to be perfect. This also makes load balance for the upper box +perfect. The positioning of the cut is done iteratively, by a +bisectioning method (median search). Note that counting particles on +either side of the cut requires communication between all processors +at each iteration. That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors -assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the particles -in the box in two. The recursion continues until every processor is -assigned a sub-box of the entire simulation domain, and owns the +assigned to each box make a new cut in one dimension of that box, +splitting the box, the subset of processors, and the particles in the +box in two. The recursion continues until every processor is assigned +a sub-box of the entire simulation domain, and owns the (weighted) particles in that sub-box. :line @@ -368,7 +376,7 @@ of about 0.8 often results in the best performance, since the number of neighbors is likely to overestimate the ideal weight. This weight style is useful for systems where there are different -cutoffs used for different pairs of interations, or the density +cutoffs used for different pairs of interactions, or the density fluctuates, or a large number of particles are in the vicinity of a wall, or a combination of these effects. If a simulation uses multiple neighbor lists, this weight style will use the first suitable @@ -402,7 +410,7 @@ decrease the weights so that the ratio of max weight to min weight decreases by {factor}. In both cases the intermediate weight values increase/decrease proportionally as well. A value = 1.0 has no effect on the {time} weights. As a rule of thumb, effective values to use -are typicall between 0.5 and 1.2. Note that the timer quantities +are typically between 0.5 and 1.2. Note that the timer quantities mentioned above can be affected by communication which occurs in the middle of the operations, e.g. pair styles with intermediate exchange of data witin the force computation, and likewise for KSpace solves. diff --git a/doc/src/body.txt b/doc/src/body.txt index 0ea975539d..d44f82d4cc 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -82,7 +82,7 @@ internal stress that induces fragmentation :ul then the interaction between pairs of particles is likely to be more complex than the summation of simple sub-particle interactions. An example is contact or frictional forces between particles with planar -sufaces that inter-penetrate. +surfaces that inter-penetrate. These are additional LAMMPS commands that can be used with body particles of different styles @@ -105,7 +105,7 @@ in the sections below. The {nparticle} body style represents body particles as a rigid body with a variable number N of sub-particles. It is provided as a -vanillia, prototypical example of a body particle, although as +vanilla, prototypical example of a body particle, although as mentioned above, the "fix rigid"_fix_rigid.html command already duplicates its functionality. @@ -140,7 +140,7 @@ for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The coordinates of each sub-particle are specified as its x,y,z displacement from the center-of-mass of the body particle. The @@ -218,7 +218,7 @@ wish; see the "read_data"_read_data.html command for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt index 0b5731dcb4..400c3e0be4 100644 --- a/doc/src/bond_hybrid.txt +++ b/doc/src/bond_hybrid.txt @@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. Unlike other bond styles, the hybrid bond style does not store bond coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when retarting a simulation from a restart +files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify bond_coeff commands. [Related commands:] diff --git a/doc/src/bond_oxdna_fene.txt b/doc/src/bond_oxdna.txt similarity index 69% rename from doc/src/bond_oxdna_fene.txt rename to doc/src/bond_oxdna.txt index 23018c2ab7..3a10058812 100644 --- a/doc/src/bond_oxdna_fene.txt +++ b/doc/src/bond_oxdna.txt @@ -6,20 +6,20 @@ :line -bond_style oxdna_fene command :h3 +bond_style oxdna/fene command :h3 [Syntax:] -bond_style oxdna_fene :pre +bond_style oxdna/fene :pre [Examples:] -bond_style oxdna_fene +bond_style oxdna/fene bond_coeff * 2.0 0.25 0.7525 :pre [Description:] -The {oxdna_fene} bond style uses the potential +The {oxdna/fene} bond style uses the potential :c,image(Eqs/bond_oxdna_fene.jpg) @@ -37,14 +37,14 @@ Delta (distance) r0 (distance) :ul NOTE: This bond style has to be used together with the corresponding oxDNA pair styles -for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk} -and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of -"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients +for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} +and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of +"pair_style oxdna/excv"_pair_oxdna.html). The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/. +Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. A technical report with more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA can be found "here"_PDF/USER-CGDNA-overview.pdf. @@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html +"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt index ee35672aa1..169d56ecbe 100644 --- a/doc/src/bonds.txt +++ b/doc/src/bonds.txt @@ -15,7 +15,7 @@ Bond Styles :h1 bond_morse bond_none bond_nonlinear - bond_oxdna_fene + bond_oxdna bond_quartic bond_table bond_zero diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index c6556e0fc9..2c7a890d4c 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -101,11 +101,11 @@ Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions: change_box all x final -10 20 -create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre +create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre change_box all x final -10 20 boundary f s s create_atoms 1 single -5 5 5 -change_box boundary s s s # this will work :pre +change_box all boundary s s s # this will work :pre NOTE: Unlike the earlier "displace_box" version of this command, atom remapping is NOT performed by default. This command allows remapping @@ -258,8 +258,8 @@ command. :line The {ortho} and {triclinic} keywords convert the simulation box to be -orthogonal or triclinic (non-orthongonal). See "this -section"_Section_howto#howto_13 for a discussion of how non-orthongal +orthogonal or triclinic (non-orthogonal). See "this +section"_Section_howto#howto_13 for a discussion of how non-orthogonal boxes are represented in LAMMPS. The simulation box is defined as either orthogonal or triclinic when @@ -289,7 +289,7 @@ the create_box command is encountered in the input script. The {remap} keyword remaps atom coordinates from the last saved box size/shape to the current box state. For example, if you stretch the box in the x dimension or tilt it in the xy plane via the {x} and {xy} -keywords, then the {remap} commmand will dilate or tilt the atoms to +keywords, then the {remap} command will dilate or tilt the atoms to conform to the new box size/shape, as if the atoms moved with the box as it deformed. diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 667938768b..8248d654d3 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -39,7 +39,7 @@ sizes and shapes. Again there is one tile per processor. To acquire information for nearby atoms, communication must now be done with a more complex pattern of neighboring processors. -Note that this command does not actually define a partitoining of the +Note that this command does not actually define a partitioning of the simulation box (a domain decomposition), rather it determines what kinds of decompositions are allowed and the pattern of communication used to enable the decomposition. A decomposition is created when the diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 8ecfd81af1..eed190aeb2 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -235,7 +235,7 @@ section of "this page"_Section_commands.html#cmd_5. "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"ti"_compute_ti.html - thermodyanmic integration free energy values +"ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 439ff5192c..813da15eea 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -22,7 +22,7 @@ compute 1 fluid angmom/chunk molchunk :pre [Description:] -Define a computation that calculates the angular momemtum of multiple +Define a computation that calculates the angular momentum of multiple chunks of atoms. In LAMMPS, chunks are collections of atoms defined by a "compute diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 0a48ccb5be..4e4b03d167 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -18,8 +18,8 @@ lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l zero or more keyword/value pairs may be appended :l keyword = {axes} :l {axes} value = {no} or {yes} - {no} = do not calulate 3 symmetry axes - {yes} = calulate 3 symmetry axes :pre + {no} = do not calculate 3 symmetry axes + {yes} = calculate 3 symmetry axes :pre :ule [Examples:] @@ -108,7 +108,7 @@ symmetry axis, followed by the second, and third symmetry axes in columns 5-7 and 8-10. The centrosymmetry values are unitless values >= 0.0. Their magnitude -depends on the lattice style due to the number of contibuting neighbor +depends on the lattice style due to the number of contributing neighbor pairs in the summation in the formula above. And it depends on the local defects surrounding the central atom, as described above. For the {axes yes} case, the vector components are also unitless, since diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index e6083ad615..b3b09ffa71 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -386,7 +386,7 @@ If {compress yes} is set, and the {compress} keyword comes before the {limit} keyword, the compression operation is performed first, as described below, which resets {Nchunk}. The {limit} keyword is then applied to the new {Nchunk} value, exactly as described in the -preceeding paragraph. Note that in this case, all atoms will end up +preceding paragraph. Note that in this case, all atoms will end up with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or compute/fix/variable value) may have been > {Nc}, because of the compression operation. @@ -459,7 +459,7 @@ The original chunk IDs (before renumbering) can be accessed by the which outputs the original IDs as one of the columns in its global output array. For example, using the "compute cluster/atom" command discussed above, the original 5 unique chunk IDs might be atom IDs -(27,4982,58374,857838,1000000). After compresion, these will be +(27,4982,58374,857838,1000000). After compression, these will be renumbered to (1,2,3,4,5). The original values (27,...,1000000) can be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command, or by using the "fix ave/time"_fix_ave_time.html command in @@ -538,7 +538,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to to the first or last bin in both the radial and axis dimensions. If {discard} is set to {mixed}, which is the default, the radial dimension is treated the same as for {discard} = no. But for the axis -dimensinon, it will only have its chunk ID set to the first or last +dimension, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in the axis dimension. This is the case if the {bound} keyword settings are {lower} and {upper}, which is the default. If the {bound} keyword diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 9867d86efb..74240b515d 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -42,7 +42,7 @@ performed on mono-component systems. The CNA calculation can be sensitive to the specified cutoff value. You should insure the appropriate nearest neighbors of an atom are -found within the cutoff distance for the presumed crystal strucure. +found within the cutoff distance for the presumed crystal structure. E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest neighbors for perfect BCC crystals. These formulas can be used to obtain a good cutoff distance: diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index a5fdb224bc..b0e0c14e42 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -25,7 +25,7 @@ Define a computation that calculates the center-of-mass of the group of atoms, including all effects due to atoms passing thru periodic boundaries. -A vector of three quantites is calculated by this compute, which +A vector of three quantities is calculated by this compute, which are the x,y,z coordinates of the center of mass. NOTE: The coordinates of an atom contribute to the center-of-mass in diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 0367b2fe95..854a5778ec 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -70,7 +70,7 @@ The ID of the previously specified "compute orientorder/atom"_compute_orientorder/atom command is specified as {orientorderID}. The compute must invoke its {components} option to calculate components of the {Ybar_lm} vector for each atoms, as -described in its documenation. Note that orientorder/atom compute +described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the orientorder/atom compute is larger than the specified {threshold}, diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 94f49492d1..918fbf65ef 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -47,7 +47,7 @@ any command that uses per-atom values from a compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (damage) >= 0.0. +The per-atom vector values are unitless numbers (damage) >= 0.0. [Restrictions:] diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index 04409f7e45..ce00f7f12a 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -50,7 +50,7 @@ This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (theta) >= 0.0. +The per-atom vector values are unitless numbers (theta) >= 0.0. [Restrictions:] diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 566dcfc0a0..decf0bc8b9 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -25,7 +25,7 @@ Define a computation that calculates the current displacement of each atom in the group from its original coordinates, including all effects due to atoms passing thru periodic boundaries. -A vector of four quantites per atom is calculated by this compute. +A vector of four quantities per atom is calculated by this compute. The first 3 elements of the vector are the dx,dy,dz displacements. The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + dz*dz). diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index d1ebd72ae5..5e3a0c8599 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -14,7 +14,7 @@ compute ID group-ID event/displace threshold :pre ID, group-ID are documented in "compute"_compute.html command event/displace = style name of this compute command -threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul +threshold = minimum distance any particle must move to trigger an event (distance units) :ul [Examples:] @@ -37,7 +37,7 @@ further than the threshold distance. NOTE: If the system is undergoing significant center-of-mass motion, due to thermal motion, an external force, or an initial net momentum, then this compute will not be able to distinguish that motion from -local atom displacements and may generate "false postives." +local atom displacements and may generate "false positives." [Output info:] diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index f62efcff2e..3136b1fd18 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -55,7 +55,7 @@ M is the actual length of the input vector, then an output value of 0.0 is assigned to the atom. An example of how this command is useful, is in the context of -"chunks" which are static or dyanmic subsets of atoms. The "compute +"chunks" which are static or dynamic subsets of atoms. The "compute chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs to each atom. It's output can be used as the {index} parameter for this command. Various other computes with "chunk" in their style @@ -192,7 +192,7 @@ reference thermodynamic keywords and various other attributes of atoms, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating a vector of global quantities which the {index} parameter will reference for -assignement of global values to atoms. +assignment of global values to atoms. :line @@ -207,7 +207,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the -corresponsing input values are in. +corresponding input values are in. [Restrictions:] none diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 720d26ce76..e8adac3deb 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -38,7 +38,7 @@ subtracted to a group of atoms. The compute takes three arguments which are IDs of other "computes"_compute.html. One calculates per-atom kinetic energy ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the -third calcualtes per-atom stress ({stress-ID}). +third calculates per-atom stress ({stress-ID}). NOTE: These other computes should provide values for all the atoms in the group this compute specifies. That means the other computes could @@ -83,7 +83,7 @@ The heat flux can be output every so many timesteps (e.g. via the post-processing operation, an autocorrelation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. -The "fix ave/correlate"_fix_ave_correlate.html command can calclate +The "fix ave/correlate"_fix_ave_correlate.html command can calculate the autocorrelation. The trap() function in the "variable"_variable.html command can calculate the integral. diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index 59a459b0d7..b0dbb12aea 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section defined and examples of how they can be used to measure properties of a system. -This compute calculates the 6 components of the symmetric intertia +This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The calculation includes all effects due to atoms passing thru periodic boundaries. diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index 42dbca255d..f806c5e292 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -33,7 +33,7 @@ passing thru periodic boundaries. For computation of the non-Gaussian parameter of mean-squared displacement, see the "compute msd/nongauss"_compute_msd_nongauss.html command. -A vector of four quantites is calculated by this compute. The first 3 +A vector of four quantities is calculated by this compute. The first 3 elements of the vector are the squared dx,dy,dz displacements, summed and averaged over atoms in the group. The 4th element is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 7382ca87de..7f31b61ed0 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section defined and examples of how they can be used to measure properties of a system. -Four quantites are calculated by this compute for each chunk. The +Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the center-of-mass. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index b92ceaacde..198da999e0 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -30,12 +30,12 @@ Define a computation that calculates the mean-squared displacement (MSD) and non-Gaussian parameter (NGP) of the group of atoms, including all effects due to atoms passing thru periodic boundaries. -A vector of three quantites is calculated by this compute. The first +A vector of three quantities is calculated by this compute. The first element of the vector is the total squared dx,dy,dz displacements drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the fourth power of these displacements drfourth = (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the -group. The 3rd component is the nonGaussian diffusion paramter NGP = +group. The 3rd component is the nonGaussian diffusion parameter NGP = 3*drfourth/(5*drsquared*drsquared), i.e. :c,image(Eqs/compute_msd_nongauss.jpg) @@ -48,7 +48,7 @@ others. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calcluated. +displacment of each atom is calculated. See the "compute msd"_compute_msd.html doc page for further important NOTEs, which also apply to this compute. diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index d2b34ed110..0602dab81b 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -43,7 +43,7 @@ style van der Waals interaction or not) is tallied in {evdwl}. If as a global scalar by this compute. This is useful when using "pair_style hybrid"_pair_hybrid.html if you want to know the portion of the total energy contributed by one sub-style. If {evalue} is -specfied as {evdwl} or {ecoul}, then just that portion of the energy +specified as {evdwl} or {ecoul}, then just that portion of the energy is stored as a global scalar. NOTE: The energy returned by the {evdwl} keyword does not include tail @@ -52,7 +52,7 @@ corrections, even if they are enabled via the Some pair styles tally additional quantities, e.g. a breakdown of potential energy into a dozen or so components is tallied by the -"pair_style reax"_pair_reax.html commmand. These values (1 or more) +"pair_style reax"_pair_reax.html command. These values (1 or more) are stored as a global vector by this compute. See the doc page for "individual pair styles"_pair_style.html for info on these values. diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 0d420b2202..0121210994 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -47,7 +47,7 @@ force cutoff distance for that interaction, as defined by the "pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html commands. -The value {dist} is the distance bewteen the pair of atoms. +The value {dist} is the distance between the pair of atoms. The value {eng} is the interaction energy for the pair of atoms. diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index 8e2fd17f24..6de3a79e5b 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -51,7 +51,7 @@ these terms is included in the pair energy, not the dihedral energy. The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, as specified by the "kspace_style pppm"_kspace_style.html command. -For PPPM, the calcluation requires 1 extra FFT each timestep that +For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This "document"_PDF/kspace.pdf describes how the long-range per-atom energy calculation is performed. diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index 75491cfb14..788213fc65 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -44,7 +44,7 @@ This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (lambda) >= 0.0. +The per-atom vector values are unitless numbers (lambda) >= 0.0. [Restrictions:] diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 9e8c2a3b46..ae62859b17 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias. Also note that the N in the first formula above is really degrees-of-freedom divided by d = dimensionality, where the DOF value -is calcluated by the temperature compute. See the various "compute +is calculated by the temperature compute. See the various "compute temperature"_compute.html styles for details. A compute of this style with the ID of "thermo_press" is created when diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index 3bed9c0677..b9d4944b30 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -64,7 +64,7 @@ can only be used if the {compress} keyword was set to {yes} for the "compute chunk/atom"_compute_chunk_atom.html command referenced by chunkID. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compresed chunk ID of 3 may correspond to an original +to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID (molecule ID in this case) of 415. The {id} attribute will then be 415 for the 3rd chunk. diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index 1c9de277bc..acbc0e4f0c 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -73,7 +73,7 @@ post-process a dump file to calculate it. This is because using the which may slow down your simulation. If you specify a {Rcut} <= force cutoff, you will force an additional neighbor list to be built at every timestep this command is invoked (or every reneighboring -timestep, whichever is less frequent), which is inefficent. LAMMPS +timestep, whichever is less frequent), which is inefficient. LAMMPS will warn you if this is the case. If you specify a {Rcut} > force cutoff, you must insure ghost atom information out to {Rcut} + {skin} is communicated, via the "comm_modify cutoff"_comm_modify.html diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 5cdd58fbc2..077ad57d81 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -123,7 +123,7 @@ The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of the COM velocity and force on the COM of the body. The {omegax}, {omegay}, and {omegaz} attributes are the angular -velocity componennts of the body around its COM. +velocity components of the body around its COM. The {angmomx}, {angmomy}, and {angmomz} attributes are the angular momentum components of the body around its COM. diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index 658f41cdca..aadda49533 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -93,7 +93,7 @@ parameters will denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an intersecting Ewald sphere. Diffraction intensities will only be computed at the intersection of the reciprocal lattice mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the -example 3D intestiety data and the intersection of a \[010\] zone axis +example 3D intensity data and the intersection of a \[010\] zone axis in the below image. :c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg) diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index 95af1b2163..adece93343 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -35,7 +35,7 @@ any command that uses per-particle values from a compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle values will be given dimentionless, see "units"_units.html. +The per-particle values will be given dimensionless, see "units"_units.html. [Restrictions:] diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 3dc642da32..d09c8069cc 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -92,7 +92,7 @@ The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and by the methodology described in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified by the "kspace_style pppm"_kspace_style.html command. Note that for -PPPM, the calcluation requires 6 extra FFTs each timestep that +PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the cost of the PPPM calculation if it is needed on a large fraction of the simulation timesteps. diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index 43e1588fa0..495366b345 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -138,7 +138,7 @@ This compute is part of the ASPHERE 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 compute requires that atoms store angular momementum and a +This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt index 04b707bcce..f72b886cc4 100644 --- a/doc/src/compute_temp_body.txt +++ b/doc/src/compute_temp_body.txt @@ -120,7 +120,7 @@ This compute is part of the BODY 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 compute requires that atoms store angular momementum and a +This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index d565c95134..f877f6ece8 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -44,7 +44,7 @@ compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre Define a computation that calculates the temperature of a group of atoms that are also in chunks, after optionally subtracting out the center-of-mass velocity of each chunk. By specifying optional values, -it can also calulate the per-chunk temperature or energies of the +it can also calculate the per-chunk temperature or energies of the multiple chunks of atoms. In LAMMPS, chunks are collections of atoms defined by a "compute @@ -122,7 +122,7 @@ concept is somewhat ill-defined. In some cases, you can use the {adof} and {cdof} keywords to adjust the calculated degress of freedom appropriately, as explained below. -Note that the per-chunk temperature calulated by this compute and the +Note that the per-chunk temperature calculated by this compute and the "fix ave/chunk temp"_fix_ave_chunk.html command can be different. This compute calculates the temperature for each chunk for a single snapshot. Fix ave/chunk can do that but can also time average those @@ -208,7 +208,7 @@ This compute also optionally calculates a global array, if one or more of the optional values are specified. The number of rows in the array = the number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of -columns is the number of specifed values (1 or more). These values +columns is the number of specified values (1 or more). These values can be accessed by any command that uses global array values from a compute as input. Again, see "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 54eebd6d8f..3b6f774d33 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the NOTE: When using the {out} keyword with a value of {bin}, the calculated temperature for each bin does not include the -degrees-of-freedom adjustment described in the preceeding paragraph, +degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the {extra} option, which is applied to each bin. diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt index 29ada25c9c..a0d9a3c5f7 100644 --- a/doc/src/compute_vacf.txt +++ b/doc/src/compute_vacf.txt @@ -27,7 +27,7 @@ function (VACF), averaged over a group of atoms. Each atom's contribution to the VACF is its current velocity vector dotted into its initial velocity vector at the time the compute was specified. -A vector of four quantites is calculated by this compute. The first 3 +A vector of four quantities is calculated by this compute. The first 3 elements of the vector are vx * vx0 (and similarly for the y and z components), summed and averaged over atoms in the group. Vx is the current x-component of velocity for the atom, vx0 is the initial diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index ea573a1356..d084fcee66 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -217,6 +217,10 @@ This compute is part of the VORONOI 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. +It also requiers you have a copy of the Voro++ library built and +installed on your system. See instructions on obtaining and +installing the Voro++ software in the src/VORONOI/README file. + [Related commands:] "dump custom"_dump.html, "dump local"_dump.html diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index ec7a6f4d8a..98c3c24a0b 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -101,7 +101,7 @@ positions. For the {random} style, N particles are added to the system at randomly generated coordinates, which can be useful for generating an amorphous system. The particles are created one by one using the -speficied random number {seed}, resulting in the same set of particles +specified random number {seed}, resulting in the same set of particles coordinates, independent of how many processors are being used in the simulation. If the {region-ID} argument is specified as NULL, then the created particles will be anywhere in the simulation box. If a @@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules are being added. The "delete_atoms"_delete_atoms.html command can be used to remove overlapping atoms or molecules. +NOTE: You cannot use any of the styles explained above to create atoms +that are outside the simulation box; they will just be ignored by +LAMMPS. This is true even if you are using shrink-wrapped box +boundaries, as specified by the "boundary"_boundary.html command. +However, you can first use the "change_box"_change_box.html command to +temporarily expand the box, then add atoms via create_atoms, then +finally use change_box command again if needed to re-shrink-wrap the +new atoms. See the "change_box"_change_box.html doc page for an +example of how to do this, using the create_atoms {single} style to +insert a new atom outside the current simulation box. + :line Individual atoms are inserted by this command, unless the {mol} diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt index bddc0c0ec8..8cb40eff44 100644 --- a/doc/src/dihedral_hybrid.txt +++ b/doc/src/dihedral_hybrid.txt @@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. Unlike other dihedral styles, the hybrid dihedral style does not store dihedral coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when retarting a simulation from a +restart files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify dihedral_coeff commands. [Related commands:] diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 5f8ee1ee88..1c65b1cdbf 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -225,7 +225,7 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they repesent a bounding box. See "this +of xlo, etc, since they represent a bounding box. See "this section"_Section_howto.html#howto_12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are @@ -545,7 +545,7 @@ that the coordinate values may be far outside the box bounds printed with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will -have the corresponding cooordinate increased or decreased by 1.0. +have the corresponding coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt index b84817327b..f15d20f849 100644 --- a/doc/src/dump_custom_vtk.txt +++ b/doc/src/dump_custom_vtk.txt @@ -211,7 +211,7 @@ charge. There are several options for outputting atom coordinates. The {x}, {y}, {z} attributes are used to write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). -Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the +Additionally, you can use {xs}, {ys}, {zs} if you want to also save the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you @@ -224,7 +224,7 @@ values may be far outside the box bounds printed with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will have the corresponding -cooordinate increased or decreased by 1.0. +coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index f5085846df..3fa267d2b0 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -99,7 +99,7 @@ included in the image or movie and how it appears. A series of such images can easily be manually converted into an animated movie of your simulation or the process can be automated without writing the intermediate files using the dump movie style; see further details -below. Other dump styles store snapshots of numerical data asociated +below. Other dump styles store snapshots of numerical data associated with atoms in various formats, as discussed on the "dump"_dump.html doc page. @@ -237,7 +237,7 @@ diameter, which can be used as the {diameter} setting. :line -The various kewords listed above control how the image is rendered. +The various keywords listed above control how the image is rendered. As listed below, all of the keywords have defaults, most of which you will likely not need to change. The "dump modify"_dump_modify.html also has options specific to the dump image style, particularly for @@ -261,7 +261,7 @@ the input script defines, e.g. Angstroms. The {bond} keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being in the specified group and due to other selection criteria -(e.g. region, threshhold settings of the +(e.g. region, threshold settings of the "dump_modify"_dump_modify.html command). By default, bonds are drawn if they are defined in the input data file as read by the "read_data"_read_data.html command. Using {none} for both the bond @@ -356,7 +356,7 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent and how they are drawn by this dump image command. For all the body styles, individual atoms can be either a @@ -442,7 +442,7 @@ degrees. The {center} keyword determines the point in simulation space that will be at the center of the image. {Cx}, {Cy}, and {Cz} are -speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is +specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is the center of the simulation box. These values do not have to be between 0.0 and 1.0, if you want the simulation box to be offset from the center of the image. Note, however, that if you choose strange @@ -476,8 +476,8 @@ smaller. {Zfactor} must be a value > 0.0. The {persp} keyword determines how much depth perspective is present in the image. Depth perspective makes lines that are parallel in simulation space appear non-parallel in the image. A {pfactor} value -of 0.0 means that parallel lines will meet at infininty (1.0/pfactor), -which is an orthographic rendering with no persepctive. A {pfactor} +of 0.0 means that parallel lines will meet at infinity (1.0/pfactor), +which is an orthographic rendering with no perspective. A {pfactor} value between 0.0 and 1.0 will introduce more perspective. A {pfactor} value > 1 will create a highly skewed image with a large amount of perspective. @@ -638,7 +638,7 @@ pipe:: Input/output error :pre which can be safely ignored. Other warnings and errors have to be addressed according to the FFmpeg documentation. One known issue is that certain movie file formats (e.g. MPEG level 1 -and 2 format streams) have video bandwith limits that can be crossed +and 2 format streams) have video bandwidth limits that can be crossed when rendering too large of image sizes. Typical warnings look like this: diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 0cf30e3c92..b5daa6416e 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -426,7 +426,7 @@ regions. The {scale} keyword applies only to the dump {atom} style. A scale value of {yes} means atom coords are written in normalized units from -0.0 to 1.0 in each box dimension. If the simluation box is triclinic +0.0 to 1.0 in each box dimension. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. A value of {no} means they are written in absolute distance units (e.g. Angstroms or sigma). @@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold. If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values -which may be useful for the comparision operator. Boolean values can +which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the "variable"_variable.html command doc page for details. diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 0238d9b4f2..8943192176 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -67,7 +67,7 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre [NOTE:] -If you are trying to replace a deprectated fix ave/spatial command +If you are trying to replace a deprecated 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 @@ -189,7 +189,7 @@ chunk/atom"_compute_chunk_atom.html command must remain constant. If the {ave} keyword is set to {running} or {window} then {Nchunk} must remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold {Nchunk} constant -for the appropriate time windows, by not allowing it to re-calcualte +for the appropriate time windows, by not allowing it to re-calculate {Nchunk}, which can also affect how it assigns chunk IDs to atoms. More details are given on the "compute chunk/atom"_compute_chunk_atom.html doc page. @@ -301,7 +301,7 @@ sample values" divided by {Nrepeat}. In other words it is an average of an average. If the {norm} setting is {none}, a similar computation as for the -{sample} seting is done, except the individual "average sample values" +{sample} setting is done, except the individual "average sample values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by the number of atoms in the sample. The output value for the chunk on the @@ -410,7 +410,7 @@ chunk/atom"_compute_chunk_atom.html command supports them. The OrigID column is only used if the {compress} keyword was set to {yes} for the "compute chunk/atom"_compute_chunk_atom.html command. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed -to remove chunk IDs with no atoms assigned to them. Thus a compresed +to remove chunk IDs with no atoms assigned to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID or molecule ID of 415. The OrigID column will list 415 for the 3rd chunk. diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index bd097f291a..371f2f66a8 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -64,7 +64,7 @@ fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\] [Description:] Use one or more global scalar values as inputs every few timesteps, -calculate time correlations bewteen them at varying time intervals, +calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output @@ -219,7 +219,7 @@ to {upper} then each input value is correlated with every succeeding value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l If {type} is set -to {lower} then each input value is correlated with every preceeding +to {lower} then each input value is correlated with every preceding value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l If {type} is set to {auto/upper} then each input value is correlated diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 569cdc96cf..266e3f0e38 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -33,7 +33,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title vector = all input values are global vectors or global arrays {ave} args = {one} or {running} or {window M} one = output a new average value every Nfreq steps - running = output cummulative average of all previous Nfreq steps + running = output cumulative average of all previous Nfreq steps window M = output average of M most recent Nfreq steps {start} args = Nstart Nstart = start averaging on this timestep @@ -223,7 +223,7 @@ output as-is without further averaging. If the {ave} setting is {running}, then the values produced on timesteps that are multiples of {Nfreq} are summed and averaged in a -cummulative sense before being output. Each output value is thus the +cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the "unfix"_unfix.html @@ -320,7 +320,7 @@ input values are averaged and {mode} = vector. The global array has # of rows = length of the input vectors and # of columns = number of inputs. -If the fix prouduces a scalar or vector, then the scalar and each +If the fix produces a scalar or vector, then the scalar and each element of the vector can be either "intensive" or "extensive", depending on whether the values contributing to the scalar or vector element are "intensive" or "extensive". If the fix produces an array, diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 8473fa8152..f148e6f996 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -15,12 +15,12 @@ fix ID group-ID balance Nfreq thresh style args keyword args ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l balance = style name of this fix command :l Nfreq = perform dynamic load balancing every this many steps :l -thresh = imbalance threshhold that must be exceeded to perform a re-balance :l +thresh = imbalance threshold that must be exceeded to perform a re-balance :l style = {shift} or {rcb} :l shift args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -63,14 +63,14 @@ perform "static" balancing, before or between runs, see the Load-balancing is typically most useful if the particles in the simulation box have a spatially-varying density distribution or -where the computational cost varies signficantly between different +where the computational cost varies significantly between different atoms. E.g. a model of a vapor/liquid interface, or a solid with an irregular-shaped geometry containing void regions, or "hybrid pair style simulations"_pair_hybrid.html which combine pair styles with different computational cost. In these cases, the LAMMPS default of dividing the simulation box volume into a regular-spaced grid of 3d bricks, with one equal-volume sub-domain -per procesor, may assign numbers of particles per processor in a +per processor, may assign numbers of particles per processor in a way that the computational effort varies significantly. This can lead to poor performance when the simulation is run in parallel. @@ -78,7 +78,7 @@ The balancing can be performed with or without per-particle weighting. With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically induces a different number of atoms assigned to each processor. NOTE: The weighting options listed above are documented with the @@ -216,7 +216,7 @@ for a single value, except that the bounds used for each bisectioning take advantage of information from neighboring cuts if possible, as well as counts of particles at the bounds on either side of each cuts, which themselves were cuts in previous iterations. The latter is used -to infer a density of pariticles near each of the current cuts. At +to infer a density of particles near each of the current cuts. At each iteration, the count of particles on either side of each plane is tallied. If the counts do not match the target value for the plane, the position of the cut is adjusted based on the local density. The @@ -239,7 +239,7 @@ assigned, particles migrate to their new owning processor as part of the normal reneighboring procedure. NOTE: At each rebalance operation, the bisectioning for each cutting -plane (line in 2d) typcially starts with low and high bounds separated +plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks based on the local density, as described above, which should typically be 1/2 or more every @@ -249,7 +249,7 @@ typically be positioned to better than 1 part in 1000 accuracy be accurate to better than 1 part in a million. Thus there is no need to set {Niter} to a large value. This is especially true if you are rebalancing often enough that each time you expect only an incremental -adjustement in the cutting planes is necessary. LAMMPS will check if +adjustment in the cutting planes is necessary. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than {Niter} and exit early. @@ -275,7 +275,7 @@ at each iteration. That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the atoms in +box, splitting the box, the subset of processors, and the atoms in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the atoms in that sub-box. diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 98ba472327..83364b9efb 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -79,8 +79,8 @@ part of bonds, angles, etc. NOTE: One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though one molecule -becomes two moleclues due to the broken bond, all atoms in both new -moleclues retain their original molecule IDs. +becomes two molecules due to the broken bond, all atoms in both new +molecules retain their original molecule IDs. Computationally, each timestep this fix operates, it loops over all the bonds in the system and computes distances between pairs of bonded @@ -122,7 +122,7 @@ by this fix are "intensive". These are the 2 quantities: (1) # of bonds broken on the most recent breakage timestep -(2) cummulative # of bonds broken :ul +(2) cumulative # of bonds broken :ul 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 diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index 3d00b60844..a44c3103dd 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -118,8 +118,8 @@ of new bonds, angles, etc. NOTE: One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though two molecules -become one moleclue due to the created bond, all atoms in the new -moleclue retain their original molecule IDs. +become one molecule due to the created bond, all atoms in the new +molecule retain their original molecule IDs. If the {atype} keyword is used and if an angle potential is defined via the "angle_style"_angle_style.html command, then any new 3-body @@ -218,7 +218,7 @@ by this fix are "intensive". These are the 2 quantities: (1) # of bonds created on the most recent creation timestep -(2) cummulative # of bonds created :ul +(2) cumulative # of bonds created :ul 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 diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 38c5e17c60..ca7069e247 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -81,7 +81,7 @@ by this processor on this timestep. The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the "read_data"_read_data.html comand. +in the data file, read by the "read_data"_read_data.html command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then swaps will conserve chain length. For a particular momoner there will @@ -124,7 +124,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the "compute_modify"_compute_modify.html command or print this temperature -during thermodyanmic output via the "thermo_style +during thermodynamic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. @@ -151,8 +151,8 @@ the Boltzmann criterion. This fix computes two statistical quantities as a global 2-vector of output, which can be accessed by various "output commands"_Section_howto.html#howto_15. The first component of the -vector is the cummulative number of swaps performed by all processors. -The second component of the vector is the cummulative number of swaps +vector is the cumulative number of swaps performed by all processors. +The second component of the vector is the cumulative number of swaps attempted (whether accepted or rejected). Note that a swap "attempt" only occurs when swap partners meeting the criteria described above are found on a particular timestep. The vector values calculated by @@ -168,7 +168,7 @@ This fix is part of the MC 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 setings of the "special_bond" command must be 0,1,1 in order to +The settings of the "special_bond" command must be 0,1,1 in order to use this fix, which is typical of bead-spring chains with FENE or harmonic bonds. This means that pairwise interactions between bonded atoms are turned off, but are turned on between atoms two or three diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 96701b170e..83e5a82652 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -54,7 +54,7 @@ The external pressure tensor is specified using one or more of the keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are -varied together during the mimimization. +varied together during the minimization. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -103,7 +103,7 @@ far. In all cases, the particle positions at each iteration are unaffected by the chosen value, except that all particles are displaced by the same amount, different on each iteration. -NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz} +NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz} can sometimes result in arbitrarily large values of the tilt factors, i.e. a dramatically deformed simulation box. This typically indicates that there is something badly wrong with how the simulation was @@ -122,7 +122,7 @@ well-defined minimization problem. This is because the objective function being minimized changes if the box size/shape changes. In practice this means the minimizer can get "stuck" before you have reached the desired tolerance. The solution to this is to restart the -minmizer from the new adjusted box size/shape, since that creates a +minimizer from the new adjusted box size/shape, since that creates a new objective function valid for the new box size/shape. Repeat as necessary until the box size/shape has reached its new equilibrium. diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index 9edd660b04..c943cde489 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -44,7 +44,7 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap. The data file read by the "read_data" must contain the topology of all the CMAP interactions, similar to the topology data for bonds, angles, -dihedrals, etc. Specically it should have a line like this +dihedrals, etc. Specially it should have a line like this in its header section: N crossterms :pre diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index e2be03f46b..e48dedacd9 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -59,7 +59,7 @@ always apply to the entire system and there can only be one instance of the colvars fix at a time. The colvars fix will only communicate the minimum information necessary and the colvars library supports multiple, completely independent collective variables, so there is -no restriction to functionaliry by limiting the number of colvars fixes. +no restriction to functionality by limiting the number of colvars fixes. The {input} keyword allows to specify a state file that would contain the restart information required in order to continue a calculation from @@ -100,7 +100,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index a19f42c77c..cd4d6adfdf 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -107,7 +107,7 @@ When choosing the values of the four constants, it is best to first pick a value and sign for {alpha} that is consistent with the magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp} should then be tested over a large positive range keeping {Ki}={Kd}=0. -A good value for {Kp} will produce a fast reponse in {pvar}, without +A good value for {Kp} will produce a fast response in {pvar}, without overshooting the {setpoint}. For many applications, proportional feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where there is a substantial lag time in the response of {pvar} to a change @@ -175,7 +175,7 @@ equal-style versus internal-style variable interchangeably. [Restart, fix_modify, output, run start/stop, minimize info:] -Currenlty, no information about this fix is written to "binary restart +Currently, 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. diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 1478d47df1..8c3a9fa499 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -580,10 +580,10 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] You cannot apply x, y, or z deformations to a dimension that is -shrink-wrapped via the "boundary"_boundary.html comamnd. +shrink-wrapped via the "boundary"_boundary.html command. You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in -xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd. +xy) that is shrink-wrapped via the "boundary"_boundary.html command. [Related commands:] diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index ea9c5643dd..a1dd5f6434 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l deposit = style name of this fix command :l N = # of atoms or molecules to insert :l -type = atom type to assign to inserted atoms (offset for moleclue insertion) :l +type = atom type to assign to inserted atoms (offset for molecule insertion) :l M = insert a single atom or molecule every M steps :l seed = random # seed (positive integer) :l one or more keyword/value pairs may be appended to args :l @@ -140,7 +140,7 @@ the molecule. If the molecule template contains more than one molecule, the relative probability of depositing each molecule can be specified by the -{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are +{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are specified, where N is the number of molecules in the template. Each time a molecule is deposited, a random number is used to sample from the list of relative probabilities. The N values must sum to 1.0. @@ -192,7 +192,7 @@ LAMMPS prints a warning message. NOTE: If you are inserting finite size particles or a molecule or rigid body consisting of finite-size particles, then you should typically set R larger than the distance at which any inserted -particle may overlap with either a previouly inserted particle or an +particle may overlap with either a previously inserted particle or an existing particle. LAMMPS will issue a warning if R is smaller than this value, based on the radii of existing and inserted particles. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 8fc72bbdad..42778d7978 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -17,7 +17,7 @@ eos/table = style name of this fix command style = {linear} = method of interpolation file = filename containing the tabulated equation of state N = use N values in {linear} tables -keyword = name of table keyword correponding to table file :ul +keyword = name of table keyword corresponding to table file :ul [Examples:] diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 749642f57c..e8d515e1f3 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -17,7 +17,7 @@ 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 +keyword = name of table keyword corresponding to table file file2 = filename containing the heats of formation of each species (optional) deltaHf = heat of formation for a single species in energy units (optional) energyCorr = energy correction in energy units (optional) diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index 0243cbe977..ed6c6d0377 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -31,9 +31,9 @@ fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre [Description:] Remove M atoms from the simulation every N steps. This can be used, -for example, to model evaporation of solvent particles or moleclues +for example, to model evaporation of solvent particles or molecules (i.e. drying) of a system. Every N steps, the number of atoms in the -fix group and within the specifed region are counted. M of these are +fix group and within the specified region are counted. M of these are chosen at random and deleted. If there are less than M eligible particles, then all of them are deleted. @@ -74,7 +74,7 @@ are relevant to this fix. This fix computes a global scalar, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative number of deleted atoms. The scalar value calculated by +cumulative number of deleted atoms. The scalar value calculated by this fix is "intensive". No parameter of this fix can be used with the {start/stop} keywords of diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index 79b5abe5b0..ca7625e2d0 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -62,7 +62,7 @@ as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are optimal for a given application and the system of choice can be obtained from "(GLE4MD)"_#GLE4MD. -Equilibrium sampling a temperature T is obtained by specifiying the +Equilibrium sampling a temperature T is obtained by specifying the target value as the {Tstart} and {Tstop} arguments, so that the diffusion matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that @@ -116,7 +116,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index 04b0fd091e..2cf1665c30 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -76,7 +76,7 @@ specified as an equal-style "variable"_variable.html. If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the quantity. You should -insure that the variable calculates a result in the approriate units, +insure that the variable calculates a result in the appropriate units, e.g. force/mass or degrees. Equal-style variables can specify formulas with various mathematical diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index c9295eca69..3f7650466f 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -15,15 +15,16 @@ fix ID group-ID halt N attribute operator avalue keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l halt = style name of this fix command :l N = check halt condition every N steps :l -attribute = hstyle or v_name :l - hstyle = {bondmax} +attribute = {bondmax} or {tlimit} or v_name :l + bondmax = length of longest bond in the system + tlimit = elapsed CPU time v_name = name of "equal-style variable"_variable.html :pre operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l avalue = numeric value to compare attribute to :l -string = text string to print with optional variable names :l zero or more keyword/value pairs may be appended :l -keyword = {error} :l - {error} value = {hard} or {soft} or {continue} :pre +keyword = {error} or {message} :l + {error} value = {hard} or {soft} or {continue} + {message} value = {yes} or {no} :pre :ule [Examples:] @@ -40,14 +41,33 @@ specified by the "run"_run.html or "minimize"_minimize.html command. The specified group-ID is ignored by this fix. -The specified {attribute} can be one of the {hstyle} options listed -above, or an "equal-style variable"_variable.html referenced as -{v_name}, where "name" is the name of a variable that has been defined -previously in the input script. +The specified {attribute} can be one of the options listed above, +namely {bondmax} or {tlimit}, or an "equal-style +variable"_variable.html referenced as {v_name}, where "name" is the +name of a variable that has been defined previously in the input +script. -The only {hstyle} option currently implemented is {bondmax}. This -will loop over all bonds in the system, compute their current -lengths, and set {attribute} to the longest bond distance. +The {bondmax} attribute will loop over all bonds in the system, +compute their current lengths, and set {attribute} to the longest bond +distance. + +The {tlimit} attribute queries the elapsed CPU time (in seconds) since +the current run began, and sets {attribute} to that value. This is an +alternative way to limit the length of a simulation run, similar to +the "timer"_timer.html timeout command. There are two differences in +using this method versus the timer command option. The first is that +the clock starts at the beginning of the current run (not when the +timer or fix command is specified), so that any setup time for the run +is not included in the elapsed time. The second is that the timer +invocation and syncing across all processors (via MPI_Allreduce) is +not performed once every {N} steps by this command. Instead it is +performed (typically) only a small number of times and the elapsed +times are used to predict when the end-of-the-run will be. Both of +these attributes can be useful when performing benchmark calculations +for a desired length of time with minmimal overhead. For example, if +a run is performing 1000s of timesteps/sec, the overhead for syncing +the timer frequently across a large number of processors may be +non-negligble. Equal-style variables evaluate to a numeric value. See the "variable"_variable.html command for a description. They calculate @@ -100,6 +120,14 @@ Note that you may wish use the "unfix"_unfix.html command on the fix halt ID, so that the same condition is not immediately triggered in a subsequent run. +The optional {message} keyword determines whether a message is printed +to the screen and logfile when the half condition is triggered. If +{message} is set to yes, a one line message with the values that +triggered the halt is printed. If {message} is set to no, no message +is printed; the run simply exits. The latter may be desirable for +post-processing tools that extract thermodyanmic information from log +files. + [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart @@ -118,4 +146,4 @@ This fix is not invoked during "energy minimization"_minimize.html. [Default:] -The option defaults are error = hard. +The option defaults are error = hard and message = yes. diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index be13925897..c9a791ae4e 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -107,7 +107,7 @@ fashion. For the latter, see the {start} and {stop} keywords of the "run"_run.html command and the {elaplong} keyword of "thermo_style custom"_thermo_style.html for details. -For example, if a spherical indenter's x-position is specfied as v_x, +For example, if a spherical indenter's x-position is specified as v_x, then this variable definition will keep it's center at a relative position in the simulation box, 1/4 of the way from the left edge to the right edge, even if the box size changes: @@ -121,7 +121,7 @@ variable x equal "2.5 + 5*elaplong*dt" variable x equal vdisplace(2.5,5) :pre If a spherical indenter's radius is specified as v_r, then these -variable definitions will grow the size of the indenter at a specfied +variable definitions will grow the size of the indenter at a specified rate. variable r0 equal 0.0 diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index b387117d83..a3d0fb7eaa 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -307,7 +307,7 @@ setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index 4b09d695b9..d3112d529d 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -80,7 +80,7 @@ setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index 62265a3bc1..fc6203b0f2 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -328,7 +328,7 @@ fix must be used in conjunction with the "lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or -"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specifiy +"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify their own value for the force coupling constant. [Related commands:] diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index afdfa9e892..9c95cdc452 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -53,7 +53,7 @@ default method for computing P. For fixes that calculate a contribution to the potential energy of the system, the {energy} keyword will include that contribution in thermodynamic output of potential energy. This is because the {energy -yes} setting must be specfied to include the fix's global or per-atom +yes} setting must be specified to include the fix's global or per-atom energy in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 9bbe252c1f..7cb40ad132 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -58,7 +58,7 @@ nve"_fix_nve.html command). It is up to you to decide whether periodic boundaries are appropriate with the kind of atom motion you are prescribing with this fix. -NOTE: As dicsussed below, atoms are moved relative to their initial +NOTE: As discussed below, atoms are moved relative to their initial position at the time the fix is specified. These initial coordinates are stored by the fix in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command @@ -131,7 +131,7 @@ This style also sets the velocity of each atom to (omega cross Rperp) where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the defined "atom_style"_atom_style.html assigns an angular velocity or -angular moementum or orientation to each atom ("atom +angular momentum or orientation to each atom ("atom styles"_atom_style.html sphere, ellipsoid, line, tri, body), then those properties are also updated appropriately to correspond to the atom's motion and rotation over time. diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index c613a598fe..0e09f8a9c5 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -83,7 +83,7 @@ produces additional output files. The range finder functionality (step 4) outputs files defining pair and bonded interaction ranges. The force matching functionality (step 5) outputs tabulated force files for every interaction in the system. Other diagnostic files can -also be output depending on the paramters in the MS-CG library input +also be output depending on the parameters in the MS-CG library input script. Again, see the documentation provided with the MS-CG library for more info. @@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. The MS-CG library uses C++11, which may not be supported by older compilers. The MS-CG library also has some additional numeric library -dependencies, which are describd in its documentation. +dependencies, which are described in its documentation. Currently, the MS-CG library is not setup to run in parallel with MPI, so this fix can only be used in a serial LAMMPS build and run diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index 059498a843..3d151a724b 100644 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -136,7 +136,7 @@ This fix is part of the ASPHERE 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index ad5ffd8026..3a273be595 100644 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -135,7 +135,7 @@ This fix is part of the BODY 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index 40cc7ed2b2..8fe98f1818 100644 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -161,7 +161,7 @@ This fix is part of the ASPHERE 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index c098ae216b..772920df61 100644 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -160,7 +160,7 @@ This fix is part of the BODY 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index 817e6985c5..03846a2558 100644 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -71,7 +71,7 @@ This fix is part of the ASPHERE 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt index 8cc2ceb396..5f1b271546 100644 --- a/doc/src/fix_nve_asphere_noforce.txt +++ b/doc/src/fix_nve_asphere_noforce.txt @@ -25,7 +25,7 @@ Perform updates of position and orientation, but not velocity or angular momentum for atoms in the group each timestep. In other words, the force and torque on the atoms is ignored and their velocity and angular momentum are not updated. The atom velocities and -angularm momenta are used to update their positions and orientation. +angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the @@ -49,7 +49,7 @@ This fix is part of the ASPHERE 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 7709805abf..604b5391cd 100644 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -47,7 +47,7 @@ This fix is part of the BODY 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt index 6a83d715d2..2ecec83e9c 100644 --- a/doc/src/fix_nve_limit.txt +++ b/doc/src/fix_nve_limit.txt @@ -48,8 +48,8 @@ unaltered, pressures computed by thermodynamic output will still be very large for overlapped configurations. NOTE: You should not use "fix shake"_fix_shake.html in conjunction -with this fix. That is because fix shake applies contraint forces -based on the predicted postitions of atoms after the next timestep. +with this fix. That is because fix shake applies constraint forces +based on the predicted positions of atoms after the next timestep. It has no way of knowing the timestep may change due to this fix, which will cause the constraint forces to be invalid. A better strategy is to turn off fix shake when performing initial dynamics diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 6256627724..77de1dea40 100644 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -137,7 +137,7 @@ This fix is part of the ASPHERE 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index d12903acfd..1f04b85c8b 100644 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -136,7 +136,7 @@ This fix is part of the BODY 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 requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index 2d772ba6be..e92d1640cd 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -35,7 +35,7 @@ radial velocity of electrons are also updated and thermostatted. Likewise the temperature calculated by the fix, using the compute it creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc page), is performed with a "compute -temp/deform/eff"_compute_temp_deform_eff.html commmand that includes +temp/deform/eff"_compute_temp_deform_eff.html command that includes the eFF contribution to the temperature from the electron radial velocity. diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt index 8573d99508..20ff94866e 100644 --- a/doc/src/fix_orient.txt +++ b/doc/src/fix_orient.txt @@ -31,7 +31,7 @@ The fix applies an orientation-dependent force to atoms near a planar grain boundary which can be used to induce grain boundary migration (in the direction perpendicular to the grain boundary plane). The motivation and explanation of this force and its application are -described in "(Janssens)"_#Janssens. The adaptiation to bcc crystals +described in "(Janssens)"_#Janssens. The adaptation to bcc crystals is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only applied to atoms in the fix group. diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 10a0c95c80..aad6c2bfaa 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -43,7 +43,7 @@ fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre Calculate the dynamical matrix from molecular dynamics simulations based on fluctuation-dissipation theory for a group of atoms. -Consider a crystal with \(N\) unit cells in three dimensions labelled +Consider a crystal with \(N\) unit cells in three dimensions labeled \(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is defined by three linearly independent vectors \(\mathbf\{a\}_1\), \(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped, @@ -183,7 +183,7 @@ This fix requires LAMMPS be built with an FFT library. See the [Default:] -The option defaults are sysdim = the same dimemsion as specified by +The option defaults are sysdim = the same dimension as specified by the "dimension"_dimension.html command, and nasr = 20. :line diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index 90ed84a8bf..f2c10184dd 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -107,7 +107,7 @@ atoms in the molecule. If the molecule template contains more than one molecule, the relative probability of depositing each molecule can be specified by the -{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are +{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are specified, where N is the number of molecules in the template. Each time a molecule is inserted, a random number is used to sample from the list of relative probabilities. The N values must sum to 1.0. @@ -144,7 +144,7 @@ command for the temperature compute you are using. All other keywords are optional with defaults as shown below. -The {diam} option is only used when inserting atoms and specifes the +The {diam} option is only used when inserting atoms and specifies the diameters of inserted particles. There are 3 styles: {one}, {range}, or {poly}. For {one}, all particles will have diameter {D}. For {range}, the diameter of each particle will be chosen randomly and @@ -175,7 +175,7 @@ some other way. The {vol} option specifies what volume fraction of the insertion volume will be filled with particles. For particles with a size specified by the {diam range} keyword, they are assumed to all be of -maximum diamter {Dhi} for purposes of computing their contribution to +maximum diameter {Dhi} for purposes of computing their contribution to the volume fraction. The higher the volume fraction value, the more particles are inserted diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 8c9164c25d..aef534ad25 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -121,7 +121,7 @@ as described below. Per-atom properties that are defined by the "atom style"_atom_style.html are initialized when atoms are created, e.g. by the "read_data"_read_data.html or "create_atoms"_create_atoms.html -commands. The per-atom properaties defined by this fix are not. So +commands. The per-atom properties defined by this fix are not. So you need to initialize them explicitly. This can be done by the "read_data"_read_data.html command, using its {fix} keyword and passing it the fix-ID of this fix. diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index e9769ed33b..b1a1dd5c42 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -71,7 +71,7 @@ or AMBER, can have a strong effect on energies and forces, and produces a different model than the published versions. NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used -to perform charge equliibration with the "COMB +to perform charge equilibration with the "COMB potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html command can be used to perform charge equilibration with the "ReaxFF force field"_pair_reax_c.html, although fix qeq/shielded yields the @@ -81,7 +81,7 @@ are the same. Eventually the fix qeq/reax command will be deprecated. The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the atoms) by adjusting the partial charge on individual atoms based on -interactions with their neighbors within {cutoff}. It reqires a few +interactions with their neighbors within {cutoff}. It requires a few parameters, in {metal} units, for each atom type which provided in a file specified by {qfile}. The file has the following format @@ -91,7 +91,7 @@ file specified by {qfile}. The file has the following format Ntype chi eta gamma zeta qcore :pre There is one line per atom type with the following parameters. -Only a subset of the parameters is used by each QEq style as descibed +Only a subset of the parameters is used by each QEq style as described below, thus the others can be set to 0.0 if desired. {chi} = electronegativity in energy units @@ -167,7 +167,7 @@ zero net charge. NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is non-trivial. Charges on atoms are not guaranteed to equilibrate with arbitrary choices of these parameters. We do not develop these QEq -paramters. See the examples/qeq directory for some examples. +parameters. See the examples/qeq directory for some examples. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 58a541cc9d..30c5003e72 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -42,12 +42,12 @@ Only charges on the atoms in the specified group are equilibrated. The fix relies on the pair style (COMB in this case) to calculate the per-atom electronegativity (effective force on the charges). An electronegativity equalization calculation (or QEq) is performed in an -interative fashion, which in parallel requires communication at each +iterative fashion, which in parallel requires communication at each iteration for processors to exchange charge information about nearby atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and "Rick_and_Stuart"_#Rick_and_Stuart for details. -During a run, charge equilibration is peformed every {Nevery} time +During a run, charge equilibration is performed every {Nevery} time steps. Charge equilibration is also always enforced on the first step of each run. The {precision} argument controls the tolerance for the difference in electronegativity for all atoms during charge @@ -55,7 +55,7 @@ equilibration. {Precision} is a trade-off between the cost of performing charge equilibration (more iterations) and accuracy. If the {file} keyword is used, then information about each -equilibration calculation is written to the specifed file. +equilibration calculation is written to the specified file. :line diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index d0266480a8..a26934dfb4 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -33,14 +33,14 @@ typically used in conjunction with the ReaxFF force field model as implemented in the "pair_style reax/c"_pair_reax_c.html command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html -command should be used to perform charge equliibration with the "COMB +command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the "(Aktulga)"_#Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions -with their neighbors. It reqires some parameters for each atom type. +with their neighbors. It requires some parameters for each atom type. If the {params} setting above is the word "reax/c", then these are extracted from the "pair_style reax/c"_pair_reax_c.html command and the ReaxFF force field file it reads in. If a file name is specified diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index a85e140b62..1fd1b3ca5a 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,7 +34,7 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. -The format of the output file should be self-explantory. +The format of the output file should be self-explanatory. :line diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 596ca54b67..c8ec20daaa 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -88,7 +88,7 @@ conformation. You may need to experiment to determine what value of K works best for a given application. For the case of finding a minimum energy structure for a single -molecule with particular restratins (e.g. for fitting forcefield +molecule with particular restraints (e.g. for fitting forcefield parameters or constructing a potential energy surface), commands such as the following may be useful: diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index a38948e560..e086656f5d 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -129,7 +129,7 @@ number of small rigid bodies. Each body is assigned to the atom closest to the geometrical center of the body. The fix operates using local lists of rigid bodies owned by each processor and information is exchanged and summed via local communication between neighboring -processors when ghost atom info is accumlated. +processors when ghost atom info is accumulated. NOTE: To use the {rigid/small} styles the ghost atom cutoff must be large enough to span the distance between the atom that owns the body @@ -262,7 +262,7 @@ and bond interactions within each rigid body, as they no longer contribute to the motion. The "neigh_modify exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html commands are used to do this. If the rigid bodies have strongly -overalapping atoms, you may need to turn off these interactions to +overlapping atoms, you may need to turn off these interactions to avoid numerical problems due to large equal/opposite intra-body forces swamping the contribution of small inter-body forces. @@ -325,7 +325,7 @@ simulation. The effects of these keywords are similar to those defined in "fix npt/nph"_fix_nh.html NOTE: Currently the {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and -{rigid/nph/small} styles do not support triclinic (non-orthongonal) +{rigid/nph/small} styles do not support triclinic (non-orthogonal) boxes. The target pressures for each of the 6 components of the stress tensor @@ -530,7 +530,7 @@ back into the box. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The (vxcm,vycm,vzcm) values are the velocity of the center of mass. @@ -580,7 +580,7 @@ also accounted for by this fix. :line -If your simlulation is a hybrid model with a mixture of rigid bodies +If your simulation is a hybrid model with a mixture of rigid bodies and non-rigid particles (e.g. solvent) there are several ways these rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html. diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index c0deedfa63..6a800f3865 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -21,7 +21,7 @@ solver = {lammps_rk4,rkf45} = rk4 is an explicit 4th order Runge-Kutta method; r minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45) maxSteps = maximum number of steps for the rkf45 solver (rkf45 only) relTol = relative tolerance for the rkf45 solver (rkf45 only) -absTol = absolute tolernace for the rkf45 solver (rkf45 only) +absTol = absolute tolerance for the rkf45 solver (rkf45 only) diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only) :ul [Examples:] @@ -63,7 +63,7 @@ control on the error. For error control, use the rkf45 ODE solver. The rkf45 method adjusts the step-size so that the local truncation error is held within the specified absolute and relative tolerances. The initial step-size {h0} -can be specified by the user or estimated internally. It is recommeded that the user +can be specified by the user or estimated internally. It is recommended that the user specify {h0} since this will generally reduced the number of ODE integration steps required. {h0} is defined as {dt / min_steps} if min_steps >= 1. If min_steps == 0, {h0} is estimated such that an explicit Euler method would likely produce diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index e21736b365..3523233cee 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -52,7 +52,7 @@ intensities at a single snapshot. To produce output in the image data vtk format ghost data is added outside the {Kmax} range assigned in the compute saed. The ghost data is assigned a value of -1 and can be removed setting a minimum isovolume -of 0 within the vizualiziton software. SAED images can be created by +of 0 within the visualization software. SAED images can be created by visualizing a spherical slice of the data that is centered at R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda. @@ -88,7 +88,7 @@ averaging is done; values are simply generated on timesteps :line -The output for fix ave/time/saed is a file writen with the 3rd generation +The output for fix ave/time/saed is a file written with the 3rd generation vtk image data formatting. The filename assigned by the {file} keyword is appended with _N.vtk where N is an index (0,1,2...) to account for multiple diffraction intensity outputs. diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 4f63556c52..a860aad128 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -47,7 +47,7 @@ enables a longer timestep. [SHAKE vs RATTLE:] The SHAKE algorithm was invented for schemes such as standard Verlet -timesteppnig, where only the coordinates are integrated and the +timestepping, where only the coordinates are integrated and the velocities are approximated as finite differences to the trajectories ("Ryckaert et al. (1977)"_#Ryckaert). If the velocities are integrated explicitly, as with velocity Verlet which is what LAMMPS @@ -119,7 +119,7 @@ contribution to the pressure of the system (virial) is also accounted for. NOTE: This command works by using the current forces on atoms to -caculate an additional constraint force which when added will leave +calculate an additional constraint force which when added will leave the atoms in positions that satisfy the SHAKE constraints (e.g. bond length) after the next time integration step. If you define fixes (e.g. "fix efield"_fix_efield.html) that add additional force to the @@ -133,7 +133,7 @@ forces (to atoms that fix shake operates on). The {mol} keyword should be used when other commands, such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules -on-the-fly during a simulation, and you wish to contrain the new +on-the-fly during a simulation, and you wish to constrain the new molecules via SHAKE. You specify a {template-ID} previously defined using the "molecule"_molecule.html command, which reads a file that defines the molecule. You must use the same {template-ID} that the @@ -210,7 +210,7 @@ which can lead to poor energy conservation. You can test for this in your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time. -SHAKE or RATTLE should not be used to contrain an angle at 180 degrees +SHAKE or RATTLE should not be used to constrain an angle at 180 degrees (e.g. linear CO2 molecule). This causes numeric difficulties. [Related commands:] none diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index 4ea592be1b..feb65b2312 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -27,7 +27,7 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre [Description:] -This fix creates reads a traingulated surface from a file in .STL format. +This fix creates reads a triangulated surface from a file in .STL format. For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index 3f3940cd11..68961a1512 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -30,7 +30,7 @@ location at the time the fix command was issued. At each timestep, the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position. The distance r correctly takes into account any crossings -of periodic boundary by the atom since it was in its intitial +of periodic boundary by the atom since it was in its initial position. With the (optional) dir flag, one can select in which direction the diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 13519ecfad..31660fe77a 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -54,18 +54,18 @@ fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 :pre [Description:] -Treat a group of partilces as stochastic rotation dynamics (SRD) +Treat a group of particles as stochastic rotation dynamics (SRD) particles that serve as a background solvent when interacting with big (colloidal) particles in groupbig-ID. The SRD formalism is described in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a cheap coarse-grained solvent is that SRD particles do not interact with each other, but only with the solute particles, which in LAMMPS can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spherioids or ellipsoids or line segments +bodies containing multiple spheriods or ellipsoids or line segments or triangles. The collision and rotation properties of the model imbue the SRD particles with fluid-like properties, including an effective viscosity. Thus simulations with large solute particles can -be run more quickly, to measure solute propoerties like diffusivity +be run more quickly, to measure solute properties like diffusivity and viscosity in a background fluid. The usual LAMMPS fixes for such simulations, such as "fix deform"_fix_deform.html, "fix viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html, @@ -182,7 +182,7 @@ can be used to scale down their effective collision radius by an amount {rfactor}, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation -bewteen two big particles is as small as about 0.88 sigma. Thus an +between two big particles is as small as about 0.88 sigma. Thus an {rfactor} value of 0.85 should prevent dual collisions. The {bounce} keyword can be used to limit the maximum number of @@ -230,7 +230,7 @@ error or warning is generated. Similarly, if the ratio of any bin dimension with {hgrid} exceeds (1 +/- tolerance), then an error or warning is generated. -NOTE: The fix srd command can be used with simluations the size and/or +NOTE: The fix srd command can be used with simulations the size and/or shape of the simulation box changes. This can be due to non-periodic boundary conditions or the use of fixes such as the "fix deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands @@ -241,7 +241,7 @@ box shape changes. This re-binning is always done so as to fit an integer number of bins in the current box dimension, whether it be a fixed, shrink-wrapped, or periodic boundary, as set by the "boundary"_boundary.html command. If the box size or shape changes, -then the size of the search bins must be recalculated avery +then the size of the search bins must be recalculated every reneighboring. Note that changing the SRD bin size may alter the properties of the SRD fluid, such as its viscosity. @@ -345,15 +345,15 @@ commands"_Section_howto.html#howto_15. The vector values calculated by this fix are "intensive", meaning they do not scale with the size of the simulation. Technically, the first 8 do scale with the size of the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodyanmic output. +scaled when printed as part of thermodynamic output. These are the 12 quantities. All are values for the current timestep, except for quantity 5 and the last three, each of which are -cummulative quantities since the beginning of the run. +cumulative quantities since the beginning of the run. (1) # of SRD/big collision checks performed (2) # of SRDs which had a collision -(3) # of SRD/big colllisions (including multiple bounces) +(3) # of SRD/big collisions (including multiple bounces) (4) # of SRD particles inside a big particle (5) # of SRD particles whose velocity was rescaled to be < Vmax (6) # of bins for collision searching diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 177591d8e7..9c1dd538da 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -127,7 +127,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 7e53926516..4129ad73c8 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -39,7 +39,7 @@ scaling factor from a suitably chosen (gaussian) distribution rather than having it determined from the time constant directly. In the case of {temp/csld} the velocities are updated to a linear combination of the current velocities with a gaussian distribution of velocities at -the desired temperature. Both termostats are applied every timestep. +the desired temperature. Both thermostats are applied every timestep. The thermostat is applied to only the translational degrees of freedom for the particles, which is an important consideration for finite-size @@ -136,7 +136,7 @@ These fixes are not invoked during "energy minimization"_minimize.html. These fixes compute a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to the fix. The scalar value +cumulative energy change due to the fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index f38d20d0d7..eff25297c1 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -44,7 +44,7 @@ ramped value between the {Tstart} and {Tstop} temperatures at the beginning and end of the run. NOTE: This thermostat will generate an error if the current -temperature is zero at the end of a timestep it is inovoked on. It +temperature is zero at the end of a timestep it is invoked on. It cannot rescale a zero temperature. {Tstart} can be specified as an equal-style "variable"_variable.html. @@ -134,7 +134,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt index c39651e05c..f87c1a2192 100644 --- a/doc/src/fix_temp_rescale_eff.txt +++ b/doc/src/fix_temp_rescale_eff.txt @@ -52,7 +52,7 @@ output"_thermo_style.html. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index beb9f68933..3c81d62ee0 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -41,7 +41,7 @@ can be used to extend the time scale of atomistic simulations, in particular when long time scale relaxation effects must be considered; some interesting examples are given in the review by "(Neyts)"_#Neyts. An example of a typical use case would be the modelling of chemical -vapour deposition (CVD) processes on a surface, in which impacts by +vapor deposition (CVD) processes on a surface, in which impacts by gas-phase species can be performed using MD, but subsequent relaxation of the surface is too slow to be done using MD only. Using tfMC can allow for a much faster relaxation of the surface, so that higher diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 9038a12709..a807feaec7 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -109,10 +109,10 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative kinetic energy transferred between the bottom and middle +cumulative kinetic energy transferred between the bottom and middle of the simulation box (in the {edim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are energy; see the "units"_units.html command for details. The scalar value calculated by this fix is "intensive". @@ -141,7 +141,7 @@ of this idea. When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange kinetic energy -bewteen solvent particles. +between solvent particles. [Related commands:] diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt index 2e7318da14..48dfd254a0 100644 --- a/doc/src/fix_ttm.txt +++ b/doc/src/fix_ttm.txt @@ -106,7 +106,7 @@ electron stopping coupling parameter. C_e, rho_e, and kappa_e are specified as parameters to the fix. The other quantities are derived. The form of the heat diffusion equation used here is almost the same as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the -electronic density is explicitly reprensented, rather than being part +electronic density is explicitly represented, rather than being part of the specific heat parameter. Currently, fix ttm assumes that none of the user-supplied parameters @@ -151,7 +151,7 @@ output timestep. The timestep itself is given in the first column. The next Nx*Ny*Nz columns contain the temperatures for the atomic subsystem, and the final Nx*Ny*Nz columns contain the temperatures for the electronic subsystem. The ordering of the Nx*Ny*Nz columns is -with the z index varing fastest, y the next fastest, and x the +with the z index varying fastest, y the next fastest, and x the slowest. These fixes do not change the coordinates of their atoms; they only @@ -300,7 +300,7 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info. These fixes can only be used for 3d simulations and orthogonal -simlulation boxes. You must also use periodic +simulation boxes. You must also use periodic "boundary"_boundary.html conditions. [Related commands:] diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 5bae961ada..47b3cfc67a 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -136,7 +136,7 @@ An array is produced if multiple input values are specified. The length of the vector or the number of rows in the array grows by 1 every {Nevery} timesteps. -If the fix prouduces a vector, then the entire vector will be either +If the fix produces a vector, then the entire vector will be either "intensive" or "extensive", depending on whether the values stored in the vector are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 8b9c0d3cb6..5fbbc67ca5 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -102,7 +102,7 @@ parameter. An alternative method for calculating a viscosity is to run a NEMD simulation, as described in "Section 6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations -deform the simmulation box via the "fix deform"_fix_deform.html +deform the simulation box via the "fix deform"_fix_deform.html command. Thus they cannot be run on a charged system using a "PPPM solver"_kspace_style.html since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; @@ -116,10 +116,10 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative momentum transferred between the bottom and middle of the +cumulative momentum transferred between the bottom and middle of the simulation box (in the {pdim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are momentum = mass*velocity. The scalar value calculated by this fix is "intensive". @@ -147,7 +147,7 @@ See the "Maginn paper"_#Maginn for an example of using this algorithm in a computation of alcohol molecule properties. When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange momenta bewteen +in a background solvent, you may want to only exchange momenta between solvent particles. [Related commands:] diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index 024719f057..6d76956620 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -136,7 +136,7 @@ of 1/volume. The {wall/colloid} interaction is derived by integrating over constituent LJ particles of size {sigma} within the colloid particle and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma} -in the wall. As mentioned in the preceeding paragraph, the density of +in the wall. As mentioned in the preceding paragraph, the density of particles in the wall and colloid can be different, as specified by the {epsilon} pre-factor. diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 40cd5c8c74..5f1679604e 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -85,7 +85,7 @@ versions used Kn and Kt from the pairwise interaction and hardwired dampflag to 1, rather than letting them be specified directly. This means you can set the values of the wall/particle coefficients appropriately in the current code to reproduce the results of a -prevoius Hertzian monodisperse calculation. For example, for the +previous Hertzian monodisperse calculation. For example, for the common case of a monodisperse system with particles of diameter 1, Kn, Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were previously. diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index cfee0d9977..92fb042194 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -153,7 +153,7 @@ material. [Restart, fix_modify, output, run start/stop, minimize info:] -Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix +Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes the shear friction state of atoms interacting with the wall to "binary restart files"_restart.html, so that a simulation can continue correctly if granular potentials with shear "history" effects are @@ -169,7 +169,7 @@ So you must re-define your region and if it is a moving region, define its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the region motion attributes (e.g. its velocity), then you should ensure -the postition/orientation of the region at the initial restart +the position/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. If this is not possible, you may need to ignore info in the restart file by defining a new fix wall/gran/region command in your diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 594e3db06d..4d7756c237 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -24,7 +24,7 @@ keyword = {pos} or {vel} or {ramp} or {units} :l {ramp} = use a linear velocity ramp from 0 to vz {temp} args = target damp seed extent target = target velocity for region immediately ahead of the piston - damp = damping paramter (time units) + damp = damping parameter (time units) seed = random number seed for langevin kicks extent = extent of thermostated region (distance units) {units} value = {lattice} or {box} diff --git a/doc/src/group.txt b/doc/src/group.txt index ab975af756..afa218c5a3 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -144,7 +144,7 @@ or exclude from a group. For example, these lines define a variable "eatom" that calculates the potential energy of each atom and includes it in the group if its -potential energy is above the threshhold value -3.0. +potential energy is above the threshold value -3.0. compute 1 all pe/atom compute 2 all reduce sum c_1 @@ -165,7 +165,7 @@ group command invokes it. Because the eatom variable computes the per-atom energy via the pe/atom compute, it will only be current if a run has been performed which evaluated pairwise energies, and the pe/atom compute was actually invoked during the run. Printing the -thermodyanmic info for compute 2 insures that this is the case, since +thermodynamic info for compute 2 insures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the "Variable Accuracy" section of the "variable"_variable.html doc page for more details on insuring that diff --git a/doc/src/if.txt b/doc/src/if.txt index aa93c73790..52fad5aea7 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -37,7 +37,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre [Description:] This command provides an if-then-else capability within an input -script. A Boolean expression is evaluted and the result is TRUE or +script. A Boolean expression is evaluated and the result is TRUE or FALSE. Note that as in the examples above, the expression can contain variables, as defined by the "variable"_variable.html command, which will be evaluated as part of the expression. Thus a user-defined @@ -93,7 +93,7 @@ system temperature has reached a certain value, and if so, breaks out of the loop to finish the run. Note that any variable could be checked, so long as it is current on the timestep when the run completes. As explained on the "variable"_variable.html doc page, -this can be insured by includig the variable in thermodynamic output. +this can be insured by including the variable in thermodynamic output. variable myTemp equal temp label loop diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt index a3bd9a973a..0c2beaef18 100644 --- a/doc/src/improper_hybrid.txt +++ b/doc/src/improper_hybrid.txt @@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. Unlike other improper styles, the hybrid improper style does not store improper coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when retarting a simulation from a +restart files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify improper_coeff commands. [Related commands:] diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index d1eca6d5d9..705b1cf742 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -36,7 +36,7 @@ j,k, and l. The "ring" improper style implements the improper potential introduced by Destree et al., in Equation (9) of "(Destree)"_#Destree. This potential does not affect small amplitude vibrations but is used in an -ad-hoc way to prevent the onset of accidentially large amplitude +ad-hoc way to prevent the onset of accidentally large amplitude fluctuations leading to the occurrence of a planar conformation of the three bonds i-j, j-k and j-l, an intermediate conformation toward the chiral inversion of a methine carbon. In the "Impropers" section of diff --git a/doc/src/info.txt b/doc/src/info.txt index 605dafa851..0b761ccc15 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -94,7 +94,7 @@ The {time} category prints the accumulated CPU and wall time for the process that writes output (usually MPI rank 0). The {configuration} command prints some information about the LAMMPS -version and architection and OS it is run on. Where supported, also +version and architecture and OS it is run on. Where supported, also information about the memory consumption provided by the OS is reported. diff --git a/doc/src/jump.txt b/doc/src/jump.txt index e746ea782a..1b1a209511 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -87,7 +87,7 @@ system temperature has reached a certain value, and if so, breaks out of the loop to finish the run. Note that any variable could be checked, so long as it is current on the timestep when the run completes. As explained on the "variable"_variable.html doc page, -this can be insured by includig the variable in thermodynamic output. +this can be insured by including the variable in thermodynamic output. variable myTemp equal temp label loop diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 013e61965f..cb57863ad0 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -98,7 +98,7 @@ Coulombics. The {overlap} keyword can be used in conjunction with the {minorder} keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchangeed between +that occurs when values on the FFT grid are exchanged between processors. This communication is distinct from the communication inherent in the parallel FFTs themselves, and is required because processors interpolate charge and field values using grid point values @@ -122,7 +122,7 @@ neighbor processors. The {minorder} keyword limits how small the {order} setting can become. The minimum allowed value for PPPM is 2, which is the default. If {minorder} is set to the same value as {order} then no reduction is allowed, and LAMMPS will generate an -error if the grid communcation is non-nearest-neighbor and {overlap} +error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. @@ -284,7 +284,7 @@ of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal performance and accuracy in the results is obtained when these values are different. -The {disp/auto} option controlls whether the pppm/disp is allowed to +The {disp/auto} option controls whether the pppm/disp is allowed to generate PPPM parameters automatically. If set to {no}, parameters have to be specified using the {gewald/disp}, {mesh/disp}, {force/disp/real} or {force/disp/kspace} keywords, or diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 492d1d88e7..e5c47e8230 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -131,7 +131,7 @@ reduce force aliasing errors and increase the accuracy of the method for a given mesh size. Or a coarser mesh can be used for the same target accuracy, which saves CPU time. However, there is a trade-off since FFTs on two meshes are now performed which increases the -compuation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, +computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, and "(Hockney)"_#Hockney for details of the method. For high relative accuracy, using staggered PPPM allows the mesh size @@ -174,7 +174,7 @@ using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your lo-level Makefile. This setting also changes some of the PPPM operations (e.g. mapping charge to mesh and interpolating electric fields to particles) to be performed in single precision. This option -can speed-up long-range calulations, particularly in parallel or on +can speed-up long-range calculations, particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag is discussed in "this section"_Section_start.html#start_2_4 of the manual. MSM does not currently support the -DFFT_SINGLE compiler switch. @@ -233,7 +233,7 @@ simulation cell. One way to handle this issue if you have a long simulation where the box size changes dramatically, is to break it into shorter simulations (multiple "run"_run.html commands). This works because the grid size is re-computed at the beginning of each -run. Another way to ensure the descired accuracy requirement is met +run. Another way to ensure the described accuracy requirement is met is to run a short simulation at the maximum expected tilt or length, note the required grid size, and then use the "kspace_modify"_kspace_modify.html {mesh} command to manually set the @@ -255,7 +255,7 @@ are estimated using equations 33 and 46 of "(Wang)"_#Wang. See the "kspace_modify"_kspace_modify.html command for additional options of the K-space solvers that can be set, including a {force} -option for setting an absoulte RMS error in forces, as opposed to a +option for setting an absolute RMS error in forces, as opposed to a relative RMS error. :line @@ -341,7 +341,7 @@ kspace_style none :pre Adam Hilger, NY (1989). :link(Kolafa) -[(Kolafa)] Kolafa and Perram, Molecular Simualtion, 9, 351 (1992). +[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992). :link(Petersen) [(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995). diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0e4f3a8db8..3186865fb6 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -194,6 +194,7 @@ fix_meso.html fix_meso_stationary.html fix_momentum.html fix_move.html +fix_mscg.html fix_msst.html fix_neb.html fix_nh.html @@ -218,6 +219,7 @@ fix_nve_manifold_rattle.html fix_nve_noforce.html fix_nve_sphere.html fix_nve_tri.html +fix_nvk.html fix_nvt_asphere.html fix_nvt_body.html fix_nvt_manifold_rattle.html @@ -432,6 +434,7 @@ pair_gromacs.html pair_hbond_dreiding.html pair_hybrid.html pair_kim.html +pair_kolmogorov_crespi_z.html pair_lcbop.html pair_line_lj.html pair_list.html @@ -458,7 +461,7 @@ pair_multi_lucy_rx.html pair_nb3b_harmonic.html pair_nm.html pair_none.html -pair_oxdna_excv.html +pair_oxdna.html pair_peri.html pair_polymorphic.html pair_quip.html @@ -497,7 +500,7 @@ pair_zero.html bond_class2.html bond_fene.html bond_fene_expand.html -bond_oxdna_fene.html +bond_oxdna.html bond_harmonic.html bond_harmonic_shift.html bond_harmonic_shift_cut.html diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 2de23310b8..a3f2c5d0bf 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -48,7 +48,7 @@ soft"_pair_soft.html potential can be used to un-overlap atoms while running dynamics. Note that you can minimize some atoms in the system while holding the -coordiates of other atoms fixed by applying "fix +coordinates of other atoms fixed by applying "fix setforce"_fix_setforce.html to the other atoms. See a fuller discussion of using fixes while minimizing below. @@ -58,7 +58,7 @@ which atom coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search typically evaluates forces and energies several times to set new coordinates. Currently, a backtracking algorithm is used which may not be optimal -in terms of the number of force evaulations performed, but appears to +in terms of the number of force evaluations performed, but appears to be more robust than previous line searches we've tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). @@ -201,7 +201,7 @@ minimum to the specified energy or force tolerance. Note that a cutoff Lennard-Jones potential (and others) can be shifted so that its energy is 0.0 at the cutoff via the "pair_modify"_pair_modify.html command. See the doc pages for -inidividual "pair styles"_pair_style.html for details. Note that +individual "pair styles"_pair_style.html for details. Note that Coulombic potentials always have a cutoff, unless versions with a long-range component are used (e.g. "pair_style lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 9e738cee50..ecec62256a 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -155,7 +155,7 @@ The mass and center-of-mass coordinates (Xc,Yc,Zc) are self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to -the simulation box XYZ axes, not with respect to the prinicpal axes of +the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 649e521eee..a5fa03552c 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -58,7 +58,7 @@ would see with one or more physical processors per replica. See discussion. NOTE: As explained below, a NEB calculation perfoms a damped dynamics -minimization across all the replicas. The mimimizer uses whatever +minimization across all the replicas. The minimizer uses whatever timestep you have defined in your input script, via the "timestep"_timestep.html command. Often NEB will converge more quickly if you use a timestep about 10x larger than you would normally @@ -81,7 +81,7 @@ inter-replica springs and the forces they feel and their motion is computed in the usual way due only to other atoms within their replica. Conceptually, the non-NEB atoms provide a background force field for the NEB atoms. They can be allowed to move during the NEB -minimiation procedure (which will typically induce different +minimization procedure (which will typically induce different coordinates for non-NEB atoms in different replicas), or held fixed using other LAMMPS commands such as "fix setforce"_fix_setforce.html. Note that the "partition"_partition.html command can be used to invoke @@ -97,7 +97,7 @@ Conceptually, the initial configuration for the first replica should be a state with all the atoms (NEB and non-NEB) having coordinates on one side of the energy barrier. A perfect energy minimum is not required, since atoms in the first replica experience no spring forces -from the 2nd replica. Thus the damped dynamics minimizaiton will +from the 2nd replica. Thus the damped dynamics minimization will drive the first replica to an energy minimum if it is not already there. However, you will typically get better convergence if the initial state is already at a minimum. For example, for a system with @@ -366,7 +366,7 @@ parameters. There are 2 Python scripts provided in the tools/python directory, neb_combine.py and neb_final.py, which are useful in analyzing output from a NEB calculation. Assume a NEB simulation with M replicas, and -the NEB atoms labelled with a specific atom type. +the NEB atoms labeled with a specific atom type. The neb_combine.py script extracts atom coords for the NEB atoms from all M dump files and creates a single dump file where each snapshot diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index c16b667f7d..5c149d892d 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -34,8 +34,10 @@ keyword = {delay} or {every} or {check} or {once} or {cluster} or {include} or { M,N = exclude if one atom in pair is type M, other is type N group group1-ID group2-ID group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd - molecule group-ID - groupname = exclude if both atoms are in the same molecule and in the same group + molecule/intra group-ID + group-ID = exclude if both atoms are in the same molecule and in group + molecule/inter group-ID + group-ID = exclude if both atoms are in different molecules and in group none delete all exclude settings {page} value = N @@ -52,7 +54,7 @@ neigh_modify every 2 delay 10 check yes page 100000 neigh_modify exclude type 2 3 neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 -neigh_modify exclude molecule rigid :pre +neigh_modify exclude molecule/intra rigid :pre [Description:] @@ -130,9 +132,11 @@ The {exclude type} option turns off the pairwise interaction if one atom is of type M and the other of type N. M can equal N. The {exclude group} option turns off the interaction if one atom is in the first group and the other is the second. Group1-ID can equal -group2-ID. The {exclude molecule} option turns off the interaction if -both atoms are in the specified group and in the same molecule, as -determined by their molecule ID. +group2-ID. The {exclude molecule/intra} option turns off the +interaction if both atoms are in the specified group and in the same +molecule, as determined by their molecule ID. The {exclude +molecule/inter} turns off the interaction between pairs of atoms that +have different molecule IDs and are both in the specified group. Each of the exclude options can be specified multiple times. The {exclude type} option is the most efficient option to use; it requires @@ -195,8 +199,8 @@ binsize of 1/2 the cutoff. If the "delay" setting is non-zero, then it must be a multiple of the "every" setting. -The exclude molecule option can only be used with atom styles that -define molecule IDs. +The molecule/intra and molecule/inter exclude options can only be used +with atom styles that define molecule IDs. The value of the {page} setting must be at least 10x larger than the {one} setting. This insures neighbor pages are not mostly empty diff --git a/doc/src/package.txt b/doc/src/package.txt index de7e0f5c22..02afb8d620 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -110,7 +110,7 @@ USER-OMP. If this command is specified in an input script, it must be near the top of the script, before the simulation box has been defined. This is because it specifies settings that the accelerator packages use in -their intialization, before a simultion is defined. +their initialization, before a simulation is defined. This command can also be specified from the command-line when launching LAMMPS, using the "-pk" "command-line @@ -166,7 +166,7 @@ neighbor list building is performed on the CPU. GPU neighbor list building currently cannot be used with a triclinic box. GPU neighbor list calculation currently cannot be used with "hybrid"_pair_hybrid.html pair styles. GPU neighbor lists are not -compatible with comannds that are not GPU-enabled. When a non-GPU +compatible with commands that are not GPU-enabled. When a non-GPU enabled command requires a neighbor list, it will also be built on the CPU. In these cases, it will typically be more efficient to only use CPU neighbor list builds. @@ -199,7 +199,7 @@ the default. The {split} keyword can be used for load balancing force calculations between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} < 1.0, a fixed fraction of particles is offloaded to the GPU while force -calculation for the other particles occurs simulataneously on the CPU. +calculation for the other particles occurs simultaneously on the CPU. If {split} < 0.0, the optimal fraction (based on CPU and GPU timings) is calculated every 25 timesteps, i.e. dynamic load-balancing across the CPU and GPU is performed. If {split} = 1.0, all force @@ -295,7 +295,7 @@ For more details, including examples of how to set the OMP_NUM_THREADS environment variable, see the discussion of the {Nthreads} setting on this doc page for the "package omp" command. Nthreads is a required argument for the USER-OMP package. Its meaning is exactly the same -for the USER-INTEL pacakge. +for the USER-INTEL package. NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP packages, be aware that both packages allow setting of the {Nthreads} @@ -347,7 +347,7 @@ automatically throughout the run. This typically give performance within 5 to 10 percent of the optimal fixed fraction. The {ghost} keyword determines whether or not ghost atoms, i.e. atoms -at the boundaries of proessor sub-domains, are offloaded for neighbor +at the boundaries of processor sub-domains, are offloaded for neighbor and force calculations. When the value = "no", ghost atoms are not offloaded. This option can reduce the amount of data transfer with the coprocessor and can also overlap MPI communication of forces with @@ -516,7 +516,7 @@ for OpenMPI. Check your MPI documentation for additional details. What combination of threads and MPI tasks gives the best performance is difficult to predict and can depend on many components of your input. Not all features of LAMMPS support OpenMP threading via the -USER-OMP packaage and the parallel efficiency can be very different, +USER-OMP package and the parallel efficiency can be very different, too. Optional keyword/value pairs can also be specified. Each has a @@ -527,7 +527,7 @@ multi-threaded in addition to force calculations. If {neigh} is set to {no} then neighbor list calculation is performed only by MPI tasks with no OpenMP threading. If {mode} is {yes} (the default), a multi-threaded neighbor list build is used. Using {neigh} = {yes} is -almost always faster and should produce idential neighbor lists at the +almost always faster and should produce identical neighbor lists at the expense of using more memory. Specifically, neighbor list pages are allocated for all threads at the same time and each thread works within its own pages. diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index c9dd31d57b..457a797d95 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -68,7 +68,7 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the -potentials directory of the LAMMPS distrbution, is an extended {setfl} +potentials directory of the LAMMPS distribution, is an extended {setfl} file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 08490c601a..27fb6c10fe 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -34,7 +34,7 @@ non-linear regression model. The method implements the recently proposed machine learning access to atomic forces as discussed extensively in the following publications - "(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise -of the method is to map the atomic enviornment numerically into a +of the method is to map the atomic environment numerically into a fingerprint, and use machine learning methods to create a mapping to the vectorial atomic forces. diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 6d0b1b0088..2e3083c34b 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -53,7 +53,7 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO) Potential of "(Brenner)"_#Brenner. Note that this is the so-called 2nd generation REBO from 2002, not the original REBO from 1990. As discussed below, 2nd generation REBO is closely related to the -intial AIREBO; it is just a subset of the potential energy terms. +initial AIREBO; it is just a subset of the potential energy terms. The AIREBO potential consists of three terms: diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index 49c6c8db62..4e792754b8 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively. [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html shift diff --git a/doc/src/pair_body.txt b/doc/src/pair_body.txt index 622cc88f88..7899da832b 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body.txt @@ -59,7 +59,7 @@ computed and summed. If the distance is not within the cutoff, no interactions between the body and point particle are computed. The interaction between two sub-particles, or a sub-particle and point -particle, or betwee two point particles is computed as a Lennard-Jones +particle, or between two point particles is computed as a Lennard-Jones interaction, using the standard formula :c,image(Eqs/pair_lj.jpg) diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 0dbd1fc5dd..9251fc4e70 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -36,11 +36,11 @@ developed by Pettifor ("Pettifor_1"_#Pettifor_1, "Pettifor_2"_#Pettifor_2, "Pettifor_3"_#Pettifor_3) and later updated by Murdick, Zhou, and Ward ("Murdick"_#Murdick, "Ward"_#Ward). Currently, BOP potential files for these systems are provided with -LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with +LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with only a subset of these elements, including a single element (e.g. C or Cu or Al or Ga or Zn or CdZn), can also be modeled by using the appropriate alloy file and assigning all atom types to the -singleelement or subset of elements via the pair_coeff command, as +single element or subset of elements via the pair_coeff command, as discussed below. The BOP potential consists of three terms: @@ -49,7 +49,7 @@ The BOP potential consists of three terms: where phi_ij(r_ij) is a short-range two-body function representing the repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and -beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals, +beta_(sigma,ij)(r_ij) are respectively sigma and pi bond integrals, THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and U_prom is the promotion energy for sp-valent systems. @@ -78,8 +78,8 @@ levels of the recursive representations for both the sigma and the pi bond-orders. Bond-order terms can be understood in terms of molecular orbital hopping paths based upon the Cyrot-Lackmann theorem ("Pettifor_1"_#Pettifor_1). The sigma bond-order with a half-full -valence shell is used to interpolate the bond-order expressiont that -incorporated explicite valance band filling. This pi bond-order +valence shell is used to interpolate the bond-order expression that +incorporated explicit valance band filling. This pi bond-order expression also contains also contains a three-member ring term that allows implementation of an asymmetric density of states, which helps to either stabilize or destabilize close-packed structures. The pi @@ -299,7 +299,7 @@ of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The function can contain up to 10 term thus 10 constants. The first line can contain up to five constants. If the spline has more than five terms the second line will contain the remaining constants The -following lines will then contain the constants for the remainaing g0, +following lines will then contain the constants for the remaining g0, g1, g2... (for e_1-e_1-e_2) and the other three body interactions :l :ule diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index c060856d60..92e74bbba3 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -86,7 +86,7 @@ For style {comb}, the provided potential file {ffield.comb} contains all currently-available 2nd generation COMB parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style {comb3}, the potential file {ffield.comb3} contains all -currently-available 3rd generation COMB paramterizations: O, Cu, N, C, +currently-available 3rd generation COMB parameterizations: O, Cu, N, C, H, Ti, Zn and Zr. The status of the optimization of the compounds, for example Cu2O, TiN and hydrocarbons, are given in the following table: diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index b3d5fdef27..43bd13127a 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -127,15 +127,15 @@ summation method, described in "Wolf"_#Wolf, given by: :c,image(Eqs/pair_coul_wolf.jpg) where {alpha} is the damping parameter, and erc() and erfc() are -error-fuction and complementary error-function terms. This potential +error-function and complementary error-function terms. This potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, pairwise {1/r} summation. With a -manipulation of adding and substracting a self term (for i = j) to the +manipulation of adding and subtracting a self term (for i = j) to the first and second term on the right-hand-side, respectively, and a small enough {alpha} damping parameter, the second term shrinks and the potential becomes a rapidly-converging real-space summation. With a long enough cutoff and small enough alpha parameter, the energy and -forces calcluated by the Wolf summation method approach those of the +forces calculated by the Wolf summation method approach those of the Ewald sum. So it is a means of getting effective long-range interactions with a short-range potential. @@ -188,7 +188,7 @@ but there is no conceptual problem with extending it to nitrides and carbides (such as SiC, TiN). Pair coul/strietz used by itself or with any other pair style such as EAM, MEAM, Tersoff, or LJ in hybrid/overlay mode. To do this, you would need to provide a -Streitz-Mintmire parameterizaion for the material being modeled. +Streitz-Mintmire parameterization for the material being modeled. :line @@ -222,7 +222,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502. See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb +parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index 498e1873df..fc2042a901 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -23,11 +23,11 @@ pair_coeff 1 4 78. 1.375 0.112 :pre [Description:] -Style {coul/diel} computes a Coulomb correction for implict solvent -ion interactions in which the dielectric perimittivity is distance dependent. +Style {coul/diel} computes a Coulomb correction for implicit solvent +ion interactions in which the dielectric permittivity is distance dependent. The dielectric permittivity epsilon_D(r) connects to limiting regimes: One limit is defined by a small dielectric permittivity (close to vacuum) -at or close to contact seperation between the ions. At larger separations +at or close to contact separation between the ions. At larger separations the dielectric permittivity reaches a bulk value used in the regular Coulomb interaction coul/long or coul/cut. The transition is modeled by a hyperbolic function which is incorporated @@ -48,7 +48,7 @@ Examples of the use of this type of Coulomb interaction include implicit solvent simulations of salt ions "(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi. Note that this potential is only reasonable for implicit solvent simulations -and in combiantion with coul/cut or coul/long. It is also usually combined +and in combination with coul/cut or coul/long. It is also usually combined with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi. The following coefficients must be defined for each pair of atom diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 7072b1702d..62a5faffed 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -88,7 +88,7 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), where T is the temperature set by the "pair_style"_pair_style.html command so it does not need to be specified. -For style {dpd/tstat}, the coefficiencts defined for each pair of +For style {dpd/tstat}, the coefficients defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command is the same, except that A is not included. diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index ed09ce4d99..4d3c2b2dea 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -273,7 +273,7 @@ style. However the DYNAMO {setfl} file must has two lines added to it, at the end of the file: line 1: Comment line (ignored) -line 2: N Coefficient0 Coefficient1 ... CoeffincientN :ul +line 2: N Coefficient0 Coefficient1 ... CoefficientN :ul The last line begins with the degree {N} of the polynomial function {h(x)} that modifies the cross interaction between A and B elements. diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index 6881b53434..cdfc265752 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -95,7 +95,7 @@ entries would be required, etc. At the moment, only a single element parametrization is implemented. However, the author is not aware of other -multi-element EDIP parametrizations. If you know any and +multi-element EDIP parameterization. If you know any and you are interest in that, please contact the author of the EDIP package. diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index 6be8cdc785..ee7dc99932 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -149,7 +149,7 @@ command. :line -The {limit/eradius} and {pressure/evirials} keywrods are optional. +The {limit/eradius} and {pressure/evirials} keywords are optional. Neither or both must be specified. If not specified they are unset. The {limit/eradius} keyword is used to restrain electron size from @@ -197,7 +197,7 @@ partitioning changes, the total energy remains similar). :line -NOTE: This implemention of eFF gives a reasonably accurate description +NOTE: This implementation of eFF gives a reasonably accurate description for systems containing nuclei from Z = 1-6 in "all electron" representations. For systems with increasingly non-spherical electrons, Users should use the ECP representations. ECPs are now @@ -284,7 +284,7 @@ that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. These pair styles require that particles store electron attributes -such as radius, radial velocity, and radital force, as defined by the +such as radius, radial velocity, and radial force, as defined by the "atom_style"_atom_style.html. The {electron} atom style does all of this. diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 47078f9a8f..e74bb364d4 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -97,7 +97,7 @@ pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The filename is the EIM potential file. The Na and Cl arguments (before the file name) are the two elements for which info will be -extracted from the potentail file. The first three trailing Na +extracted from the potential file. The first three trailing Na arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The final Cl argument maps LAMMPS atom type 4 to the EIM Cl element. @@ -107,7 +107,7 @@ This can be used when an {eim} potential is used as part of the that will be used with other potentials. The ffield.eim file in the {potentials} directory of the LAMMPS -distribution is formated as follows: +distribution is formatted as follows: Lines starting with # are comments and are ignored by LAMMPS. Lines starting with "global:" include three global values. The first value diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index dafba2c44c..47045a5933 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -63,7 +63,7 @@ reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). The fourth argument specifies the type of scaling that will be used -to scale the EXP-6 paramters as reactions occur. Currently, there +to scale the EXP-6 parameters as reactions occur. Currently, there are three scaling options: {exponent}, {polynomial} and {none}. Exponent scaling requires two additional arguments for scaling @@ -72,7 +72,7 @@ is computed by phi^exponent, where phi is the number of molecules represented by the coarse-grain particle and exponent is specified as a pair coefficient argument for {Rm} and {epsilon}, respectively. The {Rm} and {epsilon} parameters are multiplied by the scaling -factor to give the scaled interaction paramters for the CG particle. +factor to give the scaled interaction parameters for the CG particle. Polynomial scaling requires a filename to be specified as a pair coeff argument. The file contains the coefficients to a fifth order diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d4530d37dd..373a82fa80 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -224,7 +224,7 @@ normal direction (along the line joining the 2 sphere centers). The last 3 (8-10) the components of the relative velocity in the tangential direction. -These extra quantites can be accessed by the "compute +These extra quantities can be accessed by the "compute pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., {p10}. diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index b3c9b5b5d5..9641e294fa 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -101,13 +101,13 @@ pair_coeff settings for all possible I,J type pairs. Only I,J type pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. -NOTE: A "pair_coeff"_pair_coeff.html command can be speficied multiple +NOTE: A "pair_coeff"_pair_coeff.html command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. For other pair_styles, if the pair_coeff command is re-used for the same I.J type pair, the settings for that type pair are overwritten. For the hydrogen bond potentials this is not the case; the settings -are cummulative. This means the only way to turn off a previous +are cumulative. This means the only way to turn off a previous setting, is to re-use the pair_style command and start over. For the {hbond/dreiding/lj} style the list of coefficients is as diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 47451cf14a..7ef54e7f07 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -63,7 +63,7 @@ Note that an individual pair style can be used multiple times as a sub-style. For efficiency this should only be done if your model requires it. E.g. if you have different regions of Si and C atoms and wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potetnial for pure C for the other set (presumably with some +a Tersoff potential for pure C for the other set (presumably with some 3rd potential for Si-C interactions), then the sub-style {tersoff} could be listed twice. But if you just want to use a Lennard-Jones or other pairwise potential for several different atom type pairs in your @@ -189,7 +189,7 @@ potentials. Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise -interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4 +interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the "special_bonds"_special_bonds.html command. Different weights can be assigned to different pair hybrid sub-styles via the "pair_modify diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 04d8d23dba..5a623e5ece 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -46,7 +46,7 @@ model. You should get an error or warning message from either LAMMPS or KIM if there is an incompatibility. The argument {printflag} is optional. If it is set to a non-zero -value then a KIM dsecriptor file is printed when KIM is invoked. This +value then a KIM descriptor file is printed when KIM is invoked. This can be useful for debugging. The default is to not print this file. Only a single pair_coeff command is used with the {kim} style which diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt new file mode 100644 index 0000000000..a7bd917caa --- /dev/null +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -0,0 +1,72 @@ +"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 kolmogorov/crespi/z command :h3 + +[Syntax:] + +pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre + +[Examples:] + +pair_style hybrid/overlay kolmogorov/crespi/z 20.0 +pair_coeff * * none +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre + +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +pair_coeff * * rebo CH.airebo C C +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre + +[Description:] + +The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction +potential as described in "(KC05)"_#KC05. An important simplification is made, +which is to take all normals along the z-axis. + +:c,image(Eqs/pair_kolmogorov_crespi_z.jpg) + +It is important to have a suffiently large cutoff to ensure smooth forces. +Energies are shifted so that they go continously to zero at the cutoff assuming +that the exponential part of {Vij} (first term) decays sufficiently fast. +This shift is achieved by the last term in the equation for {Vij} above. + +This potential is intended for interactions between two layers of graphene. +Therefore, to avoid interaction between layers in multi-layered materials, +each layer should have a separate atom type and interactions should only +be computed between atom types of neighbouring layers. + +The parameter file (e.g. CC.KC), is intended for use with metal +"units"_units.html, with energies in meV. An additional parameter, {S}, +is available to facilitate scaling of energies in accordance with +"(vanWijk)"_#vanWijk. + +This potential must be used in combination with hybrid/overlay. +Other interactions can be set to zero using pair_style {none}. + +[Restrictions:] + +This fix is part of the USER-MISC 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:] + +"pair_coeff"_pair_coeff.html +"pair_none"_pair_none.html +"pair_style hybrid/overlay"_pair_hybrid.html + +[Default:] none + +:line + +:link(KC05) +[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) + +:link(vanWijk) +[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, +Physical Review Letters, 113, 135504 (2014) diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index bb1146b64e..44cfeb48e9 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -39,7 +39,7 @@ function of the line segment length and the specified sub-particle size for that particle type. If a line segment has a length L and is of type I, then the number of spheres N that represent the segment is calculated as N = L/sizeI, rounded up to an integer value. Thus if L -is not evenly divisibly by sizeI, N is incremented to include one +is not evenly divisible by sizeI, N is incremented to include one extra sphere. The centers of the spheres are spaced equally along the line segment. Imagine N+1 equally-space points, which include the 2 end points of the segment. The sphere centers are halfway between @@ -48,7 +48,7 @@ each pair of points. The LJ interaction between 2 spheres on different line segments (or a sphere on a line segment and a point particles) is computed with sub-particle epsilon, sigma, and cutoff values that are set by the -pair_coeff command, as described below. If the distance bewteen the 2 +pair_coeff command, as described below. If the distance between the 2 spheres is greater than the sub-particle cutoff, there is no interaction. This means that some pairs of sub-particles on 2 line segments may interact, but others may not. @@ -90,7 +90,7 @@ The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for line particles of type I and type J. They are used to define the N sub-particles per segment as described above. These coefficients are actually stored on a per-type basis. Thus if there are multiple -pair_coeff commmands that involve type I, as either the first or +pair_coeff commands that involve type I, as either the first or second atom type, you should use consistent values for sizeI or sizeJ in all of them. If you do not do this, the last value specified for sizeI will apply to all segments of type I. If typeI or typeJ refers @@ -112,7 +112,7 @@ cutoff is used. [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index e2af7eaeeb..fdc0b133dd 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -197,7 +197,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502. See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb +parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index a4fb3f0274..517bb3d20b 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -91,7 +91,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502. See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair style. Note that the -neighobr list cutoff for Coulomb interactions is effectively extended +neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is typically best in an efficiency sense to use a diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index 0cb0a998fe..133773abd0 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -51,7 +51,7 @@ commands, or by mixing as described below: epsilon (energy units) sigma (distance units) -innner (distance units) +inner (distance units) outer (distance units) :ul The last 2 coefficients are optional inner and outer cutoffs. If not diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 784f1f7f52..e372092cf0 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -106,7 +106,7 @@ pair_coeff 1 1 1.0 9.5 :pre The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones and Coulomb potential modified by a soft core, in order to avoid singularities during free energy calculations when sites are created -or anihilated "(Beutler)"_#Beutler, +or annihilated "(Beutler)"_#Beutler, :c,image(Eqs/pair_lj_soft.jpg) @@ -120,14 +120,14 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant which can be set by the "dielectric"_dielectric.html command. The coefficient lambda is an activation parameter. When lambda = 1 the -pair potentiel is identical to a Lennard-Jones term or a Coulomb term +pair potential is identical to a Lennard-Jones term or a Coulomb term or a combination of both. When lambda = 0 the interactions are deactivated. The transition between these two extrema is smoothed by a soft repulsive core in order to avoid singularities in potential -energy and forces when sites are created or anihilated and can overlap +energy and forces when sites are created or annihilated and can overlap "(Beutler)"_#Beutler. -The paratemers n, alpha_LJ and alpha_C are set in the +The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are @@ -164,7 +164,7 @@ Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water model. The usage of this pair style is documented in the "pair_lj"_pair_lj.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in -the "pair_coeff"_pair_coeff.html command. The paratemers n, alpha_LJ +the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. @@ -175,7 +175,7 @@ an inner and outer cutoff. The usage of this pair style is documented in the "pair_charmm"_pair_charmm.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and -before the optional eps14 and sigma14). The paratemers n, +before the optional eps14 and sigma14). The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. @@ -192,7 +192,7 @@ in several water models). NOTES: When using the core-softed Coulomb potentials with long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free energy calculation in which sites holding electrostatic charges are -being created or anihilated (using "fix adapt/fep"_fix_adapt_fep.html +being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html) it is important to adapt both the lambda activation parameter (from 0 to 1, or the reverse) and the value of the charge (from 0 to its final value, or the reverse). This diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index 5dbd7f4b80..daa2e37b68 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -94,7 +94,7 @@ Style {lubricate} requires monodisperse spherical particles; style {lubricate/poly} allows for polydisperse spherical particles. The viscosity {mu} can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style +course of a simulation, in which case in which case the pair_style setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html command for details. diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index ba46a135a2..08e53cb38c 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -140,5 +140,5 @@ for more info. :link(Lenosky) [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modelling Simulation Materials Science Enginerring, 8, 825 +Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt index 53ae53df23..f8b0c9f071 100644 --- a/doc/src/pair_mgpt.txt +++ b/doc/src/pair_mgpt.txt @@ -75,7 +75,7 @@ proceeds. After each time step, the atomic volume should be updated by the code as Omega = V/N. In addition, the volume term E_vol and the potentials v_2, v_3 and v_4 have to be removed at the end of the time step, and then respecified at the new value of Omega. In all -smulations, Omega must remain within the defined volume range for +simulations, Omega must remain within the defined volume range for E_vol and the potentials for the given material. The default option volpress yes in the "pair_coeff"_pair_coeff.html diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt index fec00ed44c..ad602db9f1 100644 --- a/doc/src/pair_mie.txt +++ b/doc/src/pair_mie.txt @@ -57,7 +57,7 @@ cutoff specified in the pair_style command is used. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the mie/cut pair styles can be mixed. -If not explicity defined, both the repulsive and attractive gamma +If not explicitly defined, both the repulsive and attractive gamma exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is {geometric}. See the "pair_modify" command for details. diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 73bc1a314f..c5e3a3c399 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -80,7 +80,7 @@ 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 +which sites are created or annihilated. The formula differs from that of {lj/cut/soft}, and is instead given by: :c,image(Eqs/pair_morse_soft.jpg) diff --git a/doc/src/pair_oxdna_excv.txt b/doc/src/pair_oxdna.txt similarity index 64% rename from doc/src/pair_oxdna_excv.txt rename to doc/src/pair_oxdna.txt index 23a727b3b9..ba2a3e4b01 100644 --- a/doc/src/pair_oxdna_excv.txt +++ b/doc/src/pair_oxdna.txt @@ -6,36 +6,36 @@ :line -pair_style oxdna_excv command :h3 -pair_style oxdna_stk command :h3 -pair_style oxdna_hbond command :h3 -pair_style oxdna_xstk command :h3 -pair_style oxdna_coaxstk command :h3 +pair_style oxdna/excv command :h3 +pair_style oxdna/stk command :h3 +pair_style oxdna/hbond command :h3 +pair_style oxdna/xstk command :h3 +pair_style oxdna/coaxstk command :h3 [Syntax:] pair_style style :pre -style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul +style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul [Examples:] -pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk -pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre [Description:] The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk} -and coaxial stacking interaction {oxdna_coaxstk} as well -as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on +excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk} +and coaxial stacking interaction {oxdna/coaxstk} as well +as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on opposite strands. The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients @@ -46,13 +46,13 @@ We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge for a detailed description of the oxDNA force field. NOTE: These pair styles have to be used together with the related oxDNA bond style -{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of -"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients +{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of +"bond_style oxdna/fene"_bond_oxdna.html). The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/. +Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. A technical report with more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA can be found "here"_PDF/USER-CGDNA-overview.pdf. @@ -67,7 +67,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html +"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html [Default:] none diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index 240d9f3bda..6ffd8122aa 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -116,7 +116,7 @@ cutoff distance for truncating interactions, and s00 and alpha are used as a bond breaking criteria. m_lambdai and m_taubi are the viscoelastic relaxation parameter and time constant, respectively. m_lambdai varies within zero to one. For very small -values of m_lambdai the viscoelsatic model responds very similar to a +values of m_lambdai the viscoelastic model responds very similar to a linear elastic model. For details please see the description in "(Mtchell2011)". diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index a90f65931b..12dcd244e2 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -45,12 +45,12 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the -parameters of the potential in XML format, the initialisation string, +parameters of the potential in XML format, the initialization string, and the map of atomic numbers. GAP potentials can be obtained from the Data repository section of "http://www.libatoms.org"_http://www.libatoms.org, where the -appropriate initialisation strings are also advised. The list of +appropriate initialization strings are also advised. The list of atomic numbers must be matched to the LAMMPS atom types specified in the LAMMPS data file or elsewhere. diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index f404fa4181..0242bab185 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -58,17 +58,17 @@ cutoff (distance units) :ul The parameters used depend on the type of the interacting particles, i.e. ellipsoids or LJ spheres. The type of a particle is determined -by the diameters specified for its 3 shape paramters. If all 3 shape +by the diameters specified for its 3 shape parameters. If all 3 shape parameters = 0.0, then the particle is treated as an LJ sphere. The epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If -the 3 shape paraemters are > 0.0, then the particle is treated as an +the 3 shape parameters are > 0.0, then the particle is treated as an ellipsoid (even if the 3 parameters are equal to each other). A12 specifies the energy prefactor which depends on the types of the two interacting particles. For ellipsoid/ellipsoid interactions, the interaction is computed by -the formulas in the supplementary docuement referenced above. A12 is +the formulas in the supplementary document referenced above. A12 is the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ units: @@ -79,8 +79,8 @@ composing the ellipsoids and epsilon_LJ determines the interaction strength of the spherical particles. For ellipsoid/LJ sphere interactions, the interaction is also computed -by the formulas in the supplementary docuement referenced above. A12 -has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for +by the formulas in the supplementary document referenced above. A12 +has a modified form (see "here"_PDF/pair_resquared_extra.pdf for details): :c,image(Eqs/pair_resquared2.jpg) diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index b9efeb8fc3..393bbc0665 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -31,7 +31,7 @@ pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions -between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to preceed a cross interaction. +between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats and integers, the {ulsph} {pair coeff} definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index c70af68b30..714188de32 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -36,7 +36,7 @@ atoms. This interactions depend on interatomic distance The parameters appearing in the upper expressions are set in the ffield.SMTBQ.Syst file where Syst corresponds to the selected system -(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +(e.g. field.SMTBQ.Al2O3). Examples for TiO2, Al2O3 are provided. A single pair_coeff command is used with the SMTBQ styles which provides the path to the potential file with parameters for needed elements. These are mapped to LAMMPS diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index f240779050..ec1c06729a 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -60,7 +60,7 @@ them. This functionality is now available in a more general form through the "fix adapt"_fix_adapt.html command, as explained below. Note that if you use an old input script and specify Astart and Astop without a cutoff, then LAMMPS will interpret that as A and a cutoff, -which is probabably not what you want. +which is probably not what you want. The "fix adapt"_fix_adapt.html command can be used to vary A for one or more pair types over the course of a simulation, in which case diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt index d25debe91b..2387056a1b 100644 --- a/doc/src/pair_sph_heatconduction.txt +++ b/doc/src/pair_sph_heatconduction.txt @@ -20,7 +20,7 @@ pair_coeff * * 1.0 2.4 :pre [Description:] The sph/heatconduction style computes heat transport between SPH particles. -The transport model is the diffusion euqation for the internal energy. +The transport model is the diffusion equation for the internal energy. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt index 21ca049272..957f901425 100644 --- a/doc/src/pair_sph_idealgas.txt +++ b/doc/src/pair_sph_idealgas.txt @@ -27,7 +27,7 @@ according to the ideal gas equation of state: where gamma = 1.4 is the heat capacity ratio, rho is the local density, and e is the internal energy per unit mass. This pair style also computes Monaghan's artificial viscosity to prevent particles -from interpentrating "(Monaghan)"_#ideal-Monoghan. +from interpenetrating "(Monaghan)"_#ideal-Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt index 8498841131..ef89c4ad3e 100644 --- a/doc/src/pair_sph_lj.txt +++ b/doc/src/pair_sph_lj.txt @@ -24,7 +24,7 @@ to the Lennard-Jones equation of state, which is computed according to Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters epsilon and sigma are set to unity. This pair style also computes Monaghan's artificial viscosity to prevent particles from -interpentrating "(Monaghan)"_#Monoghan. +interpenetrating "(Monaghan)"_#Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt index 2b0b6d119c..9177ca80b8 100644 --- a/doc/src/pair_sph_taitwater.txt +++ b/doc/src/pair_sph_taitwater.txt @@ -28,7 +28,7 @@ where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the reference density and c_0 the reference speed of sound. This pair style also computes Monaghan's artificial viscosity to -prevent particles from interpentrating "(Monaghan)"_#Monaghan. +prevent particles from interpenetrating "(Monaghan)"_#Monaghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index a951cccbc3..c1eff12cbf 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -86,7 +86,7 @@ the beginning of a run. This means you must specify the number of types in your system accordingly; usually to be one larger than what would normally be the case, e.g. via the "create_box"_create_box.html or by changing the header in your "data file"_read_data.html. The -ficitious "bond particles" are inserted at the beginning of the run, +fictitious "bond particles" are inserted at the beginning of the run, and serve as placeholders that define the position of the bonds. This allows neighbor lists to be constructed and pairwise interactions to be computed in almost the same way as is done for actual particles. diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index 6504edb2a5..ba79aee40d 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -33,7 +33,7 @@ pair_coeff * 3 morse.table ENTRY1 7.0 :pre Style {table} creates interpolation tables from potential energy and force values listed in a file(s) as a function of distance. When -performing dynamics or minimation, the interpolation tables are used +performing dynamics or minimization, the interpolation tables are used to evaluate energy and forces for pairwise interactions between particles, similar to how analytic formulas are used for other pair styles. @@ -180,7 +180,7 @@ 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 distance value in the table is not very close to the new value (i.e. round-off difference), then you will -be assingning energy/force values to a different distance, which is +be assigning energy/force values to a different distance, which is probably not what you want. LAMMPS will warn if this is occurring. If used, the parameter "BITMAP" is also followed by 2 values {rlo} and diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index e4eed927f5..42a5bbdfe2 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -42,7 +42,7 @@ triangle, for purposes of this pair style, are generated in the following manner. Assume the triangle is of type I, and sigma_II has been specified. We want a set of spheres with centers in the plane of the triangle, none of them larger in diameter than sigma_II, which -completely cover the triangle's area, but with minimial overlap and a +completely cover the triangle's area, but with minimal overlap and a minimal total number of spheres. This is done in a recursive manner. Place a sphere at the centroid of the original triangle. Calculate what diameter it must have to just cover all 3 corner points of the diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 7c18623d11..8928ca451b 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -39,6 +39,7 @@ Pair Styles :h1 pair_hbond_dreiding pair_hybrid pair_kim + pair_kolmogorov_crespi_z pair_lcbop pair_line_lj pair_list @@ -65,7 +66,7 @@ Pair Styles :h1 pair_nb3b_harmonic pair_nm pair_none - pair_oxdna_excv + pair_oxdna pair_peri pair_polymorphic pair_quip diff --git a/doc/src/partition.txt b/doc/src/partition.txt index ccef359050..9c1d560c83 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -39,7 +39,7 @@ such a variable is used in a "jump"_jump.html command. The "partition" command is another mechanism for having as input script operate differently on different partitions. It is basically a -prefix on any LAMMPS command. The commmand will only be invoked on +prefix on any LAMMPS command. The command will only be invoked on the partition(s) specified by the {style} and {N} arguments. If the {style} is {yes}, the command will be invoked on any partition diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 1ad66ee441..607c367afd 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -133,7 +133,7 @@ event. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -PRD commmand, which is the "compute +PRD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -230,7 +230,7 @@ files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For the PRD command, these contain the thermodynamic output for each replica. You will see short runs and minimizations corresponding to the dynamics and quench operations of the loop listed above. The -timestep will be reset aprpopriately depending on whether the +timestep will be reset appropriately depending on whether the operation advances time or not. After the PRD command completes, timing statistics for the PRD run are diff --git a/doc/src/processors.txt b/doc/src/processors.txt index adf2a0920f..781049af9c 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -27,7 +27,7 @@ keyword = {grid} or {map} or {part} or {file} :l {map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx} cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 - xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering + xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering {numa} arg = none {part} args = Psend Precv cstyle Psend = partition # (1 to Np) which will send its processor layout @@ -104,7 +104,7 @@ regular grid is initially created, regardless of which If load-balancing is never invoked via the "balance"_balance.html or "fix balance"_fix_balance.html commands, then the initial regular grid will persist for all simulations. If balancing is performed, some of -the methods invoked by those commands retain the logical toplogy of +the methods invoked by those commands retain the logical topology of the initial 3d grid, and the mapping of processors to the grid specified by the processors command. However the grid spacings in different dimensions may change, so that processors own sub-domains of @@ -179,7 +179,7 @@ The first non-blank, non-comment line should have Px Py Py :pre These must be compatible with the total number of processors -and the Px, Py, Pz settings of the processors commmand. +and the Px, Py, Pz settings of the processors command. This line should be immediately followed by P = Px*Py*Pz lines of the form: @@ -244,7 +244,7 @@ The {part} keyword affects the factorization of P into Px,Py,Pz. It can be useful when running in multi-partition mode, e.g. with the "run_style verlet/split"_run_style.html command. It specifies a -dependency bewteen a sending partition {Psend} and a receiving +dependency between a sending partition {Psend} and a receiving partition {Precv} which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of {Psend} and {Precv} must be integers from 1 to Np, where Np is the number of @@ -271,7 +271,7 @@ processors, it could create a 4x2x10 grid, but it will not create a 4. NOTE: If you use the "partition"_partition.html command to invoke -different "processsors" commands on different partitions, and you also +different "processors" commands on different partitions, and you also use the {part} keyword, then you must insure that both the sending and receiving partitions invoke the "processors" command that connects the 2 partitions via the {part} keyword. LAMMPS cannot easily check for diff --git a/doc/src/python.txt b/doc/src/python.txt index 7da69a0319..be6d1b215f 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -143,7 +143,7 @@ numeric or string value, as specified by the {format} keyword. As explained on the "variable"_variable.html doc page, the definition of a python-style variable associates a Python function name with the variable. This must match the {func} setting for this command. For -exampe these two commands would be self-consistent: +example these two commands would be self-consistent: variable foo python myMultiply python myMultiply return v_foo format f file funcs.py :pre @@ -174,7 +174,7 @@ a longer string, the {length} keyword can be specified with its {Nlen} value set to a larger number (the code allocates space for Nlen+1 to include the string terminator). If the Python function generates a string longer than the default 63 or the specified {Nlen}, it will be -trunctated. +truncated. :line @@ -356,7 +356,7 @@ python loop invoke :pre This has the effect of looping over a series of 10 short runs (10 timesteps each) where the pair style cutoff is increased from a value of 1.0 in distance units, in increments of 0.1. The looping stops -when the per-atom potential energy falls below a threshhold of -4.0 in +when the per-atom potential energy falls below a threshold of -4.0 in energy units. More generally, Python can be used to implement a loop with complex logic, much more so than can be created using the LAMMPS "jump"_jump.html and "if"_if.html commands. @@ -372,7 +372,7 @@ LAMMPS, more than the single value that can be passed back via a return statement. This cutoff value in the "cut" variable is then substituted (by LAMMPS) in the pair_style command that is executed next. Alternatively, the "LAMMPS command option" line could be used -in place of the 2 preceeding lines, to have Python insert the value +in place of the 2 preceding lines, to have Python insert the value into the LAMMPS command string. NOTE: When using the callback mechanism just described, recognize that @@ -384,7 +384,7 @@ file() functions, so long as the command would work if it were executed in the LAMMPS input script directly at the same point. However, a Python function can also be invoked during a run, whenever -an associated LAMMPS variable it is assigned to is evaluted. If the +an associated LAMMPS variable it is assigned to is evaluated. If the variable is an input argument to another LAMMPS command (e.g. "fix setforce"_fix_setforce.html), then the Python function will be invoked inside the class for that command, in one of its methods that is diff --git a/doc/src/quit.txt b/doc/src/quit.txt index 809fb2e38b..843d3de7f3 100644 --- a/doc/src/quit.txt +++ b/doc/src/quit.txt @@ -17,7 +17,7 @@ status = numerical exit status (optional) [Examples:] quit -if "$n > 10000" then "quit 1":pre +if "$n > 10000" then "quit 1" :pre [Description:] diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 9ddc9d8921..86c123527b 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -180,7 +180,7 @@ used appropriately when each data file is read, the values in those sections will be stored correctly in the larger data structures allocated by the use of the {extra} keywords. E.g. the substrate file can list mass and pair coefficients for type 1 silicon atoms. The -water file can list mass and pair coeffcients for type 1 and type 2 +water file can list mass and pair coefficients for type 1 and type 2 hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords will store those mass and pair coefficient values appropriately in data structures that allow for 3 atom types (Si, H, O). Of course, @@ -574,7 +574,7 @@ spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. template-atom = which atom within a template molecule the atom is template-index = which molecule within the molecule template the atom is part of theta = internal temperature of a DPD particle -triangleflag = 1 for triangular particles, 0 for point or sperhical particles +triangleflag = 1 for triangular particles, 0 for point or spherical particles volume = volume of Peridynamic particle (distance^3 units) x,y,z = coordinates of atom (distance units) :ul diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index e454c180ab..381e29f6e0 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -58,7 +58,7 @@ read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/ Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and -the simluation box dimensions. This is useful for restarting a run +the simulation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the "read_restart"_read_restart.html and "read_data"_read_data.html commands for alternative methods to do this. Also see the @@ -214,7 +214,7 @@ you wish to change this after the dump snapshot is read. If the {box} keyword is specified with a {yes} value, then the current simulation box dimensions are replaced by the dump snapshot box dimensions. If the {box} keyword is specified with a {no} value, the -current simulatoin box is unchanged. +current simulation box is unchanged. If the {purge} keyword is specified with a {yes} value, then all current atoms in the system are deleted before any of the operations diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index d59b5313fd..d0f4b16175 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -31,7 +31,7 @@ information is stored (and not stored) in a restart file is given below. Basically this operation will re-create the simulation box with all its atoms and their attributes as well as some related global settings, at the point in time it was written to the restart file by a -previous simluation. The simulation box will be partitioned into a +previous simulation. The simulation box will be partitioned into a regular 3d grid of rectangular bricks, one per processor, based on the number of processors in the current simulation and the settings of the "processors"_processors.html command. The partitioning can later be diff --git a/doc/src/region.txt b/doc/src/region.txt index 4ce230da7b..885e5e45f8 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -212,7 +212,7 @@ both of the spheres. The {units} keyword determines the meaning of the distance units used to define the region for any argument above listed as having distance -units. It also affects the scaling of the velocity vector specfied +units. It also affects the scaling of the velocity vector specified with the {vel} keyword, the amplitude vector specified with the {wiggle} keyword, and the rotation point specified with the {rotate} keyword, since they each involve a distance metric. @@ -283,9 +283,9 @@ velocity: variable dx equal ramp(0,10) region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre -Note that the initial displacemet is 0.0, though that is not required. +Note that the initial displacement is 0.0, though that is not required. -Either of these varaibles would "wiggle" the region back and forth in +Either of these variables would "wiggle" the region back and forth in the y direction: variable dy equal swiggle(0,5,100) @@ -352,7 +352,7 @@ high-coordinate flat end cap, and index 3 is the curved cone surface. In the last example above, a {cone} region is defined along the z-axis that is open at the zlo value (e.g. for use as a funnel). -For all other styles, the {open} keyword is ignored. As inidcated +For all other styles, the {open} keyword is ignored. As indicated above, this includes the {intersect} and {union} regions, though their sub-regions can be defined with the {open} keyword. diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 2e7153e38c..291558e0e5 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -53,7 +53,7 @@ top of each other. NOTE: You cannot use the replicate command on a system which has a molecule that spans the box and is bonded to itself across a periodic -boundary, so that the molecule is efffectively a loop. A simple +boundary, so that the molecule is effectively a loop. A simple example would be a linear polymer chain that spans the simulation box and bonds back to itself across the periodic boundary. More realistic examples would be a CNT (meant to be an infinitely long CNT) or a diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index da8c8d6895..860ee68033 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -40,7 +40,7 @@ rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre [Description:] -Perform a psuedo simulation run where atom information is read one +Perform a pseudo simulation run where atom information is read one snapshot at a time from a dump file(s), and energies and forces are computed on the shapshot to produce thermodynamic or other output. @@ -121,7 +121,7 @@ with the {start/stop} keywords. Note that if you define neither of the {start}/{stop} or {first}/{last} keywords, then LAMMPS treats the pseudo run as going from 0 to a huge value (effectively infinity). This means that any quantity that a fix scales as a fraction of -elapsed time in the run, will essentially remain at its intiial value. +elapsed time in the run, will essentially remain at its initial value. Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the {stop} setting you have specified. @@ -178,7 +178,7 @@ a timestep it expects to be, LAMMPS will flag an error. The various forms of LAMMPS output, as defined by the "thermo_style"_thermo_style.html, "thermo"_thermo.html, "dump"_dump.html, and "restart"_restart.html commands occur on -specific timesteps. If successvive dump snapshots skip those +specific timesteps. If successive dump snapshots skip those timesteps, then no output will be produced. E.g. if you request thermodynamic output every 100 steps, but the dump file snapshots are every 1000 steps, then you will only see thermodynamic output every diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 3154465f68..5e0c2a9ea5 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -97,7 +97,7 @@ timestep of a run unless it is a multiple of N. A restart file is written on the last timestep of a minimization if N > 0 and the minimization converges. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 2dafabebb5..b30a17686d 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -76,7 +76,7 @@ Specifically, this style performs all computation except the "kspace_style"_kspace_style.html portion of the force field on the 1st partition. This include the "pair style"_pair_style.html, "bond style"_bond_style.html, "neighbor list building"_neighbor.html, -"fixes"_fix.html including time intergration, and output. The +"fixes"_fix.html including time integration, and output. The "kspace_style"_kspace_style.html portion of the calculation is performed on the 2nd partition. @@ -105,23 +105,23 @@ to control this, e.g. procssors * * * part 1 2 multiple :pre You can also use the "partition"_partition.html command to explicitly -specity the processor layout on each partition. E.g. for 2 partitions +specify the processor layout on each partition. E.g. for 2 partitions of 60 and 15 processors each: partition yes 1 processors 3 4 5 partition yes 2 processors 3 1 5 :pre When you run in 2-partition mode with the {verlet/split} style, the -thermodyanmic data for the entire simulation will be output to the log +thermodynamic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and screen.0 by default; see the "-plog and -pscreen command-line switches"_Section_start.html#start_7 to change this. The log and screen file for the 2nd partition will not contain thermodynamic -output beyone the 1st timestep of the run. +output beyond the 1st timestep of the run. See "Section 5"_Section_accelerate.html of the manual for performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignemnt of +style. One important performance consideration is the assignment of logical processors in the 2 partitions to the physical cores of a parallel machine. The "processors"_processors.html command has options to support this, and strategies are discussed in @@ -182,7 +182,7 @@ for hybrid coarse-grained/all-atom models. The {hybrid} keyword requires as many level assignments as there are hybrid substyles, which assigns each sub-style to a rRESPA level, following their order of definition in the pair_style command. Since the {hybrid} keyword -operates on pair style computations, it is mututally exclusive with +operates on pair style computations, it is mutually exclusive with either the {pair} or the {inner}/{middle}/{outer} keywords. When using rRESPA (or for any MD simulation) care must be taken to diff --git a/doc/src/set.txt b/doc/src/set.txt index 42ede23b85..659eecd30d 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -374,7 +374,7 @@ header of the data file read by the "read_data"_read_data.html command. These keywords do not allow use of an atom-style variable. Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat -capacity, and density of smmothed particle hydrodynamics (SPH) +capacity, and density of smoothed particle hydrodynamics (SPH) particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 70c6a3031b..127719cdb5 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -91,7 +91,7 @@ a disabled suffix is turned back on. The use of these 2 commands lets your input script use a standard LAMMPS style (i.e. a non-accelerated variant), which can be useful for testing or benchmarking purposes. Of course this is also possible by not using any suffix commands, and -explictly appending or not appending the suffix to the relevant +explicitly appending or not appending the suffix to the relevant commands in your input script. NOTE: The default "run_style"_run_style.html verlet is invoked prior to diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 5b0f5a006c..04c7d708f6 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -130,7 +130,7 @@ transition event. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -TAD commmand, which is the "compute +TAD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -144,7 +144,7 @@ NEB is determined by the {neb_style} keyword and must be a damped dynamics minimizer. The tolerances and limits for each NEB calculation can be set by the {neb} keyword. As discussed on the "neb"_neb.html, it is often advantageous to use a larger timestep for -NEB than for normal dyanmics. Since the size of the timestep set by +NEB than for normal dynamics. Since the size of the timestep set by the "timestep"_timestep.html command is used by TAD for performing dynamics, there is a {neb_step} keyword which can be used to set a larger timestep for each NEB calculation if desired. @@ -258,7 +258,7 @@ number of replicas or processors. Note that within a single state, the dynamics will typically temporarily continue beyond the event that is ultimately chosen, until -the stopping criterionis satisfied. When the event is eventually +the stopping criterion is satisfied. When the event is eventually executed, the timestep counter is reset to the value when the event was detected. Similarly, after each quench and NEB minimization, the timestep counter is reset to the value at the start of the diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt index 6faea206f4..1d5d34995c 100644 --- a/doc/src/thermo.txt +++ b/doc/src/thermo.txt @@ -30,7 +30,7 @@ The content and format of what is printed is controlled by the "thermo_style"_thermo_style.html and "thermo_modify"_thermo_modify.html commands. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 6cdb8a3cc8..36ec7bf12e 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -36,7 +36,7 @@ args = list of arguments for a particular style :l elaplong = timesteps since start of initial run in a series of runs dt = timestep size time = simulation time - cpu = elapsed CPU time in seconds + cpu = elapsed CPU time in seconds since start of this run tpcpu = time per CPU second spcpu = timesteps per CPU second cpuremain = estimated CPU time remaining in run @@ -226,7 +226,7 @@ simulation time, also in time "units"_units.html, which is simply not been reset. If the timestep has changed (e.g. via "fix dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via the "reset_timestep" command), then the simulation time is effectively -a cummulative value up to the current point. +a cumulative value up to the current point. The {cpu} keyword is elapsed CPU seconds since the beginning of this run. The {tpcpu} and {spcpu} keywords are measures of how fast your @@ -236,7 +236,7 @@ time per CPU second, where simulation time is in time picoseconds per CPU second. The {spcpu} keyword is the number of timesteps per CPU second. Both quantities are on-the-fly metrics, measured relative to the last time they were invoked. Thus if you are -printing out thermodyamic output every 100 timesteps, the two keywords +printing out thermodynamic output every 100 timesteps, the two keywords will continually output the time and timestep rate for the last 100 steps. The {tpcpu} keyword does not attempt to track any changes in timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html @@ -289,7 +289,7 @@ The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See "this section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic periodic cells, including a precise defintion +description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, {lz}, {yz}, {xz}, {xy}. diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 358ec75a53..39a6c542b7 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -16,7 +16,7 @@ timer args :pre {off} = do not collect or print any timing information {loop} = collect only the total time for the simulation loop {normal} = collect timer information broken down by sections (default) - {full} = like {normal} but also include CPU and thread utilzation + {full} = like {normal} but also include CPU and thread utilization {sync} = explicitly synchronize MPI tasks between sections {nosync} = do not synchronize MPI tasks between sections (default) {timeout} elapse = set walltime limit to {elapse} @@ -48,11 +48,11 @@ detailed per section information. With the {normal} setting, timing information for portions of the timestep (pairwise calculations, neighbor list construction, output, etc) are collected as well as information about load imbalances for those sections across -procsessors. The {full} setting adds information about CPU +processors. The {full} setting adds information about CPU utilization and thread utilization, when multi-threading is enabled. With the {sync} setting, all MPI tasks are synchronized at each timer -call which measures load imbalance for each section more accuractly, +call which measures load imbalance for each section more accurately, though it can also slow down the simulation by prohibiting overlapping independent computations on different MPI ranks Using the {nosync} setting (which is the default) turns this synchronization off. diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index c2f4a16207..518b90854b 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -72,17 +72,17 @@ In both these force fields hydrogen atoms are treated as non-polarizable. :l The motion of of the Drude particles can be calculated by minimizing -the energy of the induced dipoles at each timestep, by an interative, +the energy of the induced dipoles at each timestep, by an iterative, self-consistent procedure. The Drude particles can be massless and therefore do not contribute to the kinetic energy. However, the -relaxed method is computationall slow. An extended-lagrangian method +relaxed method is computational slow. An extended-lagrangian method can be used to calculate the positions of the Drude particles, but this requires them to have mass. It is important in this case to decouple the degrees of freedom associated with the Drude oscillators from those of the normal atoms. Thermalizing the Drude dipoles at temperatures comparable to the rest of the simulation leads to several problems (kinetic energy transfer, very short timestep, etc.), which -can be remediated by the "cold Drude" technique ("Lamoureux and +can be remediate by the "cold Drude" technique ("Lamoureux and Roux"_#Lamoureux). Two closely related models are used to represent polarization through @@ -270,7 +270,7 @@ be stable, for example if the atomic polarizability is too high for instance, a DP can escape from its DC and be captured by another DC, which makes the force and energy diverge and the simulation crash. Even without reaching this extreme case, the correlation -between nearby dipoles on the same molecule may be exagerated. Often, +between nearby dipoles on the same molecule may be exaggerated. Often, special bond relations prevent bonded neighboring atoms to see the charge of each other's DP, so that the problem does not always appear. It is possible to use screened dipole dipole interactions by using the diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index 6966bb90b9..5d3491782e 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -328,7 +328,7 @@ IPyLammps Examples :h2 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this directory and navigate to one of them. If you compiled and installed -a LAMMPS shared library with execeptions, PNG, JPEG and FFMPEG support +a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. Validating a dihedral potential :h3 diff --git a/doc/src/units.txt b/doc/src/units.txt index 87436b6307..0b856dcc68 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -73,7 +73,7 @@ dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon) electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon density = mass/volume, where rho* = rho sigma^dim :ul -Note that for LJ units, the default mode of thermodyamic output via +Note that for LJ units, the default mode of thermodynamic output via the "thermo_style"_thermo_style.html command is to normalize all extensive quantities by the number of atoms. E.g. potential energy is extensive because it is summed over atoms, so it is output as diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 29d50a2b8e..e32e82ef4d 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -501,7 +501,7 @@ the group. :line -Numers, constants, and thermo keywords :h4 +Numbers, constants, and thermo keywords :h4 Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. @@ -576,7 +576,7 @@ returns 0.0. These relational and logical operators can be used as a masking or selection operation in a formula. For example, the number of atoms -whose properties satifsy one or more criteria could be calculated by +whose properties satisfy one or more criteria could be calculated by taking the returned per-atom vector of ones and zeroes and passing it to the "compute reduce"_compute_reduce.html command. @@ -623,7 +623,7 @@ Floor() if the largest integer not greater than its argument. Round() is the nearest integer to its argument. The ramp(x,y) function uses the current timestep to generate a value -linearly intepolated between the specified x,y values over the course +linearly interpolated between the specified x,y values over the course of a run, according to this formula: value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre @@ -669,7 +669,7 @@ sequence of output timesteps: The stride(x,y,z) function uses the current timestep to generate a new timestep. X,y >= 0 and z > 0 and x <= y are required. The generated timesteps increase in increments of z, from x to y, i.e. it generates -the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then +the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used @@ -781,7 +781,7 @@ is for a vector-style variable where "name" is replaced by the name of the variable. These functions operate on a global vector of inputs and reduce it to -a single scalar value. This is analagous to the operation of the +a single scalar value. This is analogous to the operation of the "compute reduce"_compute_reduce.html command, which performs similar operations on per-atom and local vectors. @@ -1068,7 +1068,7 @@ in the reference should be replaced by the name of a variable defined elsewhere in the input script. As discussed on this doc page, equal-style variables generate a single -global numeric value, vector-style variables gerarate a vector of +global numeric value, vector-style variables generate a vector of global numeric values, and atom-style and atomfile-style variables generate a per-atom vector of numeric values. All other variables store one or more strings. @@ -1169,7 +1169,7 @@ would print out both the current and initial volume periodically during the run. Note that it is a mistake to enclose a variable formula in double -quotes if it contains variables preceeded by $ signs. For example, +quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre @@ -1214,7 +1214,7 @@ three kinds of behavior: (1) The variable may be evaluated accurately. If it contains references to a compute or fix, and these values were calculated on -the last timestep of a preceeding run, then they will be accessed and +the last timestep of a preceding run, then they will be accessed and used by the variable and the result will be accurate. (2) LAMMPS may not be able to evaluate the variable and will generate diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index ae32a94e84..840716085f 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -53,7 +53,7 @@ support optional arguments and thus LAMMPS needs to be able to cleanly separate the two sets of args. Note that if the specified filename uses wildcard characters "*" or -"%", as supported by the "dump"_dump.html commmand, they will operate +"%", as supported by the "dump"_dump.html command, they will operate in the same fashion to create the new filename(s). Normally, "dump image"_dump_image.html files require a filename with a "*" character for the timestep. That is not the case for the write_dump command; no @@ -78,7 +78,7 @@ else LAMMPS will generate an error message. For example, it is not possible to dump per-atom energy with this command before a run has been performed, since no energies and forces have yet been calculated. See the "variable"_variable.html doc page -sectinn on Variable Accuracy for more information on this topic. +section on Variable Accuracy for more information on this topic. [Related commands:] diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index 2b4950519a..9cca50b3bf 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -299,4 +299,11 @@ more information about the code and its uses. epub_author = 'The LAMMPS Developers' +# configure spelling extension if present +import importlib.util +spelling_spec = importlib.util.find_spec("sphinxcontrib.spelling") +if spelling_spec: + extensions.append('sphinxcontrib.spelling') + spelling_lang='en_US' + spelling_word_list_filename='false_positives.txt' diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt new file mode 100644 index 0000000000..fb08e4e97e --- /dev/null +++ b/doc/utils/sphinx-config/false_positives.txt @@ -0,0 +1,2667 @@ +aa +aat +abc +abf +absTol +Acc +Accelrys +acceptor +Acceptor +acceptors +accomodate +accuracies +ach +achived +achives +ackland +Ackland +acolor +acos +Acta +actinide 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+wih +Wirnsberger +wirtes +witin +wn +Wolde +Worley +Wriggers +Wurtzite +www +wx +Wx +wy +Wy +wz +Wz +xa +xAVX +xb +Xc +xcm +Xcm +xCORE +Xeon +xflag +xhi +xHost +Xiaowang +xk +xlat +xlo +xmax +Xmax +xmgrace +xMIC +xmovie +Xmovie +xmu +Xmu +XP +XPlor +xrd +xs +xstk +xsu +xtc +xu +Xu +xy +xyz +xz +xzhou +Yamada +Ybar +ybox +Yc +ycm +Yeh +yellowgreen +yflag +yhi +yi +ylat +ylo +Yoshida +ys +ysu +yu +Yu +yukawa +Yukawa +yx +yy +yz +Zannoni +zbl +ZBL +Zc +zcm +Zepeda +zflag +Zhang +zhi +Zhou +Zhu +zi +Zi +ziegenhain +Ziegenhain +Zj +zlim +zlo +zN +zs +zsu +zu +zx +zy +Zybin +zz diff --git a/doc/utils/txt2html/README.html b/doc/utils/txt2html/README.html index 90ddaa1c49..b92214425e 100644 --- a/doc/utils/txt2html/README.html +++ b/doc/utils/txt2html/README.html @@ -205,7 +205,7 @@ which are converted into HTML.
  • "}" (right bracket) --> turn-off italics by inserting a </I> -

    If a backspace '\' preceeds any of the bold/italic mark-up characters, +

    If a backspace '\' precedes any of the bold/italic mark-up characters, then mark-up is not performed; the mark-up character is simply left in the text.

    diff --git a/doc/utils/txt2html/txt2html.cpp b/doc/utils/txt2html/txt2html.cpp index d7f411be9b..ff71c262c8 100644 --- a/doc/utils/txt2html/txt2html.cpp +++ b/doc/utils/txt2html/txt2html.cpp @@ -561,7 +561,7 @@ void substitute(string &s) string punctuation = ".,?!;:()"; // substitute for bold & italic markers - // if preceeded by \ char, then leave markers in text + // if preceded by \ char, then leave markers in text n = s.find_first_of("[]{}"); while (n != string::npos) { diff --git a/examples/KAPPA/README b/examples/KAPPA/README index ee70766d94..d025797bfa 100644 --- a/examples/KAPPA/README +++ b/examples/KAPPA/README @@ -85,7 +85,7 @@ Kappa = 3.45 (4) in.mp dQ = 15087 / 100 / 18.82^2 / 2 - 15087 = cummulative delta energy, tallied by fix thermal/conductivity + 15087 = cumulative delta energy, tallied by fix thermal/conductivity 100 = 20,000 steps at 0.005 tau timestep = run time in tau xy box area = 18.82^2 divide by 2 since energy flux goes in 2 directions due to periodic z diff --git a/examples/README b/examples/README index 87f14779ac..5880bb78d7 100644 --- a/examples/README +++ b/examples/README @@ -93,7 +93,7 @@ peri: Peridynamic model of cylinder impacted by indenter pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script -qeq: use of QEQ pacakge for charge equilibration +qeq: use of QEQ package for charge equilibration reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void diff --git a/examples/USER/atc/README b/examples/USER/atc/README index f3a852dfe3..aa874f3300 100644 --- a/examples/USER/atc/README +++ b/examples/USER/atc/README @@ -65,7 +65,7 @@ elastic: in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field @@ -146,7 +146,7 @@ elastic: in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field diff --git a/examples/USER/atc/fluids/in.bar1d_fluids b/examples/USER/atc/fluids/in.bar1d_fluids index 63ef0e2744..af152bfbab 100644 --- a/examples/USER/atc/fluids/in.bar1d_fluids +++ b/examples/USER/atc/fluids/in.bar1d_fluids @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d b/examples/USER/atc/thermal/in.bar1d index e8b61c412a..5591f7177d 100644 --- a/examples/USER/atc/thermal/in.bar1d +++ b/examples/USER/atc/thermal/in.bar1d @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# temperature is initially 20 everywhere and the left boundary BC is fixed at 40. # The result should show heat diffusing through the FEM to the MD and back out # to the FEM on the right. Insufficient time is captured to reach the linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_all_atoms b/examples/USER/atc/thermal/in.bar1d_all_atoms index 6b855f37b1..2c8851137f 100644 --- a/examples/USER/atc/thermal/in.bar1d_all_atoms +++ b/examples/USER/atc/thermal/in.bar1d_all_atoms @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_combined b/examples/USER/atc/thermal/in.bar1d_combined index 1f960dbab7..767544d2d4 100644 --- a/examples/USER/atc/thermal/in.bar1d_combined +++ b/examples/USER/atc/thermal/in.bar1d_combined @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing the boundaries should be observed, diff --git a/examples/USER/atc/thermal/in.bar1d_flux b/examples/USER/atc/thermal/in.bar1d_flux index 0103f00b5b..eae32ec5b2 100644 --- a/examples/USER/atc/thermal/in.bar1d_flux +++ b/examples/USER/atc/thermal/in.bar1d_flux @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/USER/atc/thermal/in.bar1d_frac_step index ca722e79aa..eddec44b52 100644 --- a/examples/USER/atc/thermal/in.bar1d_frac_step +++ b/examples/USER/atc/thermal/in.bar1d_frac_step @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_hoover b/examples/USER/atc/thermal/in.bar1d_hoover index 50e8f02166..2f0518d0d2 100644 --- a/examples/USER/atc/thermal/in.bar1d_hoover +++ b/examples/USER/atc/thermal/in.bar1d_hoover @@ -1,6 +1,6 @@ # AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_interpolate b/examples/USER/atc/thermal/in.bar1d_interpolate index e7db0d3856..0333bf117d 100644 --- a/examples/USER/atc/thermal/in.bar1d_interpolate +++ b/examples/USER/atc/thermal/in.bar1d_interpolate @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/atc/thermal/in.bar1d_lumped b/examples/USER/atc/thermal/in.bar1d_lumped index eb305a6252..153f7b632d 100644 --- a/examples/USER/atc/thermal/in.bar1d_lumped +++ b/examples/USER/atc/thermal/in.bar1d_lumped @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff --git a/examples/USER/lb/confined_colloid/in.confined_colloids b/examples/USER/lb/confined_colloid/in.confined_colloids index 37cd52e621..b7b8958e9a 100755 --- a/examples/USER/lb/confined_colloid/in.confined_colloids +++ b/examples/USER/lb/confined_colloid/in.confined_colloids @@ -67,7 +67,7 @@ timestep 0.0006 #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix). # Use the standard LB integration scheme, a fluid density = 1.0, # fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003. diff --git a/examples/USER/lb/microrheology/in.microrheology_default_gamma b/examples/USER/lb/microrheology/in.microrheology_default_gamma index 4937a2cb20..8c3b684ff7 100755 --- a/examples/USER/lb/microrheology/in.microrheology_default_gamma +++ b/examples/USER/lb/microrheology/in.microrheology_default_gamma @@ -61,7 +61,7 @@ group FluidAtoms type 2 #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix). # Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid # density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003. diff --git a/examples/USER/lb/microrheology/in.microrheology_set_gamma b/examples/USER/lb/microrheology/in.microrheology_set_gamma index 7b84bdaf63..1f744220f0 100755 --- a/examples/USER/lb/microrheology/in.microrheology_set_gamma +++ b/examples/USER/lb/microrheology/in.microrheology_set_gamma @@ -61,7 +61,7 @@ group FluidAtoms type 2 #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the rigid_pc_sphere # fix). # Use the LB integration scheme of Ollila et. al. (for stability reasons, diff --git a/examples/USER/lb/planewall/in.planewall_default_gamma b/examples/USER/lb/planewall/in.planewall_default_gamma index bf0cfcb3c7..83f42ebddd 100755 --- a/examples/USER/lb/planewall/in.planewall_default_gamma +++ b/examples/USER/lb/planewall/in.planewall_default_gamma @@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box #---------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # All of the particles in the simulation apply a force to the fluid. -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix. # Use the standard LB integration scheme, a fluid density = 1.0, # fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0. diff --git a/examples/USER/lb/planewall/in.planewall_set_gamma b/examples/USER/lb/planewall/in.planewall_set_gamma index a048411b01..47d8266a1c 100755 --- a/examples/USER/lb/planewall/in.planewall_set_gamma +++ b/examples/USER/lb/planewall/in.planewall_set_gamma @@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box #---------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # All of the particles in the simulation apply a force to the fluid. -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the rigid_pc_sphere # fix). # Use the LB integration scheme of Ollila et. al. (for stability reasons, diff --git a/examples/USER/lb/polymer/data.polymer b/examples/USER/lb/polymer/data.polymer index d3c39ad39b..da974446cb 100755 --- a/examples/USER/lb/polymer/data.polymer +++ b/examples/USER/lb/polymer/data.polymer @@ -1,1040 +1,1040 @@ -Position data for a 32-bead polymer consisting of 31-vertex extended spheres - -992 atoms -31 bonds - -2 atom types -1 bond types - -0 40 xlo xhi -0 40 ylo yhi -0 40 zlo zhi - -Atoms - -1 1 21.0439 24.2646 23.1337 1 -2 2 20.3839 24.2646 23.3669 1 -3 2 20.8557 23.6306 23.3629 1 -4 2 21.5866 23.883 23.3569 1 -5 2 21.5866 24.6463 23.3569 1 -6 2 20.8558 24.8987 23.3629 1 -7 2 20.3839 24.2646 22.9005 1 -8 2 20.8558 23.6306 22.9045 1 -9 2 21.5866 23.883 22.9105 1 -10 2 21.5866 24.6463 22.9105 1 -11 2 20.8557 24.8987 22.9045 1 -12 2 21.6158 24.2646 23.5374 1 -13 2 21.2339 24.8002 23.5425 1 -14 2 20.595 24.6026 23.5511 1 -15 2 20.595 23.9267 23.5511 1 -16 2 21.2339 23.7291 23.5425 1 -17 2 21.6158 24.2646 22.73 1 -18 2 21.2339 24.8002 22.7249 1 -19 2 20.595 24.6026 22.7163 1 -20 2 20.595 23.9267 22.7163 1 -21 2 21.2339 23.7291 22.7249 1 -22 2 21.3444 24.2646 23.7659 1 -23 2 21.1464 24.5394 23.7693 1 -24 2 20.8215 24.436 23.7749 1 -25 2 20.8215 24.0933 23.7749 1 -26 2 21.1464 23.9899 23.7693 1 -27 2 21.3444 24.2646 22.5015 1 -28 2 21.1464 24.5394 22.4981 1 -29 2 20.8214 24.436 22.4925 1 -30 2 20.8214 24.0933 22.4925 1 -31 2 21.1464 23.9899 22.4981 1 -32 1 21.5789 25.5745 23.3738 2 -33 2 20.9189 25.5745 23.6069 2 -34 2 21.3907 24.9404 23.603 2 -35 2 22.1216 25.1929 23.597 2 -36 2 22.1216 25.9562 23.597 2 -37 2 21.3907 26.2086 23.603 2 -38 2 20.9189 25.5745 23.1406 2 -39 2 21.3907 24.9404 23.1446 2 -40 2 22.1216 25.1929 23.1505 2 -41 2 22.1216 25.9562 23.1505 2 -42 2 21.3907 26.2086 23.1446 2 -43 2 22.1507 25.5745 23.7775 2 -44 2 21.7688 26.1101 23.7826 2 -45 2 21.13 25.9125 23.7912 2 -46 2 21.13 25.2365 23.7912 2 -47 2 21.7688 25.039 23.7826 2 -48 2 22.1507 25.5745 22.97 2 -49 2 21.7688 26.1101 22.965 2 -50 2 21.13 25.9125 22.9563 2 -51 2 21.13 25.2365 22.9563 2 -52 2 21.7688 25.039 22.965 2 -53 2 21.8794 25.5745 24.006 2 -54 2 21.6814 25.8493 24.0094 2 -55 2 21.3564 25.7458 24.015 2 -56 2 21.3564 25.4032 24.015 2 -57 2 21.6814 25.2997 24.0094 2 -58 2 21.8794 25.5745 22.7416 2 -59 2 21.6814 25.8493 22.7382 2 -60 2 21.3564 25.7458 22.7326 2 -61 2 21.3564 25.4032 22.7326 2 -62 2 21.6814 25.2997 22.7382 2 -63 1 22.5101 25.4302 22.2914 3 -64 2 21.8501 25.4302 22.5246 3 -65 2 22.322 24.7961 22.5206 3 -66 2 23.0528 25.0485 22.5146 3 -67 2 23.0528 25.8118 22.5146 3 -68 2 22.322 26.0643 22.5206 3 -69 2 21.8501 25.4302 22.0582 3 -70 2 22.322 24.7961 22.0622 3 -71 2 23.0528 25.0485 22.0682 3 -72 2 23.0528 25.8118 22.0682 3 -73 2 22.322 26.0643 22.0622 3 -74 2 23.082 25.4302 22.6951 3 -75 2 22.7001 25.9657 22.7002 3 -76 2 22.0612 25.7682 22.7088 3 -77 2 22.0612 25.0922 22.7088 3 -78 2 22.7001 24.8947 22.7002 3 -79 2 23.082 25.4302 21.8877 3 -80 2 22.7001 25.9657 21.8826 3 -81 2 22.0612 25.7682 21.874 3 -82 2 22.0612 25.0922 21.874 3 -83 2 22.7001 24.8947 21.8826 3 -84 2 22.8107 25.4302 22.9236 3 -85 2 22.6126 25.705 22.927 3 -86 2 22.2877 25.6015 22.9326 3 -87 2 22.2877 25.2589 22.9326 3 -88 2 22.6126 25.1554 22.927 3 -89 2 22.8107 25.4302 21.6592 3 -90 2 22.6126 25.705 21.6558 3 -91 2 22.2877 25.6015 21.6502 3 -92 2 22.2877 25.2589 21.6502 3 -93 2 22.6126 25.1554 21.6558 3 -94 1 23.895 25.0537 22.2951 4 -95 2 23.235 25.0537 22.5282 4 -96 2 23.7068 24.4196 22.5243 4 -97 2 24.4377 24.672 22.5183 4 -98 2 24.4377 25.4353 22.5183 4 -99 2 23.7068 25.6877 22.5243 4 -100 2 23.235 25.0537 22.0619 4 -101 2 23.7068 24.4196 22.0659 4 -102 2 24.4377 24.672 22.0718 4 -103 2 24.4377 25.4353 22.0718 4 -104 2 23.7068 25.6877 22.0659 4 -105 2 24.4668 25.0537 22.6988 4 -106 2 24.0849 25.5892 22.7039 4 -107 2 23.4461 25.3916 22.7125 4 -108 2 23.4461 24.7157 22.7125 4 -109 2 24.0849 24.5181 22.7039 4 -110 2 24.4668 25.0537 21.8913 4 -111 2 24.0849 25.5892 21.8863 4 -112 2 23.4461 25.3916 21.8776 4 -113 2 23.4461 24.7157 21.8776 4 -114 2 24.0849 24.5181 21.8863 4 -115 2 24.1955 25.0537 22.9273 4 -116 2 23.9975 25.3284 22.9307 4 -117 2 23.6725 25.225 22.9363 4 -118 2 23.6725 24.8823 22.9363 4 -119 2 23.9975 24.7789 22.9307 4 -120 2 24.1955 25.0537 21.6629 4 -121 2 23.9975 25.3284 21.6595 4 -122 2 23.6725 25.225 21.6538 4 -123 2 23.6725 24.8823 21.6538 4 -124 2 23.9975 24.7789 21.6595 4 -125 1 24.6582 26.0898 21.6598 5 -126 2 23.9982 26.0898 21.893 5 -127 2 24.4701 25.4557 21.889 5 -128 2 25.2009 25.7081 21.883 5 -129 2 25.2009 26.4714 21.883 5 -130 2 24.4701 26.7238 21.889 5 -131 2 23.9982 26.0898 21.4266 5 -132 2 24.4701 25.4557 21.4306 5 -133 2 25.2009 25.7081 21.4366 5 -134 2 25.2009 26.4714 21.4366 5 -135 2 24.4701 26.7238 21.4306 5 -136 2 25.2301 26.0898 22.0635 5 -137 2 24.8482 26.6253 22.0686 5 -138 2 24.2093 26.4277 22.0772 5 -139 2 24.2093 25.7518 22.0772 5 -140 2 24.8482 25.5542 22.0686 5 -141 2 25.2301 26.0898 21.2561 5 -142 2 24.8482 26.6253 21.251 5 -143 2 24.2093 26.4277 21.2424 5 -144 2 24.2093 25.7518 21.2424 5 -145 2 24.8482 25.5542 21.251 5 -146 2 24.9587 26.0898 22.292 5 -147 2 24.7607 26.3645 22.2954 5 -148 2 24.4358 26.2611 22.301 5 -149 2 24.4358 25.9185 22.301 5 -150 2 24.7607 25.815 22.2954 5 -151 2 24.9587 26.0898 21.0276 5 -152 2 24.7607 26.3645 21.0242 5 -153 2 24.4358 26.2611 21.0186 5 -154 2 24.4358 25.9184 21.0186 5 -155 2 24.7607 25.815 21.0242 5 -156 1 25.7401 26.9511 22.0433 6 -157 2 25.0801 26.9511 22.2765 6 -158 2 25.552 26.3171 22.2725 6 -159 2 26.2828 26.5695 22.2666 6 -160 2 26.2828 27.3328 22.2666 6 -161 2 25.552 27.5852 22.2725 6 -162 2 25.0801 26.9511 21.8102 6 -163 2 25.552 26.3171 21.8141 6 -164 2 26.2828 26.5695 21.8201 6 -165 2 26.2828 27.3328 21.8201 6 -166 2 25.552 27.5852 21.8141 6 -167 2 26.312 26.9511 22.4471 6 -168 2 25.9301 27.4867 22.4521 6 -169 2 25.2912 27.2891 22.4608 6 -170 2 25.2912 26.6132 22.4608 6 -171 2 25.9301 26.4156 22.4521 6 -172 2 26.312 26.9511 21.6396 6 -173 2 25.9301 27.4867 21.6345 6 -174 2 25.2912 27.2891 21.6259 6 -175 2 25.2912 26.6132 21.6259 6 -176 2 25.9301 26.4156 21.6345 6 -177 2 26.0406 26.9511 22.6755 6 -178 2 25.8426 27.2259 22.6789 6 -179 2 25.5177 27.1225 22.6845 6 -180 2 25.5177 26.7798 22.6845 6 -181 2 25.8426 26.6764 22.6789 6 -182 2 26.0406 26.9511 21.4111 6 -183 2 25.8426 27.2259 21.4077 6 -184 2 25.5177 27.1225 21.4021 6 -185 2 25.5177 26.7798 21.4021 6 -186 2 25.8426 26.6764 21.4077 6 -187 1 26.6309 26.6387 20.9623 7 -188 2 25.9709 26.6387 21.1955 7 -189 2 26.4427 26.0047 21.1916 7 -190 2 27.1736 26.2571 21.1856 7 -191 2 27.1736 27.0204 21.1856 7 -192 2 26.4427 27.2728 21.1916 7 -193 2 25.9709 26.6387 20.7292 7 -194 2 26.4427 26.0047 20.7331 7 -195 2 27.1736 26.2571 20.7391 7 -196 2 27.1736 27.0204 20.7391 7 -197 2 26.4427 27.2728 20.7331 7 -198 2 27.2028 26.6387 21.3661 7 -199 2 26.8208 27.1743 21.3712 7 -200 2 26.182 26.9767 21.3798 7 -201 2 26.182 26.3008 21.3798 7 -202 2 26.8208 26.1032 21.3712 7 -203 2 27.2027 26.6387 20.5586 7 -204 2 26.8209 27.1743 20.5535 7 -205 2 26.182 26.9767 20.5449 7 -206 2 26.182 26.3008 20.5449 7 -207 2 26.8208 26.1032 20.5535 7 -208 2 26.9314 26.6387 21.5946 7 -209 2 26.7334 26.9135 21.598 7 -210 2 26.4084 26.81 21.6036 7 -211 2 26.4084 26.4674 21.6036 7 -212 2 26.7334 26.364 21.598 7 -213 2 26.9314 26.6387 20.3301 7 -214 2 26.7334 26.9135 20.3267 7 -215 2 26.4084 26.8101 20.3211 7 -216 2 26.4084 26.4674 20.3211 7 -217 2 26.7334 26.364 20.3267 7 -218 1 27.7333 27.3399 21.5562 8 -219 2 27.0733 27.3399 21.7894 8 -220 2 27.5451 26.7058 21.7855 8 -221 2 28.276 26.9582 21.7795 8 -222 2 28.276 27.7215 21.7795 8 -223 2 27.5451 27.974 21.7855 8 -224 2 27.0733 27.3399 21.3231 8 -225 2 27.5451 26.7058 21.327 8 -226 2 28.276 26.9582 21.333 8 -227 2 28.276 27.7215 21.333 8 -228 2 27.5451 27.974 21.327 8 -229 2 28.3051 27.3399 21.96 8 -230 2 27.9232 27.8754 21.9651 8 -231 2 27.2844 27.6779 21.9737 8 -232 2 27.2844 27.0019 21.9737 8 -233 2 27.9232 26.8043 21.9651 8 -234 2 28.3051 27.3399 21.1525 8 -235 2 27.9232 27.8754 21.1474 8 -236 2 27.2844 27.6779 21.1388 8 -237 2 27.2844 27.0019 21.1388 8 -238 2 27.9232 26.8044 21.1474 8 -239 2 28.0338 27.3399 22.1885 8 -240 2 27.8358 27.6147 22.1919 8 -241 2 27.5108 27.5112 22.1975 8 -242 2 27.5108 27.1686 22.1975 8 -243 2 27.8358 27.0651 22.1919 8 -244 2 28.0338 27.3399 20.924 8 -245 2 27.8358 27.6147 20.9206 8 -246 2 27.5108 27.5112 20.915 8 -247 2 27.5108 27.1686 20.915 8 -248 2 27.8358 27.0651 20.9206 8 -249 1 28.2741 26.7179 22.7311 9 -250 2 27.6141 26.7179 22.9642 9 -251 2 28.086 26.0838 22.9603 9 -252 2 28.8168 26.3362 22.9543 9 -253 2 28.8168 27.0995 22.9543 9 -254 2 28.086 27.352 22.9603 9 -255 2 27.6141 26.7179 22.4979 9 -256 2 28.086 26.0838 22.5019 9 -257 2 28.8168 26.3362 22.5078 9 -258 2 28.8168 27.0995 22.5078 9 -259 2 28.086 27.352 22.5019 9 -260 2 28.846 26.7179 23.1348 9 -261 2 28.4641 27.2534 23.1399 9 -262 2 27.8252 27.0559 23.1485 9 -263 2 27.8252 26.3799 23.1485 9 -264 2 28.4641 26.1823 23.1399 9 -265 2 28.846 26.7179 22.3273 9 -266 2 28.4641 27.2534 22.3223 9 -267 2 27.8252 27.0559 22.3136 9 -268 2 27.8252 26.3799 22.3136 9 -269 2 28.4641 26.1823 22.3223 9 -270 2 28.5746 26.7179 23.3633 9 -271 2 28.3766 26.9927 23.3667 9 -272 2 28.0517 26.8892 23.3723 9 -273 2 28.0517 26.5466 23.3723 9 -274 2 28.3766 26.4431 23.3667 9 -275 2 28.5746 26.7179 22.0989 9 -276 2 28.3766 26.9927 22.0955 9 -277 2 28.0517 26.8892 22.0899 9 -278 2 28.0517 26.5466 22.0899 9 -279 2 28.3766 26.4431 22.0955 9 -280 1 26.9358 26.2738 22.9979 10 -281 2 26.2757 26.2738 23.2311 10 -282 2 26.7476 25.6397 23.2271 10 -283 2 27.4785 25.8921 23.2211 10 -284 2 27.4785 26.6554 23.2211 10 -285 2 26.7476 26.9079 23.2271 10 -286 2 26.2757 26.2738 22.7647 10 -287 2 26.7476 25.6397 22.7687 10 -288 2 27.4785 25.8921 22.7747 10 -289 2 27.4785 26.6554 22.7747 10 -290 2 26.7476 26.9079 22.7687 10 -291 2 27.5076 26.2738 23.4016 10 -292 2 27.1257 26.8093 23.4067 10 -293 2 26.4869 26.6118 23.4154 10 -294 2 26.4869 25.9358 23.4154 10 -295 2 27.1257 25.7382 23.4067 10 -296 2 27.5076 26.2738 22.5942 10 -297 2 27.1257 26.8093 22.5891 10 -298 2 26.4869 26.6118 22.5805 10 -299 2 26.4869 25.9358 22.5805 10 -300 2 27.1257 25.7382 22.5891 10 -301 2 27.2363 26.2738 23.6301 10 -302 2 27.0383 26.5486 23.6335 10 -303 2 26.7133 26.4451 23.6391 10 -304 2 26.7133 26.1025 23.6391 10 -305 2 27.0383 25.999 23.6335 10 -306 2 27.2363 26.2738 22.3657 10 -307 2 27.0383 26.5486 22.3623 10 -308 2 26.7133 26.4451 22.3567 10 -309 2 26.7133 26.1025 22.3567 10 -310 2 27.0383 25.999 22.3623 10 -311 1 27.733 25.5139 23.9181 11 -312 2 27.0729 25.5139 24.1512 11 -313 2 27.5448 24.8798 24.1473 11 -314 2 28.2756 25.1323 24.1413 11 -315 2 28.2756 25.8956 24.1413 11 -316 2 27.5448 26.148 24.1473 11 -317 2 27.0729 25.5139 23.6849 11 -318 2 27.5448 24.8798 23.6889 11 -319 2 28.2756 25.1323 23.6948 11 -320 2 28.2756 25.8956 23.6948 11 -321 2 27.5448 26.148 23.6889 11 -322 2 28.3048 25.5139 24.3218 11 -323 2 27.9229 26.0494 24.3269 11 -324 2 27.284 25.8519 24.3355 11 -325 2 27.284 25.1759 24.3355 11 -326 2 27.9229 24.9784 24.3269 11 -327 2 28.3048 25.5139 23.5143 11 -328 2 27.9229 26.0494 23.5093 11 -329 2 27.284 25.8519 23.5006 11 -330 2 27.284 25.1759 23.5006 11 -331 2 27.9229 24.9784 23.5093 11 -332 2 28.0335 25.5139 24.5503 11 -333 2 27.8354 25.7887 24.5537 11 -334 2 27.5105 25.6852 24.5593 11 -335 2 27.5105 25.3426 24.5593 11 -336 2 27.8354 25.2391 24.5537 11 -337 2 28.0335 25.5139 23.2859 11 -338 2 27.8354 25.7887 23.2825 11 -339 2 27.5105 25.6852 23.2769 11 -340 2 27.5105 25.3426 23.2769 11 -341 2 27.8354 25.2391 23.2825 11 -342 1 28.8712 25.1256 24.7012 12 -343 2 28.2111 25.1256 24.9344 12 -344 2 28.683 24.4916 24.9305 12 -345 2 29.4138 24.744 24.9245 12 -346 2 29.4138 25.5073 24.9245 12 -347 2 28.683 25.7597 24.9305 12 -348 2 28.2111 25.1256 24.4681 12 -349 2 28.683 24.4916 24.472 12 -350 2 29.4138 24.744 24.478 12 -351 2 29.4138 25.5073 24.478 12 -352 2 28.683 25.7597 24.472 12 -353 2 29.443 25.1256 25.105 12 -354 2 29.0611 25.6612 25.11 12 -355 2 28.4222 25.4636 25.1187 12 -356 2 28.4222 24.7877 25.1187 12 -357 2 29.0611 24.5901 25.11 12 -358 2 29.443 25.1256 24.2975 12 -359 2 29.0611 25.6612 24.2924 12 -360 2 28.4222 25.4636 24.2838 12 -361 2 28.4222 24.7877 24.2838 12 -362 2 29.0611 24.5901 24.2924 12 -363 2 29.1717 25.1256 25.3335 12 -364 2 28.9736 25.4004 25.3368 12 -365 2 28.6487 25.2969 25.3425 12 -366 2 28.6487 24.9543 25.3425 12 -367 2 28.9736 24.8509 25.3368 12 -368 2 29.1717 25.1256 24.069 12 -369 2 28.9736 25.4004 24.0656 12 -370 2 28.6487 25.297 24.06 12 -371 2 28.6487 24.9543 24.06 12 -372 2 28.9736 24.8509 24.0656 12 -373 1 30.0053 25.4778 25.507 13 -374 2 29.3453 25.4778 25.7401 13 -375 2 29.8172 24.8438 25.7362 13 -376 2 30.548 25.0962 25.7302 13 -377 2 30.548 25.8595 25.7302 13 -378 2 29.8172 26.1119 25.7362 13 -379 2 29.3453 25.4778 25.2738 13 -380 2 29.8172 24.8438 25.2777 13 -381 2 30.548 25.0962 25.2837 13 -382 2 30.548 25.8595 25.2837 13 -383 2 29.8172 26.1119 25.2777 13 -384 2 30.5772 25.4778 25.9107 13 -385 2 30.1953 26.0134 25.9158 13 -386 2 29.5564 25.8158 25.9244 13 -387 2 29.5564 25.1399 25.9244 13 -388 2 30.1953 24.9423 25.9158 13 -389 2 30.5772 25.4778 25.1032 13 -390 2 30.1953 26.0134 25.0982 13 -391 2 29.5564 25.8158 25.0895 13 -392 2 29.5564 25.1399 25.0895 13 -393 2 30.1953 24.9423 25.0982 13 -394 2 30.3058 25.4778 26.1392 13 -395 2 30.1078 25.7526 26.1426 13 -396 2 29.7829 25.6492 26.1482 13 -397 2 29.7829 25.3065 26.1482 13 -398 2 30.1078 25.2031 26.1426 13 -399 2 30.3058 25.4778 24.8747 13 -400 2 30.1078 25.7526 24.8714 13 -401 2 29.7829 25.6492 24.8657 13 -402 2 29.7829 25.3065 24.8657 13 -403 2 30.1078 25.2031 24.8714 13 -404 1 29.8427 26.8721 25.2081 14 -405 2 29.1827 26.8721 25.4413 14 -406 2 29.6545 26.238 25.4373 14 -407 2 30.3854 26.4904 25.4314 14 -408 2 30.3854 27.2537 25.4314 14 -409 2 29.6545 27.5061 25.4373 14 -410 2 29.1827 26.8721 24.975 14 -411 2 29.6545 26.238 24.9789 14 -412 2 30.3854 26.4904 24.9849 14 -413 2 30.3854 27.2537 24.9849 14 -414 2 29.6545 27.5061 24.9789 14 -415 2 30.4145 26.8721 25.6119 14 -416 2 30.0326 27.4076 25.6169 14 -417 2 29.3938 27.21 25.6256 14 -418 2 29.3938 26.5341 25.6256 14 -419 2 30.0326 26.3365 25.6169 14 -420 2 30.4145 26.8721 24.8044 14 -421 2 30.0326 27.4076 24.7993 14 -422 2 29.3938 27.21 24.7907 14 -423 2 29.3938 26.5341 24.7907 14 -424 2 30.0326 26.3365 24.7993 14 -425 2 30.1432 26.8721 25.8403 14 -426 2 29.9452 27.1468 25.8437 14 -427 2 29.6202 27.0434 25.8493 14 -428 2 29.6202 26.7007 25.8493 14 -429 2 29.9452 26.5973 25.8437 14 -430 2 30.1432 26.8721 24.5759 14 -431 2 29.9452 27.1468 24.5725 14 -432 2 29.6202 27.0434 24.5669 14 -433 2 29.6202 26.7007 24.5669 14 -434 2 29.9452 26.5973 24.5725 14 -435 1 29.3789 27.6387 26.3292 15 -436 2 28.7189 27.6387 26.5624 15 -437 2 29.1908 27.0046 26.5584 15 -438 2 29.9216 27.257 26.5524 15 -439 2 29.9216 28.0203 26.5524 15 -440 2 29.1908 28.2727 26.5584 15 -441 2 28.7189 27.6387 26.096 15 -442 2 29.1908 27.0046 26.1 15 -443 2 29.9216 27.257 26.106 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27.8997 17 -504 2 27.4254 27.352 27.9037 17 -505 2 28.1562 27.6044 27.9097 17 -506 2 28.1562 28.3677 27.9097 17 -507 2 27.4254 28.6202 27.9037 17 -508 2 28.1854 27.9861 28.5366 17 -509 2 27.8035 28.5216 28.5417 17 -510 2 27.1646 28.3241 28.5503 17 -511 2 27.1646 27.6481 28.5503 17 -512 2 27.8035 27.4506 28.5417 17 -513 2 28.1854 27.9861 27.7292 17 -514 2 27.8035 28.5216 27.7241 17 -515 2 27.1646 28.3241 27.7154 17 -516 2 27.1646 27.6481 27.7154 17 -517 2 27.8035 27.4506 27.7241 17 -518 2 27.914 27.9861 28.7651 17 -519 2 27.716 28.2609 28.7685 17 -520 2 27.3911 28.1574 28.7741 17 -521 2 27.3911 27.8148 28.7741 17 -522 2 27.716 27.7113 28.7685 17 -523 2 27.914 27.9861 27.5007 17 -524 2 27.716 28.2609 27.4973 17 -525 2 27.3911 28.1574 27.4917 17 -526 2 27.3911 27.8148 27.4917 17 -527 2 27.716 27.7113 27.4973 17 -528 1 28.7548 27.1277 28.2749 18 -529 2 28.0948 27.1277 28.508 18 -530 2 28.5666 26.4936 28.5041 18 -531 2 29.2975 26.746 28.4981 18 -532 2 29.2975 27.5093 28.4981 18 -533 2 28.5666 27.7617 28.5041 18 -534 2 28.0948 27.1277 28.0417 18 -535 2 28.5666 26.4936 28.0457 18 -536 2 29.2975 26.746 28.0516 18 -537 2 29.2975 27.5093 28.0516 18 -538 2 28.5666 27.7617 28.0457 18 -539 2 29.3267 27.1277 28.6786 18 -540 2 28.9448 27.6632 28.6837 18 -541 2 28.3059 27.4656 28.6923 18 -542 2 28.3059 26.7897 28.6923 18 -543 2 28.9448 26.5921 28.6837 18 -544 2 29.3266 27.1277 27.8711 18 -545 2 28.9448 27.6632 27.8661 18 -546 2 28.3059 27.4656 27.8574 18 -547 2 28.3059 26.7897 27.8574 18 -548 2 28.9447 26.5921 27.8661 18 -549 2 29.0553 27.1277 28.9071 18 -550 2 28.8573 27.4024 28.9105 18 -551 2 28.5323 27.299 28.9161 18 -552 2 28.5323 26.9563 28.9161 18 -553 2 28.8573 26.8529 28.9105 18 -554 2 29.0553 27.1277 27.6427 18 -555 2 28.8573 27.4024 27.6393 18 -556 2 28.5323 27.299 27.6337 18 -557 2 28.5323 26.9563 27.6337 18 -558 2 28.8573 26.8529 27.6393 18 -559 1 29.3703 27.681 29.4473 19 -560 2 28.7102 27.681 29.6805 19 -561 2 29.1821 27.0469 29.6765 19 -562 2 29.913 27.2993 29.6706 19 -563 2 29.913 28.0626 29.6706 19 -564 2 29.1821 28.3151 29.6765 19 -565 2 28.7102 27.681 29.2142 19 -566 2 29.1821 27.0469 29.2181 19 -567 2 29.913 27.2993 29.2241 19 -568 2 29.913 28.0626 29.2241 19 -569 2 29.1821 28.3151 29.2181 19 -570 2 29.9421 27.681 29.8511 19 -571 2 29.5602 28.2165 29.8561 19 -572 2 28.9214 28.019 29.8648 19 -573 2 28.9214 27.343 29.8648 19 -574 2 29.5602 27.1455 29.8561 19 -575 2 29.9421 27.681 29.0436 19 -576 2 29.5602 28.2165 29.0385 19 -577 2 28.9214 28.019 29.0299 19 -578 2 28.9214 27.343 29.0299 19 -579 2 29.5602 27.1455 29.0385 19 -580 2 29.6708 27.681 30.0795 19 -581 2 29.4728 27.9558 30.0829 19 -582 2 29.1478 27.8523 30.0885 19 -583 2 29.1478 27.5097 30.0885 19 -584 2 29.4728 27.4062 30.0829 19 -585 2 29.6708 27.681 28.8151 19 -586 2 29.4728 27.9558 28.8117 19 -587 2 29.1478 27.8523 28.8061 19 -588 2 29.1478 27.5097 28.8061 19 -589 2 29.4728 27.4062 28.8117 19 -590 1 30.1317 28.895 29.3698 20 -591 2 29.4717 28.895 29.603 20 -592 2 29.9436 28.2609 29.5991 20 -593 2 30.6744 28.5133 29.5931 20 -594 2 30.6744 29.2766 29.5931 20 -595 2 29.9436 29.5291 29.5991 20 -596 2 29.4717 28.895 29.1367 20 -597 2 29.9436 28.2609 29.1406 20 -598 2 30.6744 28.5133 29.1466 20 -599 2 30.6744 29.2766 29.1466 20 -600 2 29.9436 29.5291 29.1406 20 -601 2 30.7036 28.895 29.7736 20 -602 2 30.3217 29.4305 29.7786 20 -603 2 29.6828 29.233 29.7873 20 -604 2 29.6828 28.557 29.7873 20 -605 2 30.3217 28.3594 29.7786 20 -606 2 30.7036 28.895 28.9661 20 -607 2 30.3217 29.4305 28.961 20 -608 2 29.6828 29.233 28.9524 20 -609 2 29.6828 28.557 28.9524 20 -610 2 30.3217 28.3594 28.961 20 -611 2 30.4322 28.895 30.0021 20 -612 2 30.2342 29.1698 30.0054 20 -613 2 29.9093 29.0663 30.0111 20 -614 2 29.9093 28.7237 30.0111 20 -615 2 30.2342 28.6202 30.0054 20 -616 2 30.4322 28.895 28.7376 20 -617 2 30.2342 29.1698 28.7342 20 -618 2 29.9093 29.0663 28.7286 20 -619 2 29.9093 28.7237 28.7286 20 -620 2 30.2342 28.6202 28.7342 20 -621 1 31.4259 29.456 29.1053 21 -622 2 30.7659 29.456 29.3385 21 -623 2 31.2377 28.8219 29.3345 21 -624 2 31.9686 29.0744 29.3285 21 -625 2 31.9686 29.8377 29.3285 21 -626 2 31.2377 30.0901 29.3345 21 -627 2 30.7659 29.456 28.8721 21 -628 2 31.2377 28.8219 28.8761 21 -629 2 31.9686 29.0744 28.8821 21 -630 2 31.9686 29.8377 28.8821 21 -631 2 31.2377 30.0901 28.8761 21 -632 2 31.9977 29.456 29.509 21 -633 2 31.6158 29.9915 29.5141 21 -634 2 30.977 29.794 29.5227 21 -635 2 30.977 29.118 29.5227 21 -636 2 31.6158 28.9205 29.5141 21 -637 2 31.9977 29.456 28.7016 21 -638 2 31.6158 29.9915 28.6965 21 -639 2 30.977 29.794 28.6878 21 -640 2 30.977 29.118 28.6878 21 -641 2 31.6158 28.9205 28.6965 21 -642 2 31.7264 29.456 29.7375 21 -643 2 31.5284 29.7308 29.7409 21 -644 2 31.2034 29.6273 29.7465 21 -645 2 31.2034 29.2847 29.7465 21 -646 2 31.5284 29.1812 29.7409 21 -647 2 31.7264 29.456 28.4731 21 -648 2 31.5284 29.7308 28.4697 21 -649 2 31.2034 29.6273 28.4641 21 -650 2 31.2034 29.2847 28.4641 21 -651 2 31.5284 29.1812 28.4697 21 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28.0613 27.7243 22 -682 2 31.4033 27.9578 27.7299 22 -683 1 32.1926 27.1371 28.1123 23 -684 2 31.5325 27.1371 28.3454 23 -685 2 32.0044 26.503 28.3415 23 -686 2 32.7353 26.7554 28.3355 23 -687 2 32.7353 27.5187 28.3355 23 -688 2 32.0044 27.7712 28.3415 23 -689 2 31.5325 27.1371 27.8791 23 -690 2 32.0044 26.503 27.8831 23 -691 2 32.7353 26.7554 27.8891 23 -692 2 32.7353 27.5187 27.8891 23 -693 2 32.0044 27.7712 27.8831 23 -694 2 32.7644 27.1371 28.516 23 -695 2 32.3825 27.6726 28.5211 23 -696 2 31.7437 27.4751 28.5297 23 -697 2 31.7437 26.7991 28.5297 23 -698 2 32.3825 26.6015 28.5211 23 -699 2 32.7644 27.1371 27.7086 23 -700 2 32.3825 27.6726 27.7035 23 -701 2 31.7437 27.4751 27.6948 23 -702 2 31.7437 26.7991 27.6948 23 -703 2 32.3825 26.6015 27.7035 23 -704 2 32.4931 27.1371 28.7445 23 -705 2 32.2951 27.4119 28.7479 23 -706 2 31.9701 27.3084 28.7535 23 -707 2 31.9701 26.9658 28.7535 23 -708 2 32.2951 26.8623 28.7479 23 -709 2 32.4931 27.1371 27.4801 23 -710 2 32.2951 27.4119 27.4767 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33.3172 26.5192 28.4794 24 -741 2 33.1192 26.7939 28.476 24 -742 2 32.7942 26.6905 28.4704 24 -743 2 32.7942 26.3478 28.4704 24 -744 2 33.1192 26.2444 28.476 24 -745 1 33.3109 26.7605 30.4953 25 -746 2 32.6509 26.7605 30.7285 25 -747 2 33.1227 26.1264 30.7246 25 -748 2 33.8536 26.3789 30.7186 25 -749 2 33.8536 27.1422 30.7186 25 -750 2 33.1227 27.3946 30.7246 25 -751 2 32.6509 26.7605 30.2622 25 -752 2 33.1227 26.1264 30.2661 25 -753 2 33.8536 26.3789 30.2721 25 -754 2 33.8536 27.1422 30.2721 25 -755 2 33.1227 27.3946 30.2661 25 -756 2 33.8827 26.7605 30.8991 25 -757 2 33.5008 27.2961 30.9041 25 -758 2 32.862 27.0985 30.9128 25 -759 2 32.862 26.4226 30.9128 25 -760 2 33.5008 26.225 30.9041 25 -761 2 33.8827 26.7605 30.0916 25 -762 2 33.5008 27.2961 30.0865 25 -763 2 32.862 27.0985 30.0779 25 -764 2 32.862 26.4226 30.0779 25 -765 2 33.5008 26.225 30.0865 25 -766 2 33.6114 26.7605 31.1276 25 -767 2 33.4134 27.0353 31.1309 25 -768 2 33.0884 26.9318 31.1366 25 -769 2 33.0884 26.5892 31.1366 25 -770 2 33.4134 26.4857 31.1309 25 -771 2 33.6114 26.7605 29.8631 25 -772 2 33.4134 27.0353 29.8597 25 -773 2 33.0884 26.9318 29.8541 25 -774 2 33.0884 26.5892 29.8541 25 -775 2 33.4134 26.4857 29.8597 25 -776 1 32.6296 27.0741 31.7189 26 -777 2 31.9696 27.0741 31.952 26 -778 2 32.4414 26.4401 31.9481 26 -779 2 33.1723 26.6925 31.9421 26 -780 2 33.1723 27.4558 31.9421 26 -781 2 32.4414 27.7082 31.9481 26 -782 2 31.9696 27.0741 31.4857 26 -783 2 32.4414 26.4401 31.4897 26 -784 2 33.1723 26.6925 31.4956 26 -785 2 33.1723 27.4558 31.4956 26 -786 2 32.4414 27.7082 31.4897 26 -787 2 33.2014 27.0741 32.1226 26 -788 2 32.8195 27.6097 32.1277 26 -789 2 32.1807 27.4121 32.1363 26 -790 2 32.1807 26.7362 32.1363 26 -791 2 32.8195 26.5386 32.1277 26 -792 2 33.2014 27.0741 31.3151 26 -793 2 32.8195 27.6097 31.3101 26 -794 2 32.1807 27.4121 31.3014 26 -795 2 32.1807 26.7362 31.3014 26 -796 2 32.8195 26.5386 31.3101 26 -797 2 32.9301 27.0741 32.3511 26 -798 2 32.7321 27.3489 32.3545 26 -799 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+750 2 33.1227 27.3946 30.7246 25 +751 2 32.6509 26.7605 30.2622 25 +752 2 33.1227 26.1264 30.2661 25 +753 2 33.8536 26.3789 30.2721 25 +754 2 33.8536 27.1422 30.2721 25 +755 2 33.1227 27.3946 30.2661 25 +756 2 33.8827 26.7605 30.8991 25 +757 2 33.5008 27.2961 30.9041 25 +758 2 32.862 27.0985 30.9128 25 +759 2 32.862 26.4226 30.9128 25 +760 2 33.5008 26.225 30.9041 25 +761 2 33.8827 26.7605 30.0916 25 +762 2 33.5008 27.2961 30.0865 25 +763 2 32.862 27.0985 30.0779 25 +764 2 32.862 26.4226 30.0779 25 +765 2 33.5008 26.225 30.0865 25 +766 2 33.6114 26.7605 31.1276 25 +767 2 33.4134 27.0353 31.1309 25 +768 2 33.0884 26.9318 31.1366 25 +769 2 33.0884 26.5892 31.1366 25 +770 2 33.4134 26.4857 31.1309 25 +771 2 33.6114 26.7605 29.8631 25 +772 2 33.4134 27.0353 29.8597 25 +773 2 33.0884 26.9318 29.8541 25 +774 2 33.0884 26.5892 29.8541 25 +775 2 33.4134 26.4857 29.8597 25 +776 1 32.6296 27.0741 31.7189 26 +777 2 31.9696 27.0741 31.952 26 +778 2 32.4414 26.4401 31.9481 26 +779 2 33.1723 26.6925 31.9421 26 +780 2 33.1723 27.4558 31.9421 26 +781 2 32.4414 27.7082 31.9481 26 +782 2 31.9696 27.0741 31.4857 26 +783 2 32.4414 26.4401 31.4897 26 +784 2 33.1723 26.6925 31.4956 26 +785 2 33.1723 27.4558 31.4956 26 +786 2 32.4414 27.7082 31.4897 26 +787 2 33.2014 27.0741 32.1226 26 +788 2 32.8195 27.6097 32.1277 26 +789 2 32.1807 27.4121 32.1363 26 +790 2 32.1807 26.7362 32.1363 26 +791 2 32.8195 26.5386 32.1277 26 +792 2 33.2014 27.0741 31.3151 26 +793 2 32.8195 27.6097 31.3101 26 +794 2 32.1807 27.4121 31.3014 26 +795 2 32.1807 26.7362 31.3014 26 +796 2 32.8195 26.5386 31.3101 26 +797 2 32.9301 27.0741 32.3511 26 +798 2 32.7321 27.3489 32.3545 26 +799 2 32.4071 27.2454 32.3601 26 +800 2 32.4071 26.9028 32.3601 26 +801 2 32.7321 26.7994 32.3545 26 +802 2 32.9301 27.0741 31.0867 26 +803 2 32.7321 27.3489 31.0833 26 +804 2 32.4071 27.2454 31.0777 26 +805 2 32.4071 26.9028 31.0777 26 +806 2 32.7321 26.7994 31.0833 26 +807 1 31.7049 27.9673 32.3567 27 +808 2 31.0449 27.9673 32.5899 27 +809 2 31.5167 27.3332 32.5859 27 +810 2 32.2476 27.5856 32.5799 27 +811 2 32.2476 28.3489 32.5799 27 +812 2 31.5167 28.6014 32.5859 27 +813 2 31.0449 27.9673 32.1235 27 +814 2 31.5167 27.3332 32.1275 27 +815 2 32.2476 27.5856 32.1335 27 +816 2 32.2476 28.3489 32.1335 27 +817 2 31.5167 28.6014 32.1275 27 +818 2 32.2767 27.9673 32.7604 27 +819 2 31.8948 28.5028 32.7655 27 +820 2 31.256 28.3053 32.7742 27 +821 2 31.256 27.6293 32.7742 27 +822 2 31.8948 27.4317 32.7655 27 +823 2 32.2767 27.9673 31.953 27 +824 2 31.8948 28.5028 31.9479 27 +825 2 31.256 28.3053 31.9393 27 +826 2 31.256 27.6293 31.9393 27 +827 2 31.8948 27.4317 31.9479 27 +828 2 32.0054 27.9673 32.9889 27 +829 2 31.8074 28.2421 32.9923 27 +830 2 31.4824 28.1386 32.9979 27 +831 2 31.4824 27.796 32.9979 27 +832 2 31.8074 27.6925 32.9923 27 +833 2 32.0054 27.9673 31.7245 27 +834 2 31.8074 28.2421 31.7211 27 +835 2 31.4824 28.1386 31.7155 27 +836 2 31.4824 27.796 31.7155 27 +837 2 31.8074 27.6925 31.7211 27 +838 1 30.3399 27.7351 32.7342 28 +839 2 29.6799 27.7351 32.9674 28 +840 2 30.1517 27.101 32.9634 28 +841 2 30.8826 27.3535 32.9574 28 +842 2 30.8826 28.1168 32.9574 28 +843 2 30.1517 28.3692 32.9634 28 +844 2 29.6799 27.7351 32.5011 28 +845 2 30.1517 27.101 32.505 28 +846 2 30.8826 27.3535 32.511 28 +847 2 30.8826 28.1168 32.511 28 +848 2 30.1517 28.3692 32.505 28 +849 2 30.9117 27.7351 33.138 28 +850 2 30.5298 28.2706 33.143 28 +851 2 29.891 28.0731 33.1517 28 +852 2 29.891 27.3971 33.1517 28 +853 2 30.5298 27.1996 33.143 28 +854 2 30.9117 27.7351 32.3305 28 +855 2 30.5298 28.2706 32.3254 28 +856 2 29.891 28.0731 32.3168 28 +857 2 29.891 27.3971 32.3168 28 +858 2 30.5298 27.1996 32.3254 28 +859 2 30.6404 27.7351 33.3664 28 +860 2 30.4424 28.0099 33.3698 28 +861 2 30.1174 27.9064 33.3754 28 +862 2 30.1174 27.5638 33.3754 28 +863 2 30.4424 27.4603 33.3698 28 +864 2 30.6404 27.7351 32.102 28 +865 2 30.4424 28.0099 32.0986 28 +866 2 30.1174 27.9064 32.093 28 +867 2 30.1174 27.5638 32.093 28 +868 2 30.4424 27.4603 32.0986 28 +869 1 29.8305 28.063 34.0352 29 +870 2 29.1705 28.063 34.2684 29 +871 2 29.6424 27.429 34.2644 29 +872 2 30.3732 27.6814 34.2584 29 +873 2 30.3732 28.4447 34.2584 29 +874 2 29.6424 28.6971 34.2644 29 +875 2 29.1705 28.063 33.8021 29 +876 2 29.6424 27.429 33.806 29 +877 2 30.3732 27.6814 33.812 29 +878 2 30.3732 28.4447 33.812 29 +879 2 29.6424 28.6971 33.806 29 +880 2 30.4024 28.063 34.439 29 +881 2 30.0205 28.5986 34.444 29 +882 2 29.3816 28.401 34.4527 29 +883 2 29.3816 27.7251 34.4527 29 +884 2 30.0205 27.5275 34.444 29 +885 2 30.4024 28.063 33.6315 29 +886 2 30.0205 28.5986 33.6264 29 +887 2 29.3816 28.401 33.6178 29 +888 2 29.3816 27.7251 33.6178 29 +889 2 30.0205 27.5275 33.6264 29 +890 2 30.1311 28.063 34.6674 29 +891 2 29.933 28.3378 34.6708 29 +892 2 29.6081 28.2344 34.6764 29 +893 2 29.6081 27.8917 34.6764 29 +894 2 29.933 27.7883 34.6708 29 +895 2 30.1311 28.063 33.403 29 +896 2 29.933 28.3378 33.3996 29 +897 2 29.6081 28.2344 33.394 29 +898 2 29.6081 27.8917 33.394 29 +899 2 29.933 27.7883 33.3996 29 +900 1 30.2349 27.8319 35.3927 30 +901 2 29.5749 27.8319 35.6258 30 +902 2 30.0468 27.1978 35.6219 30 +903 2 30.7776 27.4503 35.6159 30 +904 2 30.7776 28.2136 35.6159 30 +905 2 30.0468 28.466 35.6219 30 +906 2 29.5749 27.8319 35.1595 30 +907 2 30.0468 27.1978 35.1634 30 +908 2 30.7776 27.4503 35.1694 30 +909 2 30.7776 28.2136 35.1694 30 +910 2 30.0468 28.466 35.1634 30 +911 2 30.8068 27.8319 35.7964 30 +912 2 30.4249 28.3675 35.8015 30 +913 2 29.786 28.1699 35.8101 30 +914 2 29.786 27.4939 35.8101 30 +915 2 30.4249 27.2964 35.8015 30 +916 2 30.8068 27.8319 34.9889 30 +917 2 30.4249 28.3675 34.9839 30 +918 2 29.786 28.1699 34.9752 30 +919 2 29.786 27.4939 34.9752 30 +920 2 30.4249 27.2964 34.9839 30 +921 2 30.5354 27.8319 36.0249 30 +922 2 30.3374 28.1067 36.0283 30 +923 2 30.0125 28.0032 36.0339 30 +924 2 30.0125 27.6606 36.0339 30 +925 2 30.3374 27.5571 36.0283 30 +926 2 30.5354 27.8319 34.7604 30 +927 2 30.3374 28.1067 34.7571 30 +928 2 30.0125 28.0032 34.7514 30 +929 2 30.0125 27.6606 34.7514 30 +930 2 30.3374 27.5571 34.7571 30 +931 1 30.9967 26.7242 34.8903 31 +932 2 30.3366 26.7242 35.1234 31 +933 2 30.8085 26.0901 35.1195 31 +934 2 31.5393 26.3426 35.1135 31 +935 2 31.5393 27.1059 35.1135 31 +936 2 30.8085 27.3583 35.1195 31 +937 2 30.3366 26.7242 34.6571 31 +938 2 30.8085 26.0901 34.6611 31 +939 2 31.5393 26.3426 34.6671 31 +940 2 31.5393 27.1059 34.6671 31 +941 2 30.8085 27.3583 34.6611 31 +942 2 31.5685 26.7242 35.294 31 +943 2 31.1866 27.2598 35.2991 31 +944 2 30.5478 27.0622 35.3077 31 +945 2 30.5478 26.3862 35.3077 31 +946 2 31.1866 26.1887 35.2991 31 +947 2 31.5685 26.7242 34.4866 31 +948 2 31.1866 27.2598 34.4815 31 +949 2 30.5478 27.0622 34.4728 31 +950 2 30.5478 26.3862 34.4728 31 +951 2 31.1866 26.1887 34.4815 31 +952 2 31.2972 26.7242 35.5225 31 +953 2 31.0991 26.999 35.5259 31 +954 2 30.7742 26.8955 35.5315 31 +955 2 30.7742 26.5529 35.5315 31 +956 2 31.0991 26.4494 35.5259 31 +957 2 31.2972 26.7242 34.2581 31 +958 2 31.0991 26.999 34.2547 31 +959 2 30.7742 26.8955 34.2491 31 +960 2 30.7742 26.5529 34.2491 31 +961 2 31.0991 26.4494 34.2547 31 +962 1 29.9072 26.1623 34.144 32 +963 2 29.2472 26.1623 34.3772 32 +964 2 29.719 25.5283 34.3732 32 +965 2 30.4499 25.7807 34.3672 32 +966 2 30.4499 26.544 34.3672 32 +967 2 29.719 26.7964 34.3732 32 +968 2 29.2472 26.1623 33.9109 32 +969 2 29.719 25.5282 33.9148 32 +970 2 30.4499 25.7807 33.9208 32 +971 2 30.4499 26.544 33.9208 32 +972 2 29.719 26.7964 33.9148 32 +973 2 30.479 26.1623 34.5478 32 +974 2 30.0971 26.6979 34.5528 32 +975 2 29.4583 26.5003 34.5615 32 +976 2 29.4583 25.8244 34.5615 32 +977 2 30.0971 25.6268 34.5528 32 +978 2 30.479 26.1623 33.7403 32 +979 2 30.0971 26.6979 33.7352 32 +980 2 29.4583 26.5003 33.7266 32 +981 2 29.4583 25.8244 33.7266 32 +982 2 30.0971 25.6268 33.7352 32 +983 2 30.2077 26.1623 34.7762 32 +984 2 30.0097 26.4371 34.7796 32 +985 2 29.6847 26.3336 34.7852 32 +986 2 29.6847 25.991 34.7852 32 +987 2 30.0097 25.8876 34.7796 32 +988 2 30.2077 26.1623 33.5118 32 +989 2 30.0097 26.4371 33.5084 32 +990 2 29.6847 26.3336 33.5028 32 +991 2 29.6847 25.991 33.5028 32 +992 2 30.0097 25.8875 33.5084 32 + +Bonds + +1 1 1 32 +2 1 32 63 +3 1 63 94 +4 1 94 125 +5 1 125 156 +6 1 156 187 +7 1 187 218 +8 1 218 249 +9 1 249 280 +10 1 280 311 +11 1 311 342 +12 1 342 373 +13 1 373 404 +14 1 404 435 +15 1 435 466 +16 1 466 497 +17 1 497 528 +18 1 528 559 +19 1 559 590 +20 1 590 621 +21 1 621 652 +22 1 652 683 +23 1 683 714 +24 1 714 745 +25 1 745 776 +26 1 776 807 +27 1 807 838 +28 1 838 869 +29 1 869 900 +30 1 900 931 +31 1 931 962 diff --git a/examples/USER/lb/polymer/in.polymer_default_gamma b/examples/USER/lb/polymer/in.polymer_default_gamma index 4344dc0ef8..954e5a6923 100755 --- a/examples/USER/lb/polymer/in.polymer_default_gamma +++ b/examples/USER/lb/polymer/in.polymer_default_gamma @@ -1,107 +1,107 @@ -#===========================================================================# -# polymer test # -# # -# Run consists of a lone 32-bead coarse-grained polymer # -# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # -# # -# Here, gamma (used in the calculation of the monomer-fluid interaction # -# force) is set by the user (gamma = 0.03 for this simulation...this # -# value has been calibrated a priori through simulations of the drag # -# force acting on a single particle of the same radius). # -# Sample output from this run can be found in the file: # -# 'dump.polymer.lammpstrj' # -# and viewed using, e.g., the VMD software. # -# # -#===========================================================================# - -units nano -dimension 3 -boundary p p p -atom_style hybrid molecular -special_bonds fene -read_data data.polymer - -#---------------------------------------------------------------------------- -# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing -# to ensure that the particles belonging to a given processor remain inside -# that processors lattice-Boltzmann grid. -#---------------------------------------------------------------------------- -neighbor 0.5 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude type 2 2 -neigh_modify exclude type 2 1 - -#---------------------------------------------------------------------------- -# Implement a hard-sphere interaction between the particles at the center of -# each monomer (use a truncated and shifted Lennard-Jones potential). -#---------------------------------------------------------------------------- -bond_style fene -bond_coeff 1 60.0 2.25 4.14195 1.5 -pair_style lj/cut 1.68369 -pair_coeff 1 1 4.14195 1.5 1.68369 -pair_coeff 1 2 4.14195 1.5 1.68369 -pair_coeff 2 2 0 1.0 - -mass * 0.000000771064 -timestep 0.00003 - -#---------------------------------------------------------------------------- -# ForceAtoms are the particles at the center of each monomer which -# do not interact with the fluid, but are used to implement the hard-sphere -# interactions. -# FluidAtoms are the particles representing the surface of the monomer -# which do interact with the fluid. Monomer surface is shell of radius 0.7 -#---------------------------------------------------------------------------- -group ForceAtoms type 1 -group FluidAtoms type 2 - -#--------------------------------------------------------------------------- -# Create a lattice-Boltzmann fluid covering the simulation domain. -# This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these -# particles. This is accomplished through the use of the lb/viscous -# fix). -# Uses the standard LB integration scheme, fluid viscosity = 0.023333333, -# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit, -# dm=0.0000166368. -# Use the default method to calculate the interaction force between the -# particles and the fluid. This calculation requires the surface area -# of the composite object represented by each particle node. By default -# this area is assumed equal to dx*dx; however, since this is not the case -# here, it is input through the setArea keyword (i.e. particles of type 2 -# correspond to a surface area of 0.2025=4 Pi R^2/N ). -# Use the trilinear interpolation stencil to distribute the force from -# a given particle onto the fluid mesh (results in a smaller hydrodynamic -# radius than if the Peskin stencil is used). -# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number -# seed=15003). This enables the particles to undergo Brownian motion in -# the fluid. -#---------------------------------------------------------------------------- -fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003 - -#---------------------------------------------------------------------------- -# Apply the force from the fluid to the particles, and integrate their -# motion, constraining them to move and rotate together as a single rigid -# spherical object. -# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical -# shell) should move and rotate together, this fix is applied to all of -# the atoms in the system. However, since the central atoms should not -# feel a force due to the fluid, they are excluded from the fluid force -# calculation. -#---------------------------------------------------------------------------- -fix 2 FluidAtoms lb/viscous -fix 3 all rigid molecule - -#---------------------------------------------------------------------------- -# To ensure that numerical errors do not lead to a buildup of momentum in the -# system, the momentum_lb fix is used every 10000 timesteps to zero out the -# total (particle plus fluid) momentum in the system. -#---------------------------------------------------------------------------- -fix 4 all lb/momentum 10000 linear 1 1 1 - -#---------------------------------------------------------------------------- -# Write position and velocity coordinates into a file every 2000 time steps. -#---------------------------------------------------------------------------- - -dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz -run 2000001 +#===========================================================================# +# polymer test # +# # +# Run consists of a lone 32-bead coarse-grained polymer # +# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # +# # +# Here, gamma (used in the calculation of the monomer-fluid interaction # +# force) is set by the user (gamma = 0.03 for this simulation...this # +# value has been calibrated a priori through simulations of the drag # +# force acting on a single particle of the same radius). # +# Sample output from this run can be found in the file: # +# 'dump.polymer.lammpstrj' # +# and viewed using, e.g., the VMD software. # +# # +#===========================================================================# + +units nano +dimension 3 +boundary p p p +atom_style hybrid molecular +special_bonds fene +read_data data.polymer + +#---------------------------------------------------------------------------- +# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing +# to ensure that the particles belonging to a given processor remain inside +# that processors lattice-Boltzmann grid. +#---------------------------------------------------------------------------- +neighbor 0.5 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude type 2 2 +neigh_modify exclude type 2 1 + +#---------------------------------------------------------------------------- +# Implement a hard-sphere interaction between the particles at the center of +# each monomer (use a truncated and shifted Lennard-Jones potential). +#---------------------------------------------------------------------------- +bond_style fene +bond_coeff 1 60.0 2.25 4.14195 1.5 +pair_style lj/cut 1.68369 +pair_coeff 1 1 4.14195 1.5 1.68369 +pair_coeff 1 2 4.14195 1.5 1.68369 +pair_coeff 2 2 0 1.0 + +mass * 0.000000771064 +timestep 0.00003 + +#---------------------------------------------------------------------------- +# ForceAtoms are the particles at the center of each monomer which +# do not interact with the fluid, but are used to implement the hard-sphere +# interactions. +# FluidAtoms are the particles representing the surface of the monomer +# which do interact with the fluid. Monomer surface is shell of radius 0.7 +#---------------------------------------------------------------------------- +group ForceAtoms type 1 +group FluidAtoms type 2 + +#--------------------------------------------------------------------------- +# Create a lattice-Boltzmann fluid covering the simulation domain. +# This fluid feels a force due to the particles specified through FluidAtoms +# (however, this fix does not explicitly apply a force back on to these +# particles. This is accomplished through the use of the lb/viscous +# fix). +# Uses the standard LB integration scheme, fluid viscosity = 0.023333333, +# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit, +# dm=0.0000166368. +# Use the default method to calculate the interaction force between the +# particles and the fluid. This calculation requires the surface area +# of the composite object represented by each particle node. By default +# this area is assumed equal to dx*dx; however, since this is not the case +# here, it is input through the setArea keyword (i.e. particles of type 2 +# correspond to a surface area of 0.2025=4 Pi R^2/N ). +# Use the trilinear interpolation stencil to distribute the force from +# a given particle onto the fluid mesh (results in a smaller hydrodynamic +# radius than if the Peskin stencil is used). +# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number +# seed=15003). This enables the particles to undergo Brownian motion in +# the fluid. +#---------------------------------------------------------------------------- +fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003 + +#---------------------------------------------------------------------------- +# Apply the force from the fluid to the particles, and integrate their +# motion, constraining them to move and rotate together as a single rigid +# spherical object. +# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical +# shell) should move and rotate together, this fix is applied to all of +# the atoms in the system. However, since the central atoms should not +# feel a force due to the fluid, they are excluded from the fluid force +# calculation. +#---------------------------------------------------------------------------- +fix 2 FluidAtoms lb/viscous +fix 3 all rigid molecule + +#---------------------------------------------------------------------------- +# To ensure that numerical errors do not lead to a buildup of momentum in the +# system, the momentum_lb fix is used every 10000 timesteps to zero out the +# total (particle plus fluid) momentum in the system. +#---------------------------------------------------------------------------- +fix 4 all lb/momentum 10000 linear 1 1 1 + +#---------------------------------------------------------------------------- +# Write position and velocity coordinates into a file every 2000 time steps. +#---------------------------------------------------------------------------- + +dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz +run 2000001 diff --git a/examples/USER/lb/polymer/in.polymer_setgamma b/examples/USER/lb/polymer/in.polymer_setgamma index b5108a60fa..75b8d67ada 100755 --- a/examples/USER/lb/polymer/in.polymer_setgamma +++ b/examples/USER/lb/polymer/in.polymer_setgamma @@ -1,105 +1,105 @@ -#===========================================================================# -# polymer test # -# # -# Run consists of a lone 32-bead coarse-grained polymer # -# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # -# # -# Here, gamma (used in the calculation of the monomer-fluid interaction # -# force) is set by the user (gamma = 0.03 for this simulation...this # -# value has been calibrated a priori through simulations of the drag # -# force acting on a single particle of the same radius). # -# Sample output from this run can be found in the file: # -# 'dump.polymer.lammpstrj' # -# and viewed using, e.g., the VMD software. # -# # -# Santtu Ollila # -# santtu.ollila@aalto.fi # -# Aalto University # -# August 14, 2013 # -#===========================================================================# - -units nano -dimension 3 -boundary p p p -atom_style hybrid molecular -special_bonds fene -read_data data.polymer - -#---------------------------------------------------------------------------- -# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing -# to ensure that the particles belonging to a given processor remain inside -# that processors lattice-Boltzmann grid. -#---------------------------------------------------------------------------- -neighbor 0.5 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude type 2 2 -neigh_modify exclude type 2 1 - -#---------------------------------------------------------------------------- -# Implement a hard-sphere interaction between the particles at the center of -# each monomer (use a truncated and shifted Lennard-Jones potential). -#---------------------------------------------------------------------------- -bond_style fene -bond_coeff 1 60.0 2.25 4.14195 1.5 -pair_style lj/cut 1.68369 -pair_coeff 1 1 4.14195 1.5 1.68369 -pair_coeff 1 2 4.14195 1.5 1.68369 -pair_coeff 2 2 0 1.0 - -mass * 0.000000771064 -timestep 0.00003 - -#---------------------------------------------------------------------------- -# ForceAtoms are the particles at the center of each monomer which -# do not interact with the fluid, but are used to implement the hard-sphere -# interactions. -# FluidAtoms are the particles representing the surface of the monomer -# which do interact with the fluid. -#---------------------------------------------------------------------------- -group ForceAtoms type 1 -group FluidAtoms type 2 - -#--------------------------------------------------------------------------- -# Create a lattice-Boltzmann fluid covering the simulation domain. -# This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these -# particles. This is accomplished through the use of the rigid_pc_sphere -# fix). -# Use the LB integration scheme of Ollila et. al. (for stability reasons, -# this integration scheme should be used when a large user set value for -# gamma is specified), a fluid viscosity = 0.023333333, -# fluid density= 0.0000166368, -# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368. -# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number -# seed=15003). This enables the particles to undergo Brownian motion in -# the fluid. -#---------------------------------------------------------------------------- -fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003 - -#---------------------------------------------------------------------------- -# Apply the force from the fluid to the particles, and integrate their -# motion, constraining them to move and rotate together as a single rigid -# spherical object. -# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical -# shell) should move and rotate together, this fix is applied to all of -# the atoms in the system. However, since the central atoms should not -# feel a force due to the fluid, they are excluded from the force -# calculation through the use of the 'innerNodes' keyword. -# NOTE: This fix should only be used when the user specifies a value for -# gamma (through the setGamma keyword) in the lb_fluid fix. -#---------------------------------------------------------------------------- -fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms - -#---------------------------------------------------------------------------- -# To ensure that numerical errors do not lead to a buildup of momentum in the -# system, the momentum_lb fix is used every 10000 timesteps to zero out the -# total (particle plus fluid) momentum in the system. -#---------------------------------------------------------------------------- -fix 3 all lb/momentum 10000 linear 1 1 1 - -#---------------------------------------------------------------------------- -# Write position and velocity coordinates into a file every 2000 time steps. -#---------------------------------------------------------------------------- - -dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz -run 2000001 +#===========================================================================# +# polymer test # +# # +# Run consists of a lone 32-bead coarse-grained polymer # +# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # +# # +# Here, gamma (used in the calculation of the monomer-fluid interaction # +# force) is set by the user (gamma = 0.03 for this simulation...this # +# value has been calibrated a priori through simulations of the drag # +# force acting on a single particle of the same radius). # +# Sample output from this run can be found in the file: # +# 'dump.polymer.lammpstrj' # +# and viewed using, e.g., the VMD software. # +# # +# Santtu Ollila # +# santtu.ollila@aalto.fi # +# Aalto University # +# August 14, 2013 # +#===========================================================================# + +units nano +dimension 3 +boundary p p p +atom_style hybrid molecular +special_bonds fene +read_data data.polymer + +#---------------------------------------------------------------------------- +# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing +# to ensure that the particles belonging to a given processor remain inside +# that processors lattice-Boltzmann grid. +#---------------------------------------------------------------------------- +neighbor 0.5 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude type 2 2 +neigh_modify exclude type 2 1 + +#---------------------------------------------------------------------------- +# Implement a hard-sphere interaction between the particles at the center of +# each monomer (use a truncated and shifted Lennard-Jones potential). +#---------------------------------------------------------------------------- +bond_style fene +bond_coeff 1 60.0 2.25 4.14195 1.5 +pair_style lj/cut 1.68369 +pair_coeff 1 1 4.14195 1.5 1.68369 +pair_coeff 1 2 4.14195 1.5 1.68369 +pair_coeff 2 2 0 1.0 + +mass * 0.000000771064 +timestep 0.00003 + +#---------------------------------------------------------------------------- +# ForceAtoms are the particles at the center of each monomer which +# do not interact with the fluid, but are used to implement the hard-sphere +# interactions. +# FluidAtoms are the particles representing the surface of the monomer +# which do interact with the fluid. +#---------------------------------------------------------------------------- +group ForceAtoms type 1 +group FluidAtoms type 2 + +#--------------------------------------------------------------------------- +# Create a lattice-Boltzmann fluid covering the simulation domain. +# This fluid feels a force due to the particles specified through FluidAtoms +# (however, this fix does not explicitly apply a force back on to these +# particles. This is accomplished through the use of the rigid_pc_sphere +# fix). +# Use the LB integration scheme of Ollila et. al. (for stability reasons, +# this integration scheme should be used when a large user set value for +# gamma is specified), a fluid viscosity = 0.023333333, +# fluid density= 0.0000166368, +# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368. +# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number +# seed=15003). This enables the particles to undergo Brownian motion in +# the fluid. +#---------------------------------------------------------------------------- +fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003 + +#---------------------------------------------------------------------------- +# Apply the force from the fluid to the particles, and integrate their +# motion, constraining them to move and rotate together as a single rigid +# spherical object. +# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical +# shell) should move and rotate together, this fix is applied to all of +# the atoms in the system. However, since the central atoms should not +# feel a force due to the fluid, they are excluded from the force +# calculation through the use of the 'innerNodes' keyword. +# NOTE: This fix should only be used when the user specifies a value for +# gamma (through the setGamma keyword) in the lb_fluid fix. +#---------------------------------------------------------------------------- +fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms + +#---------------------------------------------------------------------------- +# To ensure that numerical errors do not lead to a buildup of momentum in the +# system, the momentum_lb fix is used every 10000 timesteps to zero out the +# total (particle plus fluid) momentum in the system. +#---------------------------------------------------------------------------- +fix 3 all lb/momentum 10000 linear 1 1 1 + +#---------------------------------------------------------------------------- +# Write position and velocity coordinates into a file every 2000 time steps. +#---------------------------------------------------------------------------- + +dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz +run 2000001 diff --git a/examples/USER/misc/agni/Al_jpc.agni b/examples/USER/misc/agni/Al_jpc.agni new file mode 100644 index 0000000000..0a82a3c8f4 --- /dev/null +++ b/examples/USER/misc/agni/Al_jpc.agni @@ -0,0 +1,3020 @@ +# DATE: 2017-02-24 CONTRIBUTOR: Venkatesh Botu CITATION: Botu, V., Batra, R., Chapman, J., and Ramprasad, R., J. Phys. Chem. C, 121 (1), 511 (2017). +# This potential is an updated version of Al_prb.agni, which is now deprecated. +# This potential file is parameterized for metal units + +generation 1 +n_elements 1 + +element Al + +interaction Al +Rc 8.0 +Rs 0.0 +neighbors 500 +eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294 +sigma 13.8949549437 +lambda 1e-08 +b 102.870264493 +n_train 3000 +endVar + +0.000000000000000000e+00 -4.980622283254589000e+00 -2.662505672962482528e+00 -1.495155609938069619e+00 -7.333737039816567993e-01 -2.724952969791719082e-01 -6.613771156359619929e-02 -1.912092709590330940e-03 1.473705560509566359e-05 7.453680000000000305e-01 1.597331621434825659e+07 +1.000000000000000000e+00 -4.977152206916696464e+00 -2.661383130146552922e+00 -1.494564974611932495e+00 -7.326386664321046238e-01 -2.717745126429032543e-01 -6.595850089381591341e-02 -1.985476180073739681e-03 1.342170339121332597e-05 7.294220000000000148e-01 1.595073002517673187e+07 +2.000000000000000000e+00 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b/examples/USER/misc/agni/Al_prb.agni deleted file mode 100644 index a191b22220..0000000000 --- a/examples/USER/misc/agni/Al_prb.agni +++ /dev/null @@ -1,1019 +0,0 @@ -# DATE: 2016-11-11 CONTRIBUTOR: Venkatesh Botu CITATION: Botu, V. and Ramprasad, R., Phys. Rev. B, 92, 094306 (2015) -# This potential file is parameterized for metal units - -generation 1 -n_elements 1 - -element Al - -interaction Al -Rc 8.0 -Rs 0.0 -neighbors 500 -eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294 -sigma 7.54312006335 -lambda 1e-08 -b -116.143708049 -n_train 1000 -endVar - -0.000000000000000000e+00 2.819999999999999937e-02 4.599999999999999922e-02 4.839999999999999858e-02 4.259999999999999898e-02 2.900000000000000147e-02 1.370000000000000037e-02 1.580000000000000024e-03 1.189999999999999957e-05 0.000000000000000000e+00 2.926153611883024685e+06 -1.000000000000000000e+00 6.569999999999999452e-02 8.820000000000000062e-02 1.010000000000000064e-01 1.010000000000000064e-01 7.950000000000000122e-02 4.120000000000000051e-02 4.519999999999999712e-03 2.850000000000000157e-05 0.000000000000000000e+00 -2.067059602323263418e+06 -2.000000000000000000e+00 4.959999999999999964e+00 2.669999999999999929e+00 1.510000000000000009e+00 7.479999999999999982e-01 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4.070000000000000007e-02 3.470000000000000168e-02 2.199999999999999872e-02 2.929999999999999879e-03 2.019999999999999972e-05 0.000000000000000000e+00 5.212071365308906883e+06 -9.990000000000000000e+02 5.230000000000000426e+00 2.830000000000000071e+00 1.620000000000000107e+00 8.219999999999999529e-01 3.320000000000000173e-01 9.560000000000000442e-02 5.230000000000000274e-03 1.690000000000000082e-05 0.000000000000000000e+00 2.612105472888816148e+06 diff --git a/examples/USER/misc/agni/in.adatom b/examples/USER/misc/agni/in.adatom index b39b104deb..45653e6104 100644 --- a/examples/USER/misc/agni/in.adatom +++ b/examples/USER/misc/agni/in.adatom @@ -5,7 +5,7 @@ boundary p p f read_data adatom.data pair_style agni -pair_coeff * * Al_prb.agni Al +pair_coeff * * Al_jpc.agni Al neighbor 0.3 bin neigh_modify delay 2 check yes diff --git a/examples/USER/misc/agni/in.vacancy b/examples/USER/misc/agni/in.vacancy index 94226b0e9a..4f6dd0fc8c 100644 --- a/examples/USER/misc/agni/in.vacancy +++ b/examples/USER/misc/agni/in.vacancy @@ -4,7 +4,7 @@ boundary p p p read_data vacancy.data pair_style agni -pair_coeff * * Al_prb.agni Al +pair_coeff * * Al_jpc.agni Al neighbor 0.3 bin neigh_modify delay 2 check yes diff --git a/examples/USER/misc/agni/log.21Feb17.adatom.g++.1 b/examples/USER/misc/agni/log.21Feb17.adatom.g++.1 new file mode 100644 index 0000000000..5243b83ec9 --- /dev/null +++ b/examples/USER/misc/agni/log.21Feb17.adatom.g++.1 @@ -0,0 +1,87 @@ +LAMMPS (21 Feb 2017) + using 1 OpenMP thread(s) per MPI task + +processors * * 1 +units metal +boundary p p f +read_data adatom.data + orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 181 atoms + +pair_style agni +pair_coeff * * Al_jpc.agni Al +Reading potential file Al_jpc.agni with DATE: 2017-02-24 + +neighbor 0.3 bin +neigh_modify delay 2 check yes + +timestep 0.0005 +velocity all create 500 12345 +fix 1 all nvt temp 250 250 0.2 +fix 5 all momentum 1 linear 1 1 1 + +thermo 100 +thermo_style custom step ke temp + +# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.3 + ghost atom cutoff = 8.3 + binsize = 4.15, bins = 5 4 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair agni, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Memory usage per processor = 2.69795 Mbytes +Step KinEng Temp + 0 11.633413 500 + 100 4.6059939 197.964 + 200 7.3700149 316.76065 + 300 6.0443913 259.78581 + 400 6.1631189 264.88868 + 500 6.2647272 269.25577 + 600 5.2732539 226.6426 + 700 5.6514471 242.89721 + 800 6.5572407 281.8279 + 900 6.0576738 260.35669 + 1000 6.5622233 282.04205 +Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms + +Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 51.89 | 51.89 | 51.89 | 0.0 | 99.92 +Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04 +Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01 +Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00 +Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02 +Other | | 0.002483 | | | 0.00 + +Nlocal: 181 ave 181 max 181 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 563 ave 563 max 563 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 19484 ave 19484 max 19484 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19484 +Ave neighs/atom = 107.646 +Neighbor list builds = 33 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:52 diff --git a/examples/USER/misc/agni/log.21Feb17.adatom.g++.4 b/examples/USER/misc/agni/log.21Feb17.adatom.g++.4 new file mode 100644 index 0000000000..9419888e98 --- /dev/null +++ b/examples/USER/misc/agni/log.21Feb17.adatom.g++.4 @@ -0,0 +1,87 @@ +LAMMPS (21 Feb 2017) + using 1 OpenMP thread(s) per MPI task + +processors * * 1 +units metal +boundary p p f +read_data adatom.data + orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 181 atoms + +pair_style agni +pair_coeff * * Al_jpc.agni Al +Reading potential file Al_jpc.agni with DATE: 2017-02-24 + +neighbor 0.3 bin +neigh_modify delay 2 check yes + +timestep 0.0005 +velocity all create 500 12345 +fix 1 all nvt temp 250 250 0.2 +fix 5 all momentum 1 linear 1 1 1 + +thermo 100 +thermo_style custom step ke temp + +# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.3 + ghost atom cutoff = 8.3 + binsize = 4.15, bins = 5 4 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair agni, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Memory usage per processor = 3.06041 Mbytes +Step KinEng Temp + 0 11.633413 500 + 100 4.6059941 197.96401 + 200 7.3700154 316.76067 + 300 6.0443913 259.78581 + 400 6.1631193 264.8887 + 500 6.2647281 269.25581 + 600 5.2732537 226.64259 + 700 5.651448 242.89725 + 800 6.5572405 281.82789 + 900 6.0576741 260.3567 + 1000 6.562224 282.04208 +Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms + +Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.858 | 13.227 | 13.574 | 8.0 | 91.06 +Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04 +Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78 +Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00 +Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09 +Other | | 0.004066 | | | 0.03 + +Nlocal: 45.25 ave 52 max 40 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 376.5 ave 382 max 366 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 4871 ave 5578 max 4374 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 19484 +Ave neighs/atom = 107.646 +Neighbor list builds = 33 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:14 diff --git a/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1 b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1 new file mode 100644 index 0000000000..9194d78419 --- /dev/null +++ b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.1 @@ -0,0 +1,87 @@ +LAMMPS (21 Feb 2017) + using 1 OpenMP thread(s) per MPI task + +units metal +boundary p p p +read_data vacancy.data + orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 31 atoms + +pair_style agni +pair_coeff * * Al_jpc.agni Al +Reading potential file Al_jpc.agni with DATE: 2017-02-24 +neighbor 0.3 bin +neigh_modify delay 2 check yes + + +timestep 0.0005 +velocity all create 1000 12345 +fix 1 all nvt temp 900 900 200 +fix 5 all momentum 1 linear 1 1 1 + + +thermo 100 +thermo_style custom step ke etotal temp + +# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.3 + ghost atom cutoff = 8.3 + binsize = 4.15, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair agni, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Memory usage per processor = 2.73416 Mbytes +Step KinEng TotEng Temp + 0 3.8778043 3.8778043 1000 + 100 2.9986261 2.9986261 773.27937 + 200 3.6860314 3.6860314 950.54599 + 300 3.813315 3.813315 983.36961 + 400 3.7330285 3.7330285 962.6655 + 500 3.5875467 3.5875467 925.14896 + 600 3.5331529 3.5331529 911.12202 + 700 2.6509449 2.6509449 683.62008 + 800 3.3763492 3.3763492 870.68582 + 900 3.903673 3.903673 1006.6709 + 1000 3.0884824 3.0884824 796.45133 +Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms + +Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74 +Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13 +Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07 +Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00 +Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04 +Other | | 0.001521 | | | 0.02 + +Nlocal: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 869 ave 869 max 869 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 4360 ave 4360 max 4360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4360 +Ave neighs/atom = 140.645 +Neighbor list builds = 53 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4 b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4 new file mode 100644 index 0000000000..d5d8e3a481 --- /dev/null +++ b/examples/USER/misc/agni/log.21Feb17.vacancy.g++.4 @@ -0,0 +1,87 @@ +LAMMPS (21 Feb 2017) + using 1 OpenMP thread(s) per MPI task + +units metal +boundary p p p +read_data vacancy.data + orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 31 atoms + +pair_style agni +pair_coeff * * Al_jpc.agni Al +Reading potential file Al_jpc.agni with DATE: 2017-02-24 +neighbor 0.3 bin +neigh_modify delay 2 check yes + + +timestep 0.0005 +velocity all create 1000 12345 +fix 1 all nvt temp 900 900 200 +fix 5 all momentum 1 linear 1 1 1 + + +thermo 100 +thermo_style custom step ke etotal temp + +# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.3 + ghost atom cutoff = 8.3 + binsize = 4.15, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair agni, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Memory usage per processor = 2.72175 Mbytes +Step KinEng TotEng Temp + 0 3.8778044 3.8778044 1000 + 100 2.9986263 2.9986263 773.27942 + 200 3.6860315 3.6860315 950.54602 + 300 3.8133145 3.8133145 983.3695 + 400 3.7330282 3.7330282 962.66543 + 500 3.5875466 3.5875466 925.14895 + 600 3.5331523 3.5331523 911.12186 + 700 2.6509448 2.6509448 683.62005 + 800 3.3763493 3.3763493 870.68584 + 900 3.9036733 3.9036733 1006.671 + 1000 3.0884818 3.0884818 796.45116 +Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms + +Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16 +Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11 +Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14 +Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01 +Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42 +Other | | 0.004321 | | | 0.18 + +Nlocal: 7.75 ave 8 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 617.25 ave 621 max 612 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1090 ave 1131 max 993 min +Histogram: 1 0 0 0 0 0 0 0 1 2 + +Total # of neighbors = 4360 +Ave neighs/atom = 140.645 +Neighbor list builds = 53 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1 b/examples/USER/misc/agni/log.9Nov16.adatom.g++.1 deleted file mode 100644 index 1b39652b41..0000000000 --- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1 +++ /dev/null @@ -1,82 +0,0 @@ -LAMMPS (9 Nov 2016) - using 1 OpenMP thread(s) per MPI task - -processors * * 1 -units metal -boundary p p f -read_data adatom.data - orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 181 atoms - -pair_style agni -pair_coeff * * Al_prb.agni Al -Reading potential file Al_prb.agni with DATE: 2016-11-11 - -neighbor 0.3 bin -neigh_modify delay 2 check yes - -timestep 0.0005 -velocity all create 500 12345 -fix 1 all nvt temp 250 250 0.2 -fix 5 all momentum 1 linear 1 1 1 - -thermo 100 -thermo_style custom step ke temp - -# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz - -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.3 - ghost atom cutoff = 8.3 - binsize = 4.15 -> bins = 5 4 10 -Memory usage per processor = 2.37049 Mbytes -Step KinEng Temp - 0 11.633413 500 - 100 4.049974 174.06646 - 200 5.8983472 253.50889 - 300 5.3667309 230.66021 - 400 4.9343935 212.0785 - 500 5.4054496 232.32432 - 600 6.1779127 265.52452 - 700 6.3749266 273.9921 - 800 6.0701481 260.89283 - 900 6.4582394 277.57286 - 1000 6.4047444 275.27366 -Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms - -Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 20.79 | 20.79 | 20.79 | 0.0 | 99.82 -Neigh | 0.022742 | 0.022742 | 0.022742 | 0.0 | 0.11 -Comm | 0.0040836 | 0.0040836 | 0.0040836 | 0.0 | 0.02 -Output | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.00 -Modify | 0.0089345 | 0.0089345 | 0.0089345 | 0.0 | 0.04 -Other | | 0.001819 | | | 0.01 - -Nlocal: 181 ave 181 max 181 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 562 ave 562 max 562 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 18810 ave 18810 max 18810 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 18810 -Ave neighs/atom = 103.923 -Neighbor list builds = 33 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:20 diff --git a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4 b/examples/USER/misc/agni/log.9Nov16.adatom.g++.4 deleted file mode 100644 index 132e6468e2..0000000000 --- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4 +++ /dev/null @@ -1,82 +0,0 @@ -LAMMPS (9 Nov 2016) - using 1 OpenMP thread(s) per MPI task - -processors * * 1 -units metal -boundary p p f -read_data adatom.data - orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 181 atoms - -pair_style agni -pair_coeff * * Al_prb.agni Al -Reading potential file Al_prb.agni with DATE: 2016-11-11 - -neighbor 0.3 bin -neigh_modify delay 2 check yes - -timestep 0.0005 -velocity all create 500 12345 -fix 1 all nvt temp 250 250 0.2 -fix 5 all momentum 1 linear 1 1 1 - -thermo 100 -thermo_style custom step ke temp - -# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz - -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.3 - ghost atom cutoff = 8.3 - binsize = 4.15 -> bins = 5 4 10 -Memory usage per processor = 2.48695 Mbytes -Step KinEng Temp - 0 11.633413 500 - 100 4.049974 174.06646 - 200 5.8983472 253.50889 - 300 5.3667309 230.66021 - 400 4.9343935 212.0785 - 500 5.4054496 232.32432 - 600 6.1779127 265.52451 - 700 6.3749266 273.9921 - 800 6.0701481 260.89283 - 900 6.4582394 277.57286 - 1000 6.4047444 275.27366 -Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms - -Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.4176 | 5.4602 | 5.5505 | 2.3 | 91.48 -Neigh | 0.0056074 | 0.0060464 | 0.0062635 | 0.3 | 0.10 -Comm | 0.39544 | 0.48696 | 0.53111 | 7.9 | 8.16 -Output | 0.0001545 | 0.00015736 | 0.0001595 | 0.0 | 0.00 -Modify | 0.010492 | 0.011565 | 0.012588 | 0.9 | 0.19 -Other | | 0.003794 | | | 0.06 - -Nlocal: 45.25 ave 47 max 42 min -Histogram: 1 0 0 0 0 0 0 0 2 1 -Nghost: 374.75 ave 380 max 373 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 4702.5 ave 4868 max 4389 min -Histogram: 1 0 0 0 0 0 0 1 1 1 - -Total # of neighbors = 18810 -Ave neighs/atom = 103.923 -Neighbor list builds = 33 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:05 diff --git a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1 b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1 deleted file mode 100644 index 07912609ba..0000000000 --- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1 +++ /dev/null @@ -1,82 +0,0 @@ -LAMMPS (9 Nov 2016) - using 1 OpenMP thread(s) per MPI task - -units metal -boundary p p p -read_data vac.data - orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 31 atoms - -pair_style agni -pair_coeff * * Al_prb.agni Al -Reading potential file Al_prb.agni with DATE: 2016-11-11 -neighbor 0.3 bin -neigh_modify delay 2 check yes - - -timestep 0.0005 -velocity all create 1000 12345 -fix 1 all nvt temp 900 900 200 -fix 5 all momentum 1 linear 1 1 1 - - -thermo 100 -thermo_style custom step ke etotal temp - -# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz - -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.3 - ghost atom cutoff = 8.3 - binsize = 4.15 -> bins = 2 2 2 -Memory usage per processor = 2.40842 Mbytes -Step KinEng TotEng Temp - 0 3.8778043 3.8778043 1000 - 100 2.8126642 2.8126642 725.32391 - 200 3.7110413 3.7110413 956.9955 - 300 3.2361084 3.2361084 834.52081 - 400 3.4625769 3.4625769 892.92201 - 500 3.4563307 3.4563307 891.31126 - 600 2.8486344 2.8486344 734.59982 - 700 3.1183057 3.1183057 804.14208 - 800 2.9164818 2.9164818 752.09618 - 900 3.464416 3.464416 893.39629 - 1000 3.5954546 3.5954546 927.18825 -Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms - -Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.8463 | 3.8463 | 3.8463 | 0.0 | 99.44 -Neigh | 0.011294 | 0.011294 | 0.011294 | 0.0 | 0.29 -Comm | 0.0057271 | 0.0057271 | 0.0057271 | 0.0 | 0.15 -Output | 0.00014257 | 0.00014257 | 0.00014257 | 0.0 | 0.00 -Modify | 0.0029459 | 0.0029459 | 0.0029459 | 0.0 | 0.08 -Other | | 0.001395 | | | 0.04 - -Nlocal: 31 ave 31 max 31 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 878 ave 878 max 878 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4334 ave 4334 max 4334 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4334 -Ave neighs/atom = 139.806 -Neighbor list builds = 51 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4 b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4 deleted file mode 100644 index 82bd4467bc..0000000000 --- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4 +++ /dev/null @@ -1,82 +0,0 @@ -LAMMPS (9 Nov 2016) - using 1 OpenMP thread(s) per MPI task - -units metal -boundary p p p -read_data vac.data - orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 31 atoms - -pair_style agni -pair_coeff * * Al_prb.agni Al -Reading potential file Al_prb.agni with DATE: 2016-11-11 -neighbor 0.3 bin -neigh_modify delay 2 check yes - - -timestep 0.0005 -velocity all create 1000 12345 -fix 1 all nvt temp 900 900 200 -fix 5 all momentum 1 linear 1 1 1 - - -thermo 100 -thermo_style custom step ke etotal temp - -# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz - -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.3 - ghost atom cutoff = 8.3 - binsize = 4.15 -> bins = 2 2 2 -Memory usage per processor = 2.3974 Mbytes -Step KinEng TotEng Temp - 0 3.8778044 3.8778044 1000 - 100 2.8126642 2.8126642 725.32391 - 200 3.7110413 3.7110413 956.99549 - 300 3.2361084 3.2361084 834.52081 - 400 3.4625769 3.4625769 892.92201 - 500 3.4563307 3.4563307 891.31126 - 600 2.8486343 2.8486343 734.59981 - 700 3.1183057 3.1183057 804.14208 - 800 2.9164819 2.9164819 752.09618 - 900 3.4644161 3.4644161 893.39631 - 1000 3.5954546 3.5954546 927.18824 -Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms - -Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.906 | 0.99469 | 1.0291 | 5.1 | 89.61 -Neigh | 0.0026186 | 0.0027665 | 0.0028622 | 0.2 | 0.25 -Comm | 0.066125 | 0.10079 | 0.1896 | 16.2 | 9.08 -Output | 0.00012875 | 0.00014615 | 0.00018787 | 0.2 | 0.01 -Modify | 0.0080338 | 0.0083079 | 0.00861 | 0.2 | 0.75 -Other | | 0.003372 | | | 0.30 - -Nlocal: 7.75 ave 8 max 7 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Nghost: 623.5 ave 630 max 616 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1083.5 ave 1131 max 988 min -Histogram: 1 0 0 0 0 0 0 1 1 1 - -Total # of neighbors = 4334 -Ave neighs/atom = 139.806 -Neighbor list builds = 51 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel b/examples/USER/misc/gauss-diel/in.gauss-diel index 3e2be5b4d6..5aa7ae7157 100644 --- a/examples/USER/misc/gauss-diel/in.gauss-diel +++ b/examples/USER/misc/gauss-diel/in.gauss-diel @@ -81,7 +81,7 @@ group sds subtract all cions velocity all create 1. 87287 dist gaussian neighbor 1.5 multi -neigh_modify exclude molecule sds +neigh_modify exclude molecule/intra sds neigh_modify every 5 delay 0 check yes fix 1 all nve/limit 0.2 diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel-cg b/examples/USER/misc/gauss-diel/in.gauss-diel-cg index ed21016220..51032c3d32 100644 --- a/examples/USER/misc/gauss-diel/in.gauss-diel-cg +++ b/examples/USER/misc/gauss-diel/in.gauss-diel-cg @@ -81,7 +81,7 @@ group sds subtract all cions velocity all create 1. 87287 dist gaussian neighbor 1.5 multi -neigh_modify exclude molecule sds +neigh_modify exclude molecule/intra sds neigh_modify every 5 delay 0 check yes fix 1 all nve/limit 0.2 diff --git a/examples/USER/misc/gauss-diel/in.gauss-diel-split b/examples/USER/misc/gauss-diel/in.gauss-diel-split index f13859863b..b6a17371d1 100644 --- a/examples/USER/misc/gauss-diel/in.gauss-diel-split +++ b/examples/USER/misc/gauss-diel/in.gauss-diel-split @@ -84,7 +84,7 @@ group sds subtract all cions velocity all create 1. 87287 dist gaussian neighbor 1.5 multi -neigh_modify exclude molecule sds +neigh_modify exclude molecule/intra sds neigh_modify every 5 delay 0 check yes fix 1 all nve/limit 0.2 diff --git a/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene new file mode 100644 index 0000000000..6c6ad3cb7c --- /dev/null +++ b/examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene @@ -0,0 +1,266 @@ +info: xyz2data 18:31, Mon 27-02-2017 +256 atoms +2 atom types + + 0.00000000 17.04000000 xlo xhi + 0.00000000 19.67609717 ylo yhi + -20.00000000 40.00000000 zlo zhi + +Atoms + + 1 1 0.00000000 0.00000000 0.00000000 + 2 1 1.42000000 0.00000000 0.00000000 + 3 2 1.42000000 0.00000000 3.30000000 + 4 2 2.84000000 0.00000000 3.30000000 + 5 1 2.13000000 1.22975607 0.00000000 + 6 1 3.55000000 1.22975607 0.00000000 + 7 2 3.55000000 1.22975607 3.30000000 + 8 2 4.97000000 1.22975607 3.30000000 + 9 1 0.00000000 2.45951215 0.00000000 + 10 1 1.42000000 2.45951215 0.00000000 + 11 2 1.42000000 2.45951215 3.30000000 + 12 2 2.84000000 2.45951215 3.30000000 + 13 1 2.13000000 3.68926822 0.00000000 + 14 1 3.55000000 3.68926822 0.00000000 + 15 2 3.55000000 3.68926822 3.30000000 + 16 2 4.97000000 3.68926822 3.30000000 + 17 1 0.00000000 4.91902429 0.00000000 + 18 1 1.42000000 4.91902429 0.00000000 + 19 2 1.42000000 4.91902429 3.30000000 + 20 2 2.84000000 4.91902429 3.30000000 + 21 1 2.13000000 6.14878037 0.00000000 + 22 1 3.55000000 6.14878037 0.00000000 + 23 2 3.55000000 6.14878037 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14.91000000 15.98682895 0.00000000 +124 1 16.33000000 15.98682895 0.00000000 +125 1 12.78000000 17.21658503 0.00000000 +126 1 14.20000000 17.21658503 0.00000000 +127 1 14.91000000 18.44634110 0.00000000 +128 1 16.33000000 18.44634110 0.00000000 +129 2 10.00000000 10.00000000 3.30000000 diff --git a/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion b/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion new file mode 100644 index 0000000000..5e3135a8b4 --- /dev/null +++ b/examples/USER/misc/kolmogorov-crespi/in.atom-diffusion @@ -0,0 +1,45 @@ +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.graphene-adsorbant # read lammps data file +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +group adsorbant type 2 + +######################## Potential defition ######################## +pair_style hybrid/overlay kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * none +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +fix thermostat adsorbant nve +fix rigid_membrane membrane setforce 0 0 0 +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 100 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 10000 diff --git a/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene new file mode 100644 index 0000000000..3d63fc09ed --- /dev/null +++ b/examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene @@ -0,0 +1,45 @@ +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +group adsorbant type 2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.airebo C C # chemical +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 diff --git a/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion b/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion new file mode 100644 index 0000000000..5ed6542217 --- /dev/null +++ b/examples/USER/misc/kolmogorov-crespi/log.atom-diffusion @@ -0,0 +1,189 @@ +LAMMPS (17 Nov 2016) +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.graphene-adsorbant # read lammps data file + orthogonal box = (0 0 -10) to (17.04 19.6761 40) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 129 atoms +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +1 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * none +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +fix thermostat adsorbant nve +fix rigid_membrane membrane setforce 0 0 0 +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 100 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 10000 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8 -> bins = 3 3 7 +Memory usage per processor = 2.48399 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -0.02562011 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3.64823296 + 1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357 + 1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134 + 1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759 + 1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541 + 1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274 + 1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629 + 2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626 + 2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185 + 2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749 + 2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976 + 2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483 + 2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637 + 2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384 + 2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113 + 2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542 + 2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629 + 3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498 + 3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382 + 3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573 + 3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390 + 3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142 + 3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110 + 3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529 + 3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569 + 3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329 + 3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830 + 4000 0.40000000 -0.02562011 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0.00000000 3.98416189 + 5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511 + 5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053 + 5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766 + 5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492 + 5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210 + 5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330 + 6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044 + 6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758 + 6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588 + 6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945 + 6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187 + 6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331 + 6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782 + 6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023 + 6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153 + 6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129 + 7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509 + 7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482 + 7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933 + 7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400 + 7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906 + 7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907 + 7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900 + 7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492 + 7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821 + 7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091 + 8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582 + 8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999 + 8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524 + 8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734 + 8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495 + 8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148 + 8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572 + 8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951 + 8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297 + 8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901 + 9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955 + 9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674 + 9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214 + 9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704 + 9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669 + 9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122 + 9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490 + 9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553 + 9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394 + 9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233 + 10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695 +Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms + +Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s +131.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02 +Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04 +Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43 +Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47 +Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48 +Other | | 0.01361 | | | 3.56 + +Nlocal: 129 ave 129 max 129 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1867 ave 1867 max 1867 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 290 ave 290 max 290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 290 +Ave neighs/atom = 2.24806 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene b/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene new file mode 100644 index 0000000000..3a5f123633 --- /dev/null +++ b/examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene @@ -0,0 +1,192 @@ +LAMMPS (17 Nov 2016) +# Initialization +units metal +boundary p p p +atom_style atomic +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data data.bilayer-graphene # read lammps data file + orthogonal box = (0 0 -20) to (17.04 19.6761 40) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 256 atoms +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes +# Separate atom groups +group membrane type 1 +128 atoms in group membrane +group adsorbant type 2 +128 atoms in group adsorbant + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +#################################################################### +pair_coeff * * rebo CH.airebo C C # chemical +Reading potential file CH.airebo with DATE: 2011-10-25 +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range +#################################################################### + +#### Simulation settings #### +timestep 0.0001 +velocity all create 300.0 12345 +fix thermostat all nve +compute COM1 membrane com +compute COM2 adsorbant com +############################ + +# Output +#dump 1 all xyz 100 trajec.xyz +#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C" +thermo 10 +thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu +thermo_modify line one format float %14.8f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + 3 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8 -> bins = 3 3 8 +Memory usage per processor = 3.22197 Mbytes +Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] + 0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000 + 10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126 + 20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357 + 30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673 + 40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055 + 50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486 + 60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952 + 70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441 + 80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946 + 90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458 + 100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973 + 110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489 + 120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004 + 130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519 + 140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038 + 150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562 + 160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099 + 170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654 + 180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235 + 190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851 + 200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512 + 210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230 + 220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016 + 230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883 + 240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845 + 250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913 + 260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097 + 270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408 + 280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849 + 290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424 + 300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129 + 310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957 + 320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898 + 330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935 + 340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046 + 350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207 + 360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390 + 370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561 + 380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688 + 390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734 + 400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664 + 410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442 + 420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033 + 430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405 + 440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527 + 450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373 + 460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918 + 470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143 + 480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030 + 490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565 + 500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740 + 510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547 + 520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981 + 530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040 + 540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724 + 550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032 + 560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963 + 570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517 + 580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691 + 590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478 + 600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871 + 610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856 + 620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416 + 630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531 + 640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176 + 650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323 + 660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937 + 670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986 + 680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430 + 690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229 + 700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343 + 710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729 + 720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344 + 730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148 + 740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098 + 750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156 + 760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282 + 770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441 + 780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599 + 790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726 + 800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792 + 810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773 + 820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647 + 830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393 + 840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995 + 850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439 + 860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713 + 870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805 + 880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706 + 890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408 + 900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904 + 910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186 + 920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247 + 930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078 + 940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670 + 950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015 + 960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101 + 970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915 + 980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444 + 990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672 + 1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581 +Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms + +Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s +120.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25 +Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13 +Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12 +Other | | 0.008904 | | | 0.40 + +Nlocal: 64 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 11824 ave 11824 max 11824 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23648 ave 23648 max 23648 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 94592 +Ave neighs/atom = 369.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/srp/in.srp b/examples/USER/misc/srp/in.srp index 234026e9cb..018d916292 100644 --- a/examples/USER/misc/srp/in.srp +++ b/examples/USER/misc/srp/in.srp @@ -24,7 +24,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 -# auto normalization of thermo quantites is turned off by pair srp +# auto normalization of thermo quantities is turned off by pair srp # just divide by natoms variable natoms equal count(all) variable nPotEng equal c_thermo_pe/v_natoms diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README index 57e7be5394..235c66e256 100644 --- a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README +++ b/examples/USER/phonon/3-3D-FCC-Cu-EAM/README @@ -1,5 +1,5 @@ This directory illustrates the usage of fix-phonon to calculate the dynamical -matrix as well as phonon dispersion curve for FCC Cu based on EAM potentail. +matrix as well as phonon dispersion curve for FCC Cu based on EAM potential. The files under this directory: diff --git a/examples/USER/phonon/4-Graphene/README b/examples/USER/phonon/4-Graphene/README index 1e16f0af69..3791bc679c 100644 --- a/examples/USER/phonon/4-Graphene/README +++ b/examples/USER/phonon/4-Graphene/README @@ -1,5 +1,5 @@ This directory illustrates the usage of fix-phonon to calculate the dynamical -matrix as well as phonon dispersion curve for Graphene based on a Tersoff potentail. +matrix as well as phonon dispersion curve for Graphene based on a Tersoff potential. The files under this directory: diff --git a/examples/USER/tally/README b/examples/USER/tally/README index 4c2e40e76e..fcc58e6e0d 100644 --- a/examples/USER/tally/README +++ b/examples/USER/tally/README @@ -3,4 +3,4 @@ Examples and tests for USER-TALLY compute styles. The examples in this directory show where and how compute tally styles are equivalent to other facilities in LAMMPS and thus they can also be used to validate their correct function. Various columns should have -equivalent or idential output as indicated in the input. +equivalent or identical output as indicated in the input. diff --git a/examples/VISCOSITY/README b/examples/VISCOSITY/README index 88b874cd65..38bee0c58d 100644 --- a/examples/VISCOSITY/README +++ b/examples/VISCOSITY/README @@ -24,7 +24,7 @@ times; the G-K and Einstein systems need to run longer to generate good statisti The scripts were all run on a single processor. They all run in a minute or so and produce the accompanying log files and profile files -(for velocity or momemtum flux). +(for velocity or momentum flux). See the Movies page of the LAMMPS web site (http://lammps.sandia.gov/movies.html), for animations of the NEMD @@ -74,7 +74,7 @@ eta = 0.997 = running average output as last log file column eta is computed directly within the script, by performing a time integration of the formula discussed in Section 6.21 of the manual, -analagous to the formula for thermal conductivity given on the compute +analogous to the formula for thermal conductivity given on the compute heat/flux doc page - the resulting value prints at the end of the run and is in the log file @@ -84,7 +84,7 @@ eta = 1.07 eta is computed directly within the script, by performing a time integration of the formula discussed in Section 6.21 of the manual, -analagous to the formula for thermal conductivity given on the compute +analogous to the formula for thermal conductivity given on the compute heat/flux doc page - the resulting value prints at the end of the run and is in the log file diff --git a/examples/accelerate/README b/examples/accelerate/README index 2a494a1680..1fab296a53 100644 --- a/examples/accelerate/README +++ b/examples/accelerate/README @@ -130,7 +130,7 @@ lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj # 2 MPI, 4 thread/MPI Note that when running with just 1 thread/MPI, "-pk kokkos neigh half" -was speficied to use half neighbor lists which are faster when running +was specified to use half neighbor lists which are faster when running on just 1 thread. ** KOKKOS package for CUDA diff --git a/examples/rigid/in.rigid.tnr b/examples/rigid/in.rigid.tnr index 6be5ba529c..7d8d74b3cb 100644 --- a/examples/rigid/in.rigid.tnr +++ b/examples/rigid/in.rigid.tnr @@ -20,7 +20,7 @@ velocity all create 1.4 109345 group rods type 2 group tethers subtract all rods -neigh_modify exclude molecule rods delay 0 every 1 +neigh_modify exclude molecule/intra rods delay 0 every 1 # Specify the pair potentials diff --git a/potentials/Ta06A_pot.snap b/examples/snap/Ta06A.snap similarity index 100% rename from potentials/Ta06A_pot.snap rename to examples/snap/Ta06A.snap diff --git a/potentials/W_2940_2017_2.pot.snap b/examples/snap/W_2940_2017_2.snap similarity index 77% rename from potentials/W_2940_2017_2.pot.snap rename to examples/snap/W_2940_2017_2.snap index ea98d65c9e..51eee41a0a 100644 --- a/potentials/W_2940_2017_2.pot.snap +++ b/examples/snap/W_2940_2017_2.snap @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 diff --git a/examples/snap/W_2940_2017_2.snapcoeff b/examples/snap/W_2940_2017_2.snapcoeff index 98a5c50635..dcfea3feaf 100644 --- a/examples/snap/W_2940_2017_2.snapcoeff +++ b/examples/snap/W_2940_2017_2.snapcoeff @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # LAMMPS SNAP coefficients for W diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam index 7ff57c905d..e0b20005e6 100644 --- a/examples/snap/W_2940_2017_2.snapparam +++ b/examples/snap/W_2940_2017_2.snapparam @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # required rcutfac 4.73442 diff --git a/examples/snap/W.SNAP_HePair.pot b/examples/snap/W_2940_2017_2_He_JW2013.snap similarity index 82% rename from examples/snap/W.SNAP_HePair.pot rename to examples/snap/W_2940_2017_2_He_JW2013.snap index eb5ee4dfbe..45a31955b3 100644 --- a/examples/snap/W.SNAP_HePair.pot +++ b/examples/snap/W_2940_2017_2_He_JW2013.snap @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 diff --git a/examples/snap/in.snap.Ta06A b/examples/snap/in.snap.Ta06A index fc0b122948..38a24b8c06 100644 --- a/examples/snap/in.snap.Ta06A +++ b/examples/snap/in.snap.Ta06A @@ -24,7 +24,7 @@ mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # Setup output diff --git a/examples/snap/in.snap.W.2940 b/examples/snap/in.snap.W.2940 index 7d81b4c78e..e1abf861e6 100644 --- a/examples/snap/in.snap.W.2940 +++ b/examples/snap/in.snap.W.2940 @@ -24,7 +24,7 @@ mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap +include W_2940_2017_2.snap # Setup output diff --git a/examples/snap/in.snap.hybrid.WSNAP.HePair b/examples/snap/in.snap.hybrid.WSNAP.HePair index d2710bca77..1f16fa64a2 100644 --- a/examples/snap/in.snap.hybrid.WSNAP.HePair +++ b/examples/snap/in.snap.hybrid.WSNAP.HePair @@ -27,7 +27,7 @@ group tungsten type 1 group helium type 2 # choose potential -include W.SNAP_HePair.pot +include W_2940_2017_2_He_JW2013.snap # Setup output diff --git a/lib/atc/LinearSolver.cpp b/lib/atc/LinearSolver.cpp index ea31a64a74..655d6130c4 100644 --- a/lib/atc/LinearSolver.cpp +++ b/lib/atc/LinearSolver.cpp @@ -65,7 +65,7 @@ LinearSolver::LinearSolver( matrixModified_(false), allowReinitialization_(false), homogeneousBCs_(false), - bcs_(NULL), // null implies no contraints will be added later + bcs_(NULL), // null implies no constraints will be added later rhs_(NULL), rhsDense_(), b_(NULL), matrix_(A), diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index d60a9e90f7..e8c7e88324 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -1,5 +1,5 @@ -// -*- c++ -*- +// -*- c++ -*- // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars @@ -7,6 +7,7 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -23,20 +24,31 @@ bool compare(colvar::cvc *i, colvar::cvc *j) { } -colvar::colvar(std::string const &conf) - : colvarparse(conf) +colvar::colvar() +{ + // Initialize static array once and for all + init_cv_requires(); +} + + +int colvar::init(std::string const &conf) { cvm::log("Initializing a new collective variable.\n"); + colvarparse::init(conf); + int error_code = COLVARS_OK; - get_keyval(conf, "name", this->name, - (std::string("colvar")+cvm::to_str(cvm::colvars.size()+1))); + colvarmodule *cv = cvm::main(); - if (cvm::colvar_by_name(this->name) != NULL) { + get_keyval(conf, "name", this->name, + (std::string("colvar")+cvm::to_str(cv->variables()->size()+1))); + + if ((cvm::colvar_by_name(this->name) != NULL) && + (cvm::colvar_by_name(this->name) != this)) { cvm::error("Error: this colvar cannot have the same name, \""+this->name+ "\", as another colvar.\n", INPUT_ERROR); - return; + return INPUT_ERROR; } // Initialize dependency members @@ -44,14 +56,13 @@ colvar::colvar(std::string const &conf) this->description = "colvar " + this->name; - // Initialize static array once and for all - init_cv_requires(); - kinetic_energy = 0.0; potential_energy = 0.0; error_code |= init_components(conf); - if (error_code != COLVARS_OK) return; + if (error_code != COLVARS_OK) { + return cvm::get_error(); + } size_t i; @@ -59,8 +70,6 @@ colvar::colvar(std::string const &conf) if (get_keyval(conf, "scriptedFunction", scripted_function, "", colvarparse::parse_silent)) { - // Make feature available only on user request - provide(f_cv_scripted); enable(f_cv_scripted); cvm::log("This colvar uses scripted function \"" + scripted_function + "\"."); @@ -76,8 +85,8 @@ colvar::colvar(std::string const &conf) } } if (x.type() == colvarvalue::type_notset) { - cvm::error("Could not parse scripted colvar type."); - return; + cvm::error("Could not parse scripted colvar type.", INPUT_ERROR); + return INPUT_ERROR; } cvm::log(std::string("Expecting colvar value of type ") @@ -86,8 +95,9 @@ colvar::colvar(std::string const &conf) if (x.type() == colvarvalue::type_vector) { int size; if (!get_keyval(conf, "scriptedFunctionVectorSize", size)) { - cvm::error("Error: no size specified for vector scripted function."); - return; + cvm::error("Error: no size specified for vector scripted function.", + INPUT_ERROR); + return INPUT_ERROR; } x.vector1d_value.resize(size); } @@ -154,7 +164,7 @@ colvar::colvar(std::string const &conf) } } } - feature_states[f_cv_linear]->enabled = lin; + set_enabled(f_cv_linear, lin); } // Colvar is homogeneous if: @@ -168,7 +178,7 @@ colvar::colvar(std::string const &conf) homogeneous = false; } } - feature_states[f_cv_homogeneous]->enabled = homogeneous; + set_enabled(f_cv_homogeneous, homogeneous); } // Colvar is deemed periodic if: @@ -188,7 +198,7 @@ colvar::colvar(std::string const &conf) "Make sure that you know what you are doing!"); } } - feature_states[f_cv_periodic]->enabled = b_periodic; + set_enabled(f_cv_periodic, b_periodic); } // check that cvcs are compatible @@ -202,7 +212,7 @@ colvar::colvar(std::string const &conf) "by using components of different types. " "You must use the same type in order to " "sum them together.\n", INPUT_ERROR); - return; + return INPUT_ERROR; } } @@ -215,44 +225,110 @@ colvar::colvar(std::string const &conf) f.type(value()); f_accumulated.type(value()); + x_old.type(value()); + v_fdiff.type(value()); + v_reported.type(value()); + fj.type(value()); + ft.type(value()); + ft_reported.type(value()); + f_old.type(value()); + f_old.reset(); + + x_restart.type(value()); + after_restart = false; + reset_bias_force(); + // TODO use here information from the CVCs' own natural boundaries + error_code |= init_grid_parameters(conf); + + get_keyval(conf, "timeStepFactor", time_step_factor, 1); + + error_code |= init_extended_Lagrangian(conf); + error_code |= init_output_flags(conf); + + // Start in active state by default + enable(f_cv_active); + // Make sure dependency side-effects are correct + refresh_deps(); + + if (cvm::b_analysis) + parse_analysis(conf); + + if (cvm::debug()) + cvm::log("Done initializing collective variable \""+this->name+"\".\n"); + + return error_code; +} + + +int colvar::init_grid_parameters(std::string const &conf) +{ + colvarmodule *cv = cvm::main(); + get_keyval(conf, "width", width, 1.0); if (width <= 0.0) { cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR); - return; + return INPUT_ERROR; } lower_boundary.type(value()); - lower_wall.type(value()); upper_boundary.type(value()); upper_wall.type(value()); - feature_states[f_cv_scalar]->enabled = (value().type() == colvarvalue::type_scalar); + set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); if (is_enabled(f_cv_scalar)) { if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) { - provide(f_cv_lower_boundary); enable(f_cv_lower_boundary); } + std::string lw_conf, uw_conf; - get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0); - if (lower_wall_k > 0.0) { + if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) { + cvm::log("Warning: lowerWallConstant and lowerWall are deprecated, " + "please define a harmonicWalls bias instead.\n"); + lower_wall.type(value()); get_keyval(conf, "lowerWall", lower_wall, lower_boundary); - enable(f_cv_lower_wall); + lw_conf = std::string("\n\ + lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\ + lowerWalls "+cvm::to_str(lower_wall)+"\n"); } if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) { - provide(f_cv_upper_boundary); enable(f_cv_upper_boundary); } - get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0); - if (upper_wall_k > 0.0) { + if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) { + cvm::log("Warning: upperWallConstant and upperWall are deprecated, " + "please define a harmonicWalls bias instead.\n"); + upper_wall.type(value()); get_keyval(conf, "upperWall", upper_wall, upper_boundary); - enable(f_cv_upper_wall); + uw_conf = std::string("\n\ + upperWallConstant "+cvm::to_str(upper_wall_k*width*width)+"\n\ + upperWalls "+cvm::to_str(upper_wall)+"\n"); + } + + if (lw_conf.size() && uw_conf.size()) { + if (lower_wall >= upper_wall) { + cvm::error("Error: the upper wall, "+ + cvm::to_str(upper_wall)+ + ", is not higher than the lower wall, "+ + cvm::to_str(lower_wall)+".\n", + INPUT_ERROR); + return INPUT_ERROR; + } + } + + if (lw_conf.size() || uw_conf.size()) { + cvm::log("Generating a new harmonicWalls bias for compatibility purposes.\n"); + std::string const walls_conf("\n\ +harmonicWalls {\n\ + name "+this->name+"w\n\ + colvars "+this->name+"\n"+lw_conf+uw_conf+ + "}\n"); + cv->append_new_config(walls_conf); } } @@ -271,16 +347,7 @@ colvar::colvar(std::string const &conf) ", is not higher than the lower boundary, "+ cvm::to_str(lower_boundary)+".\n", INPUT_ERROR); - } - } - - if (is_enabled(f_cv_lower_wall) && is_enabled(f_cv_upper_wall)) { - if (lower_wall >= upper_wall) { - cvm::error("Error: the upper wall, "+ - cvm::to_str(upper_wall)+ - ", is not higher than the lower wall, "+ - cvm::to_str(lower_wall)+".\n", - INPUT_ERROR); + return INPUT_ERROR; } } @@ -289,83 +356,90 @@ colvar::colvar(std::string const &conf) cvm::error("Error: trying to expand boundaries that already " "cover a whole period of a periodic colvar.\n", INPUT_ERROR); + return INPUT_ERROR; } if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) { cvm::error("Error: inconsistent configuration " "(trying to expand boundaries with both " "hardLowerBoundary and hardUpperBoundary enabled).\n", INPUT_ERROR); + return INPUT_ERROR; } - get_keyval(conf, "timeStepFactor", time_step_factor, 1); + return COLVARS_OK; +} - { - bool b_extended_Lagrangian; - get_keyval(conf, "extendedLagrangian", b_extended_Lagrangian, false); - if (b_extended_Lagrangian) { - cvm::real temp, tolerance, period; +int colvar::init_extended_Lagrangian(std::string const &conf) +{ + bool b_extended_Lagrangian; + get_keyval(conf, "extendedLagrangian", b_extended_Lagrangian, false); - cvm::log("Enabling the extended Lagrangian term for colvar \""+ - this->name+"\".\n"); + if (b_extended_Lagrangian) { + cvm::real temp, tolerance, period; - // Make feature available only on user request - provide(f_cv_extended_Lagrangian); - enable(f_cv_extended_Lagrangian); - provide(f_cv_Langevin); + cvm::log("Enabling the extended Lagrangian term for colvar \""+ + this->name+"\".\n"); - // The extended mass will apply forces - enable(f_cv_gradient); + enable(f_cv_extended_Lagrangian); - xr.type(value()); - vr.type(value()); - fr.type(value()); + xr.type(value()); + vr.type(value()); + fr.type(value()); - const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature()); - if (temp <= 0.0) { - if (found) - cvm::error("Error: \"extendedTemp\" must be positive.\n", INPUT_ERROR); - else - cvm::error("Error: a positive temperature must be provided, either " - "by enabling a thermostat, or through \"extendedTemp\".\n", - INPUT_ERROR); + const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature()); + if (temp <= 0.0) { + if (found) + cvm::error("Error: \"extendedTemp\" must be positive.\n", INPUT_ERROR); + else + cvm::error("Error: a positive temperature must be provided, either " + "by enabling a thermostat, or through \"extendedTemp\".\n", + INPUT_ERROR); + return INPUT_ERROR; + } + + get_keyval(conf, "extendedFluctuation", tolerance); + if (tolerance <= 0.0) { + cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR); + return INPUT_ERROR; + } + ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance); + cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2"); + + get_keyval(conf, "extendedTimeConstant", period, 200.0); + if (period <= 0.0) { + cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR); + } + ext_mass = (cvm::boltzmann() * temp * period * period) + / (4.0 * PI * PI * tolerance * tolerance); + cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)"); + + { + bool b_output_energy; + get_keyval(conf, "outputEnergy", b_output_energy, false); + if (b_output_energy) { + enable(f_cv_output_energy); } + } - get_keyval(conf, "extendedFluctuation", tolerance); - if (tolerance <= 0.0) { - cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR); - } - ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance); - cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2"); - - get_keyval(conf, "extendedTimeConstant", period, 200.0); - if (period <= 0.0) { - cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR); - } - ext_mass = (cvm::boltzmann() * temp * period * period) - / (4.0 * PI * PI * tolerance * tolerance); - cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)"); - - { - bool b_output_energy; - get_keyval(conf, "outputEnergy", b_output_energy, false); - if (b_output_energy) { - enable(f_cv_output_energy); - } - } - - get_keyval(conf, "extendedLangevinDamping", ext_gamma, 1.0); - if (ext_gamma < 0.0) { - cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR); - } - if (ext_gamma != 0.0) { - enable(f_cv_Langevin); - ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1 - ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt()); - } + get_keyval(conf, "extendedLangevinDamping", ext_gamma, 1.0); + if (ext_gamma < 0.0) { + cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR); + return INPUT_ERROR; + } + if (ext_gamma != 0.0) { + enable(f_cv_Langevin); + ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1 + ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt()); } } + return COLVARS_OK; +} + + +int colvar::init_output_flags(std::string const &conf) +{ { bool b_output_value; get_keyval(conf, "outputValue", b_output_value, true); @@ -387,7 +461,7 @@ colvar::colvar(std::string const &conf) if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) { cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n" "The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR); - return; + return INPUT_ERROR; } } @@ -395,28 +469,7 @@ colvar::colvar(std::string const &conf) get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false); get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false); - // Start in active state by default - enable(f_cv_active); - // Make sure dependency side-effects are correct - refresh_deps(); - - x_old.type(value()); - v_fdiff.type(value()); - v_reported.type(value()); - fj.type(value()); - ft.type(value()); - ft_reported.type(value()); - f_old.type(value()); - f_old.reset(); - - x_restart.type(value()); - after_restart = false; - - if (cvm::b_analysis) - parse_analysis(conf); - - if (cvm::debug()) - cvm::log("Done initializing collective variable \""+this->name+"\".\n"); + return COLVARS_OK; } @@ -637,7 +690,7 @@ int colvar::parse_analysis(std::string const &conf) std::string runave_outfile; get_keyval(conf, "runAveOutputFile", runave_outfile, - std::string(cvm::output_prefix+"."+ + std::string(cvm::output_prefix()+"."+ this->name+".runave.traj")); size_t const this_cv_width = x.output_width(cvm::cv_width); @@ -693,7 +746,7 @@ int colvar::parse_analysis(std::string const &conf) get_keyval(conf, "corrFuncNormalize", acf_normalize, true); get_keyval(conf, "corrFuncOutputFile", acf_outfile, - std::string(cvm::output_prefix+"."+this->name+ + std::string(cvm::output_prefix()+"."+this->name+ ".corrfunc.dat")); } return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); @@ -730,11 +783,12 @@ colvar::~colvar() } // remove reference to this colvar from the CVM - for (std::vector::iterator cvi = cvm::colvars.begin(); - cvi != cvm::colvars.end(); + colvarmodule *cv = cvm::main(); + for (std::vector::iterator cvi = cv->variables()->begin(); + cvi != cv->variables()->end(); ++cvi) { if ( *cvi == this) { - cvm::colvars.erase(cvi); + cv->variables()->erase(cvi); break; } } @@ -892,7 +946,6 @@ int colvar::collect_cvc_values() cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n"); if (after_restart) { - after_restart = false; if (cvm::proxy->simulation_running()) { cvm::real const jump2 = dist2(x, x_restart) / (width*width); if (jump2 > 0.25) { @@ -1122,8 +1175,7 @@ int colvar::calc_colvar_properties() // initialize the restraint center in the first step to the value // just calculated from the cvcs - // TODO: put it in the restart information - if (cvm::step_relative() == 0) { + if (cvm::step_relative() == 0 && !after_restart) { xr = x; vr.reset(); // (already 0; added for clarity) } @@ -1148,6 +1200,8 @@ int colvar::calc_colvar_properties() ft_reported = ft; } + // At the end of the first update after a restart, we can reset the flag + after_restart = false; return COLVARS_OK; } @@ -1173,51 +1227,17 @@ cvm::real colvar::update_forces_energy() f -= fj; } - // Wall force - colvarvalue fw(x); - fw.reset(); - - if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) { - - if (cvm::debug()) - cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n"); - - // For a periodic colvar, both walls may be applicable at the same time - // in which case we pick the closer one - if ( (!is_enabled(f_cv_upper_wall)) || - (this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) { - - cvm::real const grad = this->dist2_lgrad(x, lower_wall); - if (grad < 0.0) { - fw = -0.5 * lower_wall_k * grad; - if (cvm::debug()) - cvm::log("Applying a lower wall force("+ - cvm::to_str(fw)+") to \""+this->name+"\".\n"); - } - - } else { - - cvm::real const grad = this->dist2_lgrad(x, upper_wall); - if (grad > 0.0) { - fw = -0.5 * upper_wall_k * grad; - if (cvm::debug()) - cvm::log("Applying an upper wall force("+ - cvm::to_str(fw)+") to \""+this->name+"\".\n"); - } - } - } - // At this point f is the force f from external biases that will be applied to the // extended variable if there is one if (is_enabled(f_cv_extended_Lagrangian)) { if (cvm::debug()) { - cvm::log("Updating extended-Lagrangian degrees of freedom.\n"); + cvm::log("Updating extended-Lagrangian degree of freedom.\n"); } cvm::real dt = cvm::dt(); - colvarvalue f_ext(fr.type()); + colvarvalue f_ext(fr.type()); // force acting on the extended variable f_ext.reset(); // the total force is applied to the fictitious mass, while the @@ -1226,7 +1246,7 @@ cvm::real colvar::update_forces_energy() // f_ext: total force on extended variable (including harmonic spring) // f: - initially, external biasing force // - after this code block, colvar force to be applied to atomic coordinates - // ie. spring force + wall force + // ie. spring force (fb_actual will be added just below) fr = f; f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x); f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x); @@ -1259,8 +1279,6 @@ cvm::real colvar::update_forces_energy() if (this->is_enabled(f_cv_periodic)) this->wrap(xr); } - // TODO remove the wall force - f += fw; // Now adding the force on the actual colvar (for those biases who // bypass the extended Lagrangian mass) f += fb_actual; @@ -1286,8 +1304,10 @@ cvm::real colvar::update_forces_energy() void colvar::communicate_forces() { size_t i; - if (cvm::debug()) + if (cvm::debug()) { cvm::log("Communicating forces from colvar \""+this->name+"\".\n"); + cvm::log("Force to be applied: " + cvm::to_str(f_accumulated) + "\n"); + } if (is_enabled(f_cv_scripted)) { std::vector > func_grads; @@ -1364,7 +1384,7 @@ int colvar::update_cvc_flags() active_cvc_square_norm = 0.; for (size_t i = 0; i < cvcs.size(); i++) { - cvcs[i]->feature_states[f_cvc_active]->enabled = cvc_flags[i]; + cvcs[i]->set_enabled(f_cvc_active, cvc_flags[i]); if (cvcs[i]->is_enabled()) { n_active_cvcs++; active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff; diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 2cf3d2dac5..0cbda450b8 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -227,11 +227,23 @@ public: /// Constructor - colvar(std::string const &conf); + colvar(); + + /// Main init function + int init(std::string const &conf); /// Parse the CVC configuration and allocate their data int init_components(std::string const &conf); + /// Init defaults for grid options + int init_grid_parameters(std::string const &conf); + + /// Init extended Lagrangian parameters + int init_extended_Lagrangian(std::string const &conf); + + /// Init output flags + int init_output_flags(std::string const &conf); + private: /// Parse the CVC configuration for all components of a certain type template int init_components_type(std::string const &conf, diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 48c16e887a..32cfadf3b6 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -98,7 +98,7 @@ cvm::atom_group::atom_group() cvm::atom_group::~atom_group() { - if (is_enabled(f_ag_scalable)) { + if (is_enabled(f_ag_scalable) && !b_dummy) { (cvm::proxy)->clear_atom_group(index); index = -1; } @@ -418,7 +418,7 @@ int cvm::atom_group::parse(std::string const &conf) // We need to know the fitting options to decide whether the group is scalable parse_error |= parse_fitting_options(group_conf); - if (is_available(f_ag_scalable_com) && !b_rotate) { + if (is_available(f_ag_scalable_com) && !b_rotate && !b_center) { enable(f_ag_scalable_com); enable(f_ag_scalable); } @@ -500,14 +500,16 @@ int cvm::atom_group::add_atom_numbers(std::string const &numbers_conf) int cvm::atom_group::add_index_group(std::string const &index_group_name) { - std::list::iterator names_i = cvm::index_group_names.begin(); - std::list >::iterator index_groups_i = cvm::index_groups.begin(); - for ( ; names_i != cvm::index_group_names.end() ; ++names_i, ++index_groups_i) { + colvarmodule *cv = cvm::main(); + + std::list::iterator names_i = cv->index_group_names.begin(); + std::list >::iterator index_groups_i = cv->index_groups.begin(); + for ( ; names_i != cv->index_group_names.end() ; ++names_i, ++index_groups_i) { if (*names_i == index_group_name) break; } - if (names_i == cvm::index_group_names.end()) { + if (names_i == cv->index_group_names.end()) { cvm::error("Error: could not find index group "+ index_group_name+" among those provided by the index file.\n", INPUT_ERROR); diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp index fdd2b6254c..3779c82aa3 100644 --- a/lib/colvars/colvarbias.cpp +++ b/lib/colvars/colvarbias.cpp @@ -19,20 +19,6 @@ colvarbias::colvarbias(char const *key) rank = 1; - if (bias_type == std::string("abf")) { - rank = cvm::n_abf_biases+1; - } - if (bias_type == std::string("harmonic") || - bias_type == std::string("linear")) { - rank = cvm::n_rest_biases+1; - } - if (bias_type == std::string("histogram")) { - rank = cvm::n_histo_biases+1; - } - if (bias_type == std::string("metadynamics")) { - rank = cvm::n_meta_biases+1; - } - has_data = false; b_output_energy = false; reset(); @@ -48,7 +34,11 @@ int colvarbias::init(std::string const &conf) colvarparse::init(conf); if (name.size() == 0) { + + // first initialization + cvm::log("Initializing a new \""+bias_type+"\" instance.\n"); + rank = cvm::num_biases_type(bias_type); get_keyval(conf, "name", name, bias_type+cvm::to_str(rank)); { @@ -69,7 +59,7 @@ int colvarbias::init(std::string const &conf) // lookup the associated colvars std::vector colvar_names; if (get_keyval(conf, "colvars", colvar_names)) { - if (colvars.size()) { + if (num_variables()) { cvm::error("Error: cannot redefine the colvars that a bias was already defined on.\n", INPUT_ERROR); return INPUT_ERROR; @@ -80,7 +70,7 @@ int colvarbias::init(std::string const &conf) } } - if (!colvars.size()) { + if (!num_variables()) { cvm::error("Error: no collective variables specified.\n", INPUT_ERROR); return INPUT_ERROR; } @@ -89,6 +79,8 @@ int colvarbias::init(std::string const &conf) cvm::log("Reinitializing bias \""+name+"\".\n"); } + output_prefix = cvm::output_prefix(); + get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy); return COLVARS_OK; @@ -98,7 +90,7 @@ int colvarbias::init(std::string const &conf) int colvarbias::reset() { bias_energy = 0.0; - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { colvar_forces[i].reset(); } return COLVARS_OK; @@ -132,12 +124,13 @@ int colvarbias::clear() } } + colvarmodule *cv = cvm::main(); // ...and from the colvars module - for (std::vector::iterator bi = cvm::biases.begin(); - bi != cvm::biases.end(); + for (std::vector::iterator bi = cv->biases.begin(); + bi != cv->biases.end(); ++bi) { if ( *bi == this) { - cvm::biases.erase(bi); + cv->biases.erase(bi); break; } } @@ -185,21 +178,29 @@ int colvarbias::add_colvar(std::string const &cv_name) int colvarbias::update() { - // Note: if anything is added here, it should be added also in the SMP block of calc_biases() - // TODO move here debug msg of bias update + if (cvm::debug()) { + cvm::log("Updating the "+bias_type+" bias \""+this->name+"\".\n"); + } + has_data = true; + + bias_energy = 0.0; + for (size_t ir = 0; ir < num_variables(); ir++) { + colvar_forces[ir].reset(); + } + return COLVARS_OK; } void colvarbias::communicate_forces() { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { if (cvm::debug()) { cvm::log("Communicating a force to colvar \""+ - colvars[i]->name+"\".\n"); + variables(i)->name+"\".\n"); } - colvars[i]->add_bias_force(colvar_forces[i]); + variables(i)->add_bias_force(colvar_forces[i]); } } diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h index 12397dcb8f..6d5776d3db 100644 --- a/lib/colvars/colvarbias.h +++ b/lib/colvars/colvarbias.h @@ -32,17 +32,39 @@ public: /// Add a new collective variable to this bias int add_colvar(std::string const &cv_name); - /// Add a new collective variable to this bias - size_t number_of_colvars() const + /// How many variables are defined for this bias + inline size_t num_variables() const { return colvars.size(); } + /// Access the variables vector + inline std::vector *variables() + { + return &colvars; + } + + /// Access the i-th variable + inline colvar * variables(int i) const + { + return colvars[i]; + } + /// Retrieve colvar values and calculate their biasing forces /// Return bias energy virtual int update(); - // TODO: move update_bias here (share with metadynamics) + /// \brief Compute the energy of the bias with alternative values of the + /// collective variables (suitable for bias exchange) + virtual int calc_energy(std::vector const &values = + std::vector(0)) + { + cvm::error("Error: calc_energy() not implemented.\n", COLVARS_NOT_IMPLEMENTED); + return COLVARS_NOT_IMPLEMENTED; + } + + /// Send forces to the collective variables + virtual void communicate_forces(); /// Load new configuration - force constant and/or centers only virtual int change_configuration(std::string const &conf); @@ -51,10 +73,13 @@ public: virtual cvm::real energy_difference(std::string const &conf); /// Give the total number of bins for a given bias. + // FIXME this is currently 1D only virtual int bin_num(); /// Calculate the bin index for a given bias. + // FIXME this is currently 1D only virtual int current_bin(); //// Give the count at a given bin index. + // FIXME this is currently 1D only virtual int bin_count(int bin_index); //// Share information between replicas, whatever it may be. virtual int replica_share(); @@ -62,9 +87,6 @@ public: /// Perform analysis tasks virtual void analyze() {} - /// Send forces to the collective variables - virtual void communicate_forces(); - /// \brief Constructor colvarbias(char const *key); @@ -135,6 +157,9 @@ public: return COLVARS_OK; } + /// Use this prefix for all output files + std::string output_prefix; + /// If this bias is communicating with other replicas through files, send it to them virtual int write_state_to_replicas() { @@ -162,7 +187,7 @@ protected: /// through each colvar object std::vector colvars; - /// \brief Current forces from this bias to the colvars + /// \brief Current forces from this bias to the variables std::vector colvar_forces; /// \brief Current energy of this bias (colvar_forces should be obtained by deriving this) diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index ccfa401697..d039004f09 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -30,9 +30,8 @@ int colvarbias_abf::init(std::string const &conf) { colvarbias::init(conf); - provide(f_cvb_scalar_variables); enable(f_cvb_scalar_variables); - provide(f_cvb_history_dependent); + enable(f_cvb_calc_pmf); // TODO relax this in case of VMD plugin if (cvm::temperature() == 0.0) @@ -221,9 +220,6 @@ colvarbias_abf::~colvarbias_abf() delete [] system_force; system_force = NULL; } - - if (cvm::n_abf_biases > 0) - cvm::n_abf_biases -= 1; } @@ -319,11 +315,11 @@ int colvarbias_abf::update() } // update the output prefix; TODO: move later to setup_output() function - if ( cvm::n_abf_biases == 1 && cvm::n_meta_biases == 0 ) { - // This is the only ABF bias - output_prefix = cvm::output_prefix; + if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) { + // This is the only bias computing PMFs + output_prefix = cvm::output_prefix(); } else { - output_prefix = cvm::output_prefix + "." + this->name; + output_prefix = cvm::output_prefix() + "." + this->name; } if (output_freq && (cvm::step_absolute() % output_freq) == 0) { diff --git a/lib/colvars/colvarbias_alb.cpp b/lib/colvars/colvarbias_alb.cpp index 9e414d4db4..d096ac3daf 100644 --- a/lib/colvars/colvarbias_alb.cpp +++ b/lib/colvars/colvarbias_alb.cpp @@ -40,11 +40,8 @@ int colvarbias_alb::init(std::string const &conf) { colvarbias::init(conf); - provide(f_cvb_scalar_variables); enable(f_cvb_scalar_variables); - provide(f_cvb_history_dependent); - size_t i; // get the initial restraint centers @@ -138,8 +135,6 @@ int colvarbias_alb::init(std::string const &conf) colvarbias_alb::~colvarbias_alb() { - if (cvm::n_rest_biases > 0) - cvm::n_rest_biases -= 1; } diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp index 900ad213d5..502a7455b1 100644 --- a/lib/colvars/colvarbias_histogram.cpp +++ b/lib/colvars/colvarbias_histogram.cpp @@ -24,10 +24,7 @@ int colvarbias_histogram::init(std::string const &conf) { colvarbias::init(conf); - provide(f_cvb_scalar_variables); enable(f_cvb_scalar_variables); - - provide(f_cvb_history_dependent); enable(f_cvb_history_dependent); size_t i; @@ -104,9 +101,6 @@ colvarbias_histogram::~colvarbias_histogram() delete grid; grid = NULL; } - - if (cvm::n_histo_biases > 0) - cvm::n_histo_biases -= 1; } @@ -127,14 +121,14 @@ int colvarbias_histogram::update() // At the first timestep, we need to assign out_name since // output_prefix is unset during the constructor if (cvm::step_relative() == 0) { - out_name = cvm::output_prefix + "." + this->name + ".dat"; + out_name = cvm::output_prefix() + "." + this->name + ".dat"; cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\""); } } if (out_name_dx.size() == 0) { if (cvm::step_relative() == 0) { - out_name_dx = cvm::output_prefix + "." + this->name + ".dx"; + out_name_dx = cvm::output_prefix() + "." + this->name + ".dx"; cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\""); } } diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp index 01a04d1a01..b0acfe974a 100644 --- a/lib/colvars/colvarbias_meta.cpp +++ b/lib/colvars/colvarbias_meta.cpp @@ -43,7 +43,7 @@ int colvarbias_meta::init(std::string const &conf) { colvarbias::init(conf); - provide(f_cvb_history_dependent); + enable(f_cvb_calc_pmf); get_keyval(conf, "hillWeight", hill_weight, 0.0); if (hill_weight > 0.0) { @@ -59,9 +59,9 @@ int colvarbias_meta::init(std::string const &conf) get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0); cvm::log("Half-widths of the Gaussian hills (sigma's):\n"); - for (size_t i = 0; i < colvars.size(); i++) { - cvm::log(colvars[i]->name+std::string(": ")+ - cvm::to_str(0.5 * colvars[i]->width * hill_width)); + for (size_t i = 0; i < num_variables(); i++) { + cvm::log(variables(i)->name+std::string(": ")+ + cvm::to_str(0.5 * variables(i)->width * hill_width)); } { @@ -73,8 +73,10 @@ int colvarbias_meta::init(std::string const &conf) comm = single_replica; } - // This implies gradients for all colvars - enable(f_cvb_apply_force); + // in all cases, the first replica is this bias itself + if (replicas.size() == 0) { + replicas.push_back(this); + } get_keyval(conf, "useGrids", use_grids, true); @@ -84,14 +86,14 @@ int colvarbias_meta::init(std::string const &conf) expand_grids = false; size_t i; - for (i = 0; i < colvars.size(); i++) { - colvars[i]->enable(f_cv_grid); - if (colvars[i]->expand_boundaries) { + for (i = 0; i < num_variables(); i++) { + variables(i)->enable(f_cv_grid); + if (variables(i)->expand_boundaries) { expand_grids = true; cvm::log("Metadynamics bias \""+this->name+"\""+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ ": Will expand grids when the colvar \""+ - colvars[i]->name+"\" approaches its boundaries.\n"); + variables(i)->name+"\" approaches its boundaries.\n"); } } @@ -100,7 +102,7 @@ int colvarbias_meta::init(std::string const &conf) get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent); if (get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false, colvarparse::parse_silent)) { cvm::log("Option \"saveFreeEnergyFile\" is deprecated, " - "please use \"keepFreeEnergyFiles\" instead."); + "please use \"keepFreeEnergyFile\" instead."); } get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save); @@ -154,6 +156,20 @@ int colvarbias_meta::init(std::string const &conf) get_keyval(conf, "writeHillsTrajectory", b_hills_traj, false); + init_well_tempered_params(conf); + init_ebmeta_params(conf); + + if (cvm::debug()) + cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); + + save_delimiters = false; + return COLVARS_OK; +} + + +int colvarbias_meta::init_well_tempered_params(std::string const &conf) +{ // for well-tempered metadynamics get_keyval(conf, "wellTempered", well_tempered, false); get_keyval(conf, "biasTemperature", bias_temperature, -1.0); @@ -164,8 +180,12 @@ int colvarbias_meta::init(std::string const &conf) cvm::log("Well-tempered metadynamics is used.\n"); cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n"); } + return COLVARS_OK; +} +int colvarbias_meta::init_ebmeta_params(std::string const &conf) +{ // for ebmeta target_dist = NULL; get_keyval(conf, "ebMeta", ebmeta, false); @@ -203,11 +223,6 @@ int colvarbias_meta::init(std::string const &conf) get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, 0); } - if (cvm::debug()) - cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); - - save_delimiters = false; return COLVARS_OK; } @@ -234,9 +249,6 @@ colvarbias_meta::~colvarbias_meta() delete target_dist; target_dist = NULL; } - - if (cvm::n_meta_biases > 0) - cvm::n_meta_biases -= 1; } @@ -314,23 +326,45 @@ colvarbias_meta::delete_hill(hill_iter &h) int colvarbias_meta::update() { - if (cvm::debug()) - cvm::log("Updating the metadynamics bias \""+this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); + int error_code = COLVARS_OK; + // update base class + error_code |= colvarbias::update(); + + // update grid definition, if needed + error_code |= update_grid_params(); + // add new biasing energy/forces + error_code |= update_bias(); + // update grid content to reflect new bias + error_code |= update_grid_data(); + + if (comm != single_replica && + (cvm::step_absolute() % replica_update_freq) == 0) { + // sync with the other replicas (if needed) + error_code |= replica_share(); + } + + error_code |= calc_energy(); + error_code |= calc_forces(); + + return error_code; +} + + +int colvarbias_meta::update_grid_params() +{ if (use_grids) { std::vector curr_bin = hills_energy->get_colvars_index(); + if (cvm::debug()) { + cvm::log("Metadynamics bias \""+this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ + ": current coordinates on the grid: "+ + cvm::to_str(curr_bin)+".\n"); + } if (expand_grids) { - // first of all, expand the grids, if specified - if (cvm::debug()) - cvm::log("Metadynamics bias \""+this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ - ": current coordinates on the grid: "+ - cvm::to_str(curr_bin)+".\n"); - bool changed_grids = false; int const min_buffer = (3 * (size_t) std::floor(hill_width)) + 1; @@ -339,9 +373,9 @@ int colvarbias_meta::update() std::vector new_lower_boundaries(hills_energy->lower_boundaries); std::vector new_upper_boundaries(hills_energy->upper_boundaries); - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { - if (! colvars[i]->expand_boundaries) + if (! variables(i)->expand_boundaries) continue; cvm::real &new_lb = new_lower_boundaries[i].real_value; @@ -349,10 +383,10 @@ int colvarbias_meta::update() int &new_size = new_sizes[i]; bool changed_lb = false, changed_ub = false; - if (!colvars[i]->hard_lower_boundary) + if (!variables(i)->hard_lower_boundary) if (curr_bin[i] < min_buffer) { int const extra_points = (min_buffer - curr_bin[i]); - new_lb -= extra_points * colvars[i]->width; + new_lb -= extra_points * variables(i)->width; new_size += extra_points; // changed offset in this direction => the pointer needs to // be changed, too @@ -362,21 +396,21 @@ int colvarbias_meta::update() cvm::log("Metadynamics bias \""+this->name+"\""+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ ": new lower boundary for colvar \""+ - colvars[i]->name+"\", at "+ + variables(i)->name+"\", at "+ cvm::to_str(new_lower_boundaries[i])+".\n"); } - if (!colvars[i]->hard_upper_boundary) + if (!variables(i)->hard_upper_boundary) if (curr_bin[i] > new_size - min_buffer - 1) { int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer); - new_ub += extra_points * colvars[i]->width; + new_ub += extra_points * variables(i)->width; new_size += extra_points; changed_ub = true; cvm::log("Metadynamics bias \""+this->name+"\""+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ ": new upper boundary for colvar \""+ - colvars[i]->name+"\", at "+ + variables(i)->name+"\", at "+ cvm::to_str(new_upper_boundaries[i])+".\n"); } @@ -401,7 +435,7 @@ int colvarbias_meta::update() new_hills_energy_gradients->lower_boundaries = new_lower_boundaries; new_hills_energy_gradients->upper_boundaries = new_upper_boundaries; - new_hills_energy_gradients->setup(new_sizes, 0.0, colvars.size()); + new_hills_energy_gradients->setup(new_sizes, 0.0, num_variables()); new_hills_energy->map_grid(*hills_energy); new_hills_energy_gradients->map_grid(*hills_energy_gradients); @@ -418,25 +452,32 @@ int colvarbias_meta::update() } } } + return COLVARS_OK; +} + +int colvarbias_meta::update_bias() +{ // add a new hill if the required time interval has passed - if ((cvm::step_absolute() % new_hill_freq) == 0) { + if ((cvm::step_absolute() % new_hill_freq) == 0 && + is_enabled(f_cvb_history_dependent)) { - if (cvm::debug()) + if (cvm::debug()) { cvm::log("Metadynamics bias \""+this->name+"\""+ ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ ": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n"); + } cvm::real hills_scale=1.0; if (ebmeta) { - hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); - if(cvm::step_absolute() <= long(ebmeta_equil_steps)) { - cvm::real const hills_lambda = - (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) / - (cvm::real(ebmeta_equil_steps)); - hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; - } + hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); + if(cvm::step_absolute() <= long(ebmeta_equil_steps)) { + cvm::real const hills_lambda = + (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) / + (cvm::real(ebmeta_equil_steps)); + hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; + } } if (well_tempered) { @@ -471,160 +512,165 @@ int colvarbias_meta::update() } } - // sync with the other replicas (if needed) - if (comm != single_replica) { + return COLVARS_OK; +} - // reread the replicas registry - if ((cvm::step_absolute() % replica_update_freq) == 0) { - update_replicas_registry(); - // empty the output buffer - if (replica_hills_os.is_open()) - replica_hills_os.flush(); - read_replica_files(); +int colvarbias_meta::update_grid_data() +{ + if ((cvm::step_absolute() % grids_freq) == 0) { + // map the most recent gaussians to the grids + project_hills(new_hills_begin, hills.end(), + hills_energy, hills_energy_gradients); + new_hills_begin = hills.end(); + + // TODO: we may want to condense all into one replicas array, + // including "this" as the first element + if (comm == multiple_replicas) { + for (size_t ir = 0; ir < replicas.size(); ir++) { + replicas[ir]->project_hills(replicas[ir]->new_hills_begin, + replicas[ir]->hills.end(), + replicas[ir]->hills_energy, + replicas[ir]->hills_energy_gradients); + replicas[ir]->new_hills_begin = replicas[ir]->hills.end(); + } } } - // calculate the biasing energy and forces - bias_energy = 0.0; - for (size_t ir = 0; ir < colvars.size(); ir++) { - colvar_forces[ir].reset(); + return COLVARS_OK; +} + + +int colvarbias_meta::calc_energy(std::vector const &values) +{ + size_t ir = 0; + + for (ir = 0; ir < replicas.size(); ir++) { + replicas[ir]->bias_energy = 0.0; } - if (comm == multiple_replicas) - for (size_t ir = 0; ir < replicas.size(); ir++) { - replicas[ir]->bias_energy = 0.0; - for (size_t ic = 0; ic < colvars.size(); ic++) { - replicas[ir]->colvar_forces[ic].reset(); + + std::vector const curr_bin = values.size() ? + hills_energy->get_colvars_index(values) : + hills_energy->get_colvars_index(); + + if (hills_energy->index_ok(curr_bin)) { + // index is within the grid: get the energy from there + for (ir = 0; ir < replicas.size(); ir++) { + + bias_energy += replicas[ir]->hills_energy->value(curr_bin); + if (cvm::debug()) { + cvm::log("Metadynamics bias \""+this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ + ": current coordinates on the grid: "+ + cvm::to_str(curr_bin)+".\n"); + cvm::log("Grid energy = "+cvm::to_str(bias_energy)+".\n"); } } - - if (use_grids) { - - // get the forces from the grid - - if ((cvm::step_absolute() % grids_freq) == 0) { - // map the most recent gaussians to the grids - project_hills(new_hills_begin, hills.end(), - hills_energy, hills_energy_gradients); - new_hills_begin = hills.end(); - - // TODO: we may want to condense all into one replicas array, - // including "this" as the first element - if (comm == multiple_replicas) { - for (size_t ir = 0; ir < replicas.size(); ir++) { - replicas[ir]->project_hills(replicas[ir]->new_hills_begin, - replicas[ir]->hills.end(), - replicas[ir]->hills_energy, - replicas[ir]->hills_energy_gradients); - replicas[ir]->new_hills_begin = replicas[ir]->hills.end(); - } - } - } - - std::vector curr_bin = hills_energy->get_colvars_index(); - if (cvm::debug()) - cvm::log("Metadynamics bias \""+this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ - ": current coordinates on the grid: "+ - cvm::to_str(curr_bin)+".\n"); - - if (hills_energy->index_ok(curr_bin)) { - - // within the grid: add the energy and the forces from there - - bias_energy += hills_energy->value(curr_bin); - for (size_t ic = 0; ic < colvars.size(); ic++) { - cvm::real const *f = &(hills_energy_gradients->value(curr_bin)); - colvar_forces[ic].real_value += -1.0 * f[ic]; - // the gradients are stored, not the forces - } - if (comm == multiple_replicas) - for (size_t ir = 0; ir < replicas.size(); ir++) { - bias_energy += replicas[ir]->hills_energy->value(curr_bin); - cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value(curr_bin)); - for (size_t ic = 0; ic < colvars.size(); ic++) { - colvar_forces[ic].real_value += -1.0 * f[ic]; - } - } - - } else { - - // off the grid: compute analytically only the hills at the grid's edges - - calc_hills(hills_off_grid.begin(), hills_off_grid.end(), bias_energy); - for (size_t ic = 0; ic < colvars.size(); ic++) { - calc_hills_force(ic, hills_off_grid.begin(), hills_off_grid.end(), colvar_forces); - } - - if (comm == multiple_replicas) - for (size_t ir = 0; ir < replicas.size(); ir++) { - calc_hills(replicas[ir]->hills_off_grid.begin(), - replicas[ir]->hills_off_grid.end(), - bias_energy); - for (size_t ic = 0; ic < colvars.size(); ic++) { - calc_hills_force(ic, - replicas[ir]->hills_off_grid.begin(), - replicas[ir]->hills_off_grid.end(), - colvar_forces); - } - } + } else { + // off the grid: compute analytically only the hills at the grid's edges + for (ir = 0; ir < replicas.size(); ir++) { + calc_hills(replicas[ir]->hills_off_grid.begin(), + replicas[ir]->hills_off_grid.end(), + bias_energy, + values); } } // now include the hills that have not been binned yet (starting // from new_hills_begin) - calc_hills(new_hills_begin, hills.end(), bias_energy); - for (size_t ic = 0; ic < colvars.size(); ic++) { - calc_hills_force(ic, new_hills_begin, hills.end(), colvar_forces); - } - - if (cvm::debug()) - cvm::log("Hills energy = "+cvm::to_str(bias_energy)+ - ", hills forces = "+cvm::to_str(colvar_forces)+".\n"); - - if (cvm::debug()) - cvm::log("Metadynamics bias \""+this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ - ": adding the forces from the other replicas.\n"); - - if (comm == multiple_replicas) - for (size_t ir = 0; ir < replicas.size(); ir++) { - calc_hills(replicas[ir]->new_hills_begin, - replicas[ir]->hills.end(), - bias_energy); - for (size_t ic = 0; ic < colvars.size(); ic++) { - calc_hills_force(ic, - replicas[ir]->new_hills_begin, - replicas[ir]->hills.end(), - colvar_forces); - } - if (cvm::debug()) - cvm::log("Hills energy = "+cvm::to_str(bias_energy)+ - ", hills forces = "+cvm::to_str(colvar_forces)+".\n"); + for (ir = 0; ir < replicas.size(); ir++) { + calc_hills(replicas[ir]->new_hills_begin, + replicas[ir]->hills.end(), + bias_energy); + if (cvm::debug()) { + cvm::log("Hills energy = "+cvm::to_str(bias_energy)+".\n"); } + } return COLVARS_OK; } +int colvarbias_meta::calc_forces(std::vector const &values) +{ + size_t ir = 0, ic = 0; + for (ir = 0; ir < replicas.size(); ir++) { + for (ic = 0; ic < num_variables(); ic++) { + replicas[ir]->colvar_forces[ic].reset(); + } + } + + std::vector const curr_bin = values.size() ? + hills_energy->get_colvars_index(values) : + hills_energy->get_colvars_index(); + + if (hills_energy->index_ok(curr_bin)) { + for (ir = 0; ir < replicas.size(); ir++) { + cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value(curr_bin)); + for (ic = 0; ic < num_variables(); ic++) { + // the gradients are stored, not the forces + colvar_forces[ic].real_value += -1.0 * f[ic]; + } + } + } else { + // off the grid: compute analytically only the hills at the grid's edges + for (ir = 0; ir < replicas.size(); ir++) { + for (ic = 0; ic < num_variables(); ic++) { + calc_hills_force(ic, + replicas[ir]->hills_off_grid.begin(), + replicas[ir]->hills_off_grid.end(), + colvar_forces, + values); + } + } + } + + // now include the hills that have not been binned yet (starting + // from new_hills_begin) + + if (cvm::debug()) { + cvm::log("Metadynamics bias \""+this->name+"\""+ + ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ + ": adding the forces from the other replicas.\n"); + } + + for (ir = 0; ir < replicas.size(); ir++) { + for (ic = 0; ic < num_variables(); ic++) { + calc_hills_force(ic, + replicas[ir]->new_hills_begin, + replicas[ir]->hills.end(), + colvar_forces, + values); + if (cvm::debug()) { + cvm::log("Hills forces = "+cvm::to_str(colvar_forces)+".\n"); + } + } + } + + return COLVARS_OK; +} + + + void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first, colvarbias_meta::hill_iter h_last, cvm::real &energy, std::vector const &colvar_values) { - std::vector curr_values(colvars.size()); - for (size_t i = 0; i < colvars.size(); i++) { - curr_values[i].type(colvars[i]->value()); + size_t i = 0; + std::vector curr_values(num_variables()); + for (i = 0; i < num_variables(); i++) { + curr_values[i].type(variables(i)->value()); } if (colvar_values.size()) { - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { curr_values[i] = colvar_values[i]; } } else { - for (size_t i = 0; i < colvars.size(); i++) { - curr_values[i] = colvars[i]->value(); + for (i = 0; i < num_variables(); i++) { + curr_values[i] = variables(i)->value(); } } @@ -632,11 +678,11 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first, // compute the gaussian exponent cvm::real cv_sqdev = 0.0; - for (size_t i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvarvalue const &x = curr_values[i]; colvarvalue const ¢er = h->centers[i]; cvm::real const half_width = 0.5 * h->widths[i]; - cv_sqdev += (colvars[i]->dist2(x, center)) / (half_width*half_width); + cv_sqdev += (variables(i)->dist2(x, center)) / (half_width*half_width); } // compute the gaussian @@ -658,14 +704,14 @@ void colvarbias_meta::calc_hills_force(size_t const &i, std::vector const &values) { // Retrieve the value of the colvar - colvarvalue const x(values.size() ? values[i] : colvars[i]->value()); + colvarvalue const x(values.size() ? values[i] : variables(i)->value()); // do the type check only once (all colvarvalues in the hills series // were already saved with their types matching those in the // colvars) hill_iter h; - switch (colvars[i]->value().type()) { + switch (variables(i)->value().type()) { case colvarvalue::type_scalar: for (h = h_first; h != h_last; h++) { @@ -674,7 +720,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i, cvm::real const half_width = 0.5 * h->widths[i]; forces[i].real_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * - (colvars[i]->dist2_lgrad(x, center)).real_value ); + (variables(i)->dist2_lgrad(x, center)).real_value ); } break; @@ -687,7 +733,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i, cvm::real const half_width = 0.5 * h->widths[i]; forces[i].rvector_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * - (colvars[i]->dist2_lgrad(x, center)).rvector_value ); + (variables(i)->dist2_lgrad(x, center)).rvector_value ); } break; @@ -699,7 +745,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i, cvm::real const half_width = 0.5 * h->widths[i]; forces[i].quaternion_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * - (colvars[i]->dist2_lgrad(x, center)).quaternion_value ); + (variables(i)->dist2_lgrad(x, center)).quaternion_value ); } break; @@ -710,7 +756,7 @@ void colvarbias_meta::calc_hills_force(size_t const &i, cvm::real const half_width = 0.5 * h->widths[i]; forces[i].vector1d_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * - (colvars[i]->dist2_lgrad(x, center)).vector1d_value ); + (variables(i)->dist2_lgrad(x, center)).vector1d_value ); } break; @@ -739,13 +785,13 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, // TODO: improve it by looping over a small subgrid instead of the whole grid - std::vector colvar_values(colvars.size()); - std::vector colvar_forces_scalar(colvars.size()); + std::vector colvar_values(num_variables()); + std::vector colvar_forces_scalar(num_variables()); std::vector he_ix = he->new_index(); std::vector hg_ix = (hg != NULL) ? hg->new_index() : std::vector (0); cvm::real hills_energy_here = 0.0; - std::vector hills_forces_here(colvars.size(), 0.0); + std::vector hills_forces_here(num_variables(), 0.0); size_t count = 0; size_t const print_frequency = ((hills.size() >= 1000000) ? 1 : (1000000/(hills.size()+1))); @@ -757,7 +803,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, (he->index_ok(he_ix)) && (hg->index_ok(hg_ix)); count++) { size_t i; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i); } @@ -766,7 +812,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, calc_hills(h_first, h_last, hills_energy_here, colvar_values); he->acc_value(he_ix, hills_energy_here); - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { hills_forces_here[i].reset(); calc_hills_force(i, h_first, h_last, hills_forces_here, colvar_values); colvar_forces_scalar[i] = hills_forces_here[i].real_value; @@ -795,7 +841,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, for ( ; (he->index_ok(he_ix)); ) { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i); } @@ -851,6 +897,21 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first // ********************************************************************** +int colvarbias_meta::replica_share() +{ + // sync with the other replicas (if needed) + if (comm == multiple_replicas) { + // reread the replicas registry + update_replicas_registry(); + // empty the output buffer + if (replica_hills_os.is_open()) + replica_hills_os.flush(); + read_replica_files(); + } + return COLVARS_OK; +} + + void colvarbias_meta::update_replicas_registry() { if (cvm::debug()) @@ -975,7 +1036,6 @@ void colvarbias_meta::update_replicas_registry() } } - if (cvm::debug()) cvm::log("Metadynamics bias \""+this->name+"\": the list of replicas contains "+ cvm::to_str(replicas.size())+" elements.\n"); @@ -984,7 +1044,8 @@ void colvarbias_meta::update_replicas_registry() void colvarbias_meta::read_replica_files() { - for (size_t ir = 0; ir < replicas.size(); ir++) { + // Note: we start from the 2nd replica. + for (size_t ir = 1; ir < replicas.size(); ir++) { if (! (replicas[ir])->replica_state_file_in_sync) { // if a new state file is being read, the hills file is also new @@ -1352,9 +1413,9 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) cvm::real h_weight; get_keyval(data, "weight", h_weight, hill_weight, parse_silent); - std::vector h_centers(colvars.size()); - for (size_t i = 0; i < colvars.size(); i++) { - h_centers[i].type(colvars[i]->value()); + std::vector h_centers(num_variables()); + for (size_t i = 0; i < num_variables(); i++) { + h_centers[i].type(variables(i)->value()); } { // it is safer to read colvarvalue objects one at a time; @@ -1362,14 +1423,14 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) std::string centers_input; key_lookup(data, "centers", centers_input); std::istringstream centers_is(centers_input); - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { centers_is >> h_centers[i]; } } - std::vector h_widths(colvars.size()); + std::vector h_widths(num_variables()); get_keyval(data, "widths", h_widths, - std::vector (colvars.size(), (std::sqrt(2.0 * PI) / 2.0)), + std::vector(num_variables(), (std::sqrt(2.0 * PI) / 2.0)), parse_silent); std::string h_replica = ""; @@ -1406,6 +1467,13 @@ std::istream & colvarbias_meta::read_hill(std::istream &is) int colvarbias_meta::setup_output() { + output_prefix = cvm::output_prefix(); + if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) { + // if this is not the only free energy integrator, append + // this bias's name, to distinguish it from the output of the other + // biases producing a .pmf file + output_prefix += ("."+this->name); + } if (comm == multiple_replicas) { @@ -1421,10 +1489,10 @@ int colvarbias_meta::setup_output() // those by another replica replica_hills_file = (std::string(pwd)+std::string(PATHSEP)+ - cvm::output_prefix+".colvars."+this->name+"."+replica_id+".hills"); + cvm::output_prefix()+".colvars."+this->name+"."+replica_id+".hills"); replica_state_file = (std::string(pwd)+std::string(PATHSEP)+ - cvm::output_prefix+".colvars."+this->name+"."+replica_id+".state"); + cvm::output_prefix()+".colvars."+this->name+"."+replica_id+".state"); delete[] pwd; // now register this replica @@ -1492,13 +1560,14 @@ int colvarbias_meta::setup_output() } if (b_hills_traj) { - std::string const traj_file_name(cvm::output_prefix+ + std::string const traj_file_name(cvm::output_prefix()+ ".colvars."+this->name+ ( (comm != single_replica) ? ("."+replica_id) : ("") )+ ".hills.traj"); if (!hills_traj_os.is_open()) { + cvm::backup_file(traj_file_name.c_str()); hills_traj_os.open(traj_file_name.c_str()); } if (!hills_traj_os.is_open()) @@ -1585,16 +1654,6 @@ void colvarbias_meta::write_pmf() colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy); pmf->setup(); - std::string fes_file_name_prefix(cvm::output_prefix); - - if ((cvm::n_meta_biases > 1) || (cvm::n_abf_biases > 0)) { - // if this is not the only free energy integrator, append - // this bias's name, to distinguish it from the output of the other - // biases producing a .pmf file - // TODO: fix for ABF with updateBias == no - fes_file_name_prefix += ("."+this->name); - } - if ((comm == single_replica) || (dump_replica_fes)) { // output the PMF from this instance or replica pmf->reset(); @@ -1607,7 +1666,7 @@ void colvarbias_meta::write_pmf() pmf->multiply_constant(well_temper_scale); } { - std::string const fes_file_name(fes_file_name_prefix + + std::string const fes_file_name(this->output_prefix + ((comm != single_replica) ? ".partial" : "") + (dump_fes_save ? "."+cvm::to_str(cvm::step_absolute()) : "") + @@ -1632,7 +1691,7 @@ void colvarbias_meta::write_pmf() cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature; pmf->multiply_constant(well_temper_scale); } - std::string const fes_file_name(fes_file_name_prefix + + std::string const fes_file_name(this->output_prefix + (dump_fes_save ? "."+cvm::to_str(cvm::step_absolute()) : "") + ".pmf"); diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h index a88a34ba00..01921eaf64 100644 --- a/lib/colvars/colvarbias_meta.h +++ b/lib/colvars/colvarbias_meta.h @@ -36,8 +36,20 @@ public: colvarbias_meta(char const *key); virtual int init(std::string const &conf); + virtual int init_well_tempered_params(std::string const &conf); + virtual int init_ebmeta_params(std::string const &conf); virtual ~colvarbias_meta(); + virtual int update(); + virtual int update_grid_params(); + virtual int update_bias(); + virtual int update_grid_data(); + virtual int replica_share(); + + virtual int calc_energy(std::vector const &values = + std::vector(0)); + virtual int calc_forces(std::vector const &values = + std::vector(0)); virtual std::string const get_state_params() const; virtual int set_state_params(std::string const &state_conf); @@ -102,18 +114,18 @@ protected: /// \brief Calculate the values of the hills, incrementing /// bias_energy virtual void calc_hills(hill_iter h_first, - hill_iter h_last, - cvm::real &energy, - std::vector const &values = std::vector (0)); + hill_iter h_last, + cvm::real &energy, + std::vector const &values = std::vector(0)); /// \brief Calculate the forces acting on the i-th colvar, /// incrementing colvar_forces[i]; must be called after calc_hills /// each time the values of the colvars are changed virtual void calc_hills_force(size_t const &i, - hill_iter h_first, - hill_iter h_last, - std::vector &forces, - std::vector const &values = std::vector (0)); + hill_iter h_first, + hill_iter h_last, + std::vector &forces, + std::vector const &values = std::vector(0)); /// Height of new hills diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp index 84630984e5..159d9eae64 100644 --- a/lib/colvars/colvarbias_restraint.cpp +++ b/lib/colvars/colvarbias_restraint.cpp @@ -33,17 +33,15 @@ int colvarbias_restraint::init(std::string const &conf) int colvarbias_restraint::update() { - bias_energy = 0.0; - - if (cvm::debug()) - cvm::log("Updating the restraint bias \""+this->name+"\".\n"); + // Update base class (bias_energy and colvar_forces are zeroed there) + colvarbias::update(); // Force and energy calculation - for (size_t i = 0; i < colvars.size(); i++) { - colvar_forces[i].type(colvars[i]->value()); + for (size_t i = 0; i < num_variables(); i++) { + bias_energy += restraint_potential(i); + colvar_forces[i].type(variables(i)->value()); colvar_forces[i].is_derivative(); colvar_forces[i] = restraint_force(i); - bias_energy += restraint_potential(i); } if (cvm::debug()) @@ -59,8 +57,6 @@ int colvarbias_restraint::update() colvarbias_restraint::~colvarbias_restraint() { - if (cvm::n_rest_biases > 0) - cvm::n_rest_biases -= 1; } @@ -102,18 +98,18 @@ int colvarbias_restraint_centers::init(std::string const &conf) bool null_centers = (colvar_centers.size() == 0); if (null_centers) { // try to initialize the restraint centers for the first time - colvar_centers.resize(colvars.size()); - colvar_centers_raw.resize(colvars.size()); - for (i = 0; i < colvars.size(); i++) { - colvar_centers[i].type(colvars[i]->value()); + colvar_centers.resize(num_variables()); + colvar_centers_raw.resize(num_variables()); + for (i = 0; i < num_variables(); i++) { + colvar_centers[i].type(variables(i)->value()); colvar_centers[i].reset(); - colvar_centers_raw[i].type(colvars[i]->value()); + colvar_centers_raw[i].type(variables(i)->value()); colvar_centers_raw[i].reset(); } } if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) { - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { if (cvm::debug()) { cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n"); } @@ -129,7 +125,7 @@ int colvarbias_restraint_centers::init(std::string const &conf) return INPUT_ERROR; } - if (colvar_centers.size() != colvars.size()) { + if (colvar_centers.size() != num_variables()) { cvm::error("Error: number of centers does not match " "that of collective variables.\n", INPUT_ERROR); return INPUT_ERROR; @@ -142,10 +138,10 @@ int colvarbias_restraint_centers::init(std::string const &conf) int colvarbias_restraint_centers::change_configuration(std::string const &conf) { if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) { - for (size_t i = 0; i < colvars.size(); i++) { - colvar_centers[i].type(colvars[i]->value()); + for (size_t i = 0; i < num_variables(); i++) { + colvar_centers[i].type(variables(i)->value()); colvar_centers[i].apply_constraints(); - colvar_centers_raw[i].type(colvars[i]->value()); + colvar_centers_raw[i].type(variables(i)->value()); colvar_centers_raw[i] = colvar_centers[i]; } } @@ -269,7 +265,7 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf) size_t i; if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) { - if (colvar_centers.size() != colvars.size()) { + if (colvar_centers.size() != num_variables()) { cvm::error("Error: number of target centers does not match " "that of collective variables.\n"); } @@ -308,9 +304,9 @@ int colvarbias_restraint_centers_moving::update() // at each simulation step (or stage, if applicable) // (take current stage into account: it can be non-zero // if we are restarting a staged calculation) - centers_incr.resize(colvars.size()); - for (size_t i = 0; i < colvars.size(); i++) { - centers_incr[i].type(colvars[i]->value()); + centers_incr.resize(num_variables()); + for (size_t i = 0; i < num_variables(); i++) { + centers_incr[i].type(variables(i)->value()); centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) / cvm::real( target_nstages ? (target_nstages - stage) : (target_nsteps - cvm::step_absolute())); @@ -326,10 +322,10 @@ int colvarbias_restraint_centers_moving::update() && (cvm::step_absolute() % target_nsteps) == 0 && stage < target_nstages) { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { colvar_centers_raw[i] += centers_incr[i]; colvar_centers[i] = colvar_centers_raw[i]; - colvars[i]->wrap(colvar_centers[i]); + variables(i)->wrap(colvar_centers[i]); colvar_centers[i].apply_constraints(); } stage++; @@ -341,10 +337,10 @@ int colvarbias_restraint_centers_moving::update() } else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) { // move the restraint centers in the direction of the targets // (slow growth) - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { colvar_centers_raw[i] += centers_incr[i]; colvar_centers[i] = colvar_centers_raw[i]; - colvars[i]->wrap(colvar_centers[i]); + variables(i)->wrap(colvar_centers[i]); colvar_centers[i].apply_constraints(); } } @@ -363,7 +359,7 @@ int colvarbias_restraint_centers_moving::update_acc_work() { if (b_output_acc_work) { if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { // project forces on the calculated increments at this step acc_work += colvar_forces[i] * centers_incr[i]; } @@ -381,14 +377,14 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const if (b_chg_centers) { size_t i; os << "centers "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << colvar_centers[i]; } os << "\n"; os << "centers_raw "; - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << colvar_centers_raw[i]; @@ -429,10 +425,10 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostream &os) { if (b_output_centers) { - for (size_t i = 0; i < colvars.size(); i++) { - size_t const this_cv_width = (colvars[i]->value()).output_width(cvm::cv_width); + for (size_t i = 0; i < num_variables(); i++) { + size_t const this_cv_width = (variables(i)->value()).output_width(cvm::cv_width); os << " x0_" - << cvm::wrap_string(colvars[i]->name, this_cv_width-3); + << cvm::wrap_string(variables(i)->name, this_cv_width-3); } } @@ -448,7 +444,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostrea std::ostream & colvarbias_restraint_centers_moving::write_traj(std::ostream &os) { if (b_output_centers) { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << colvar_centers[i]; @@ -539,9 +535,9 @@ int colvarbias_restraint_k_moving::update() } force_k = starting_force_k + (target_force_k - starting_force_k) * std::pow(lambda, force_k_exp); - cvm::log("Restraint " + this->name + ", stage " + - cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda)); - cvm::log("Setting force constant to " + cvm::to_str(force_k)); + cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage) + + " : lambda = " + cvm::to_str(lambda) + + ", k = " + cvm::to_str(force_k)); } // TI calculation: estimate free energy derivative @@ -557,7 +553,7 @@ int colvarbias_restraint_k_moving::update() // Square distance normalized by square colvar width cvm::real dist_sq = 0.0; - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { dist_sq += d_restraint_potential_dk(i); } @@ -569,7 +565,8 @@ int colvarbias_restraint_k_moving::update() if (cvm::step_absolute() % target_nsteps == 0 && cvm::step_absolute() > 0) { - cvm::log("Lambda= " + cvm::to_str(lambda) + " dA/dLambda= " + cvm::log("Restraint " + this->name + " Lambda= " + + cvm::to_str(lambda) + " dA/dLambda= " + cvm::to_str(restraint_FE / cvm::real(target_nsteps - target_equil_steps))); // ...and move on to the next one @@ -584,9 +581,9 @@ int colvarbias_restraint_k_moving::update() } force_k = starting_force_k + (target_force_k - starting_force_k) * std::pow(lambda, force_k_exp); - cvm::log("Restraint " + this->name + ", stage " + - cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda)); - cvm::log("Setting force constant to " + cvm::to_str(force_k)); + cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage) + + " : lambda = " + cvm::to_str(lambda) + + ", k = " + cvm::to_str(force_k)); } } @@ -721,11 +718,11 @@ int colvarbias_restraint_harmonic::init(std::string const &conf) colvarbias_restraint_centers_moving::init(conf); colvarbias_restraint_k_moving::init(conf); - for (size_t i = 0; i < colvars.size(); i++) { - if (colvars[i]->width != 1.0) - cvm::log("The force constant for colvar \""+colvars[i]->name+ + for (size_t i = 0; i < num_variables(); i++) { + if (variables(i)->width != 1.0) + cvm::log("The force constant for colvar \""+variables(i)->name+ "\" will be rescaled to "+ - cvm::to_str(force_k / (colvars[i]->width * colvars[i]->width))+ + cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+ " according to the specified width.\n"); } @@ -751,22 +748,22 @@ int colvarbias_restraint_harmonic::update() cvm::real colvarbias_restraint_harmonic::restraint_potential(size_t i) const { - return 0.5 * force_k / (colvars[i]->width * colvars[i]->width) * - colvars[i]->dist2(colvars[i]->value(), colvar_centers[i]); + return 0.5 * force_k / (variables(i)->width * variables(i)->width) * + variables(i)->dist2(variables(i)->value(), colvar_centers[i]); } colvarvalue const colvarbias_restraint_harmonic::restraint_force(size_t i) const { - return -0.5 * force_k / (colvars[i]->width * colvars[i]->width) * - colvars[i]->dist2_lgrad(colvars[i]->value(), colvar_centers[i]); + return -0.5 * force_k / (variables(i)->width * variables(i)->width) * + variables(i)->dist2_lgrad(variables(i)->value(), colvar_centers[i]); } cvm::real colvarbias_restraint_harmonic::d_restraint_potential_dk(size_t i) const { - return 0.5 / (colvars[i]->width * colvars[i]->width) * - colvars[i]->dist2(colvars[i]->value(), colvar_centers[i]); + return 0.5 / (variables(i)->width * variables(i)->width) * + variables(i)->dist2(variables(i)->value(), colvar_centers[i]); } @@ -840,6 +837,8 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co colvarbias_restraint_moving(key), colvarbias_restraint_k_moving(key) { + lower_wall_k = 0.0; + upper_wall_k = 0.0; } @@ -849,7 +848,11 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) colvarbias_restraint_moving::init(conf); colvarbias_restraint_k_moving::init(conf); - provide(f_cvb_scalar_variables); + get_keyval(conf, "lowerWallConstant", lower_wall_k, + (lower_wall_k > 0.0) ? lower_wall_k : force_k); + get_keyval(conf, "upperWallConstant", upper_wall_k, + (upper_wall_k > 0.0) ? upper_wall_k : force_k); + enable(f_cvb_scalar_variables); size_t i; @@ -857,9 +860,9 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) bool b_null_lower_walls = false; if (lower_walls.size() == 0) { b_null_lower_walls = true; - lower_walls.resize(number_of_colvars()); - for (i = 0; i < colvars.size(); i++) { - lower_walls[i].type(colvars[i]->value()); + lower_walls.resize(num_variables()); + for (i = 0; i < num_variables(); i++) { + lower_walls[i].type(variables(i)->value()); lower_walls[i].reset(); } } @@ -872,9 +875,9 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) bool b_null_upper_walls = false; if (upper_walls.size() == 0) { b_null_upper_walls = true; - upper_walls.resize(number_of_colvars()); - for (i = 0; i < colvars.size(); i++) { - upper_walls[i].type(colvars[i]->value()); + upper_walls.resize(num_variables()); + for (i = 0; i < num_variables(); i++) { + upper_walls[i].type(variables(i)->value()); upper_walls[i].reset(); } } @@ -890,17 +893,17 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) } if ((lower_walls.size() == 0) || (upper_walls.size() == 0)) { - for (i = 0; i < colvars.size(); i++) { - if (colvars[i]->is_enabled(f_cv_periodic)) { + for (i = 0; i < num_variables(); i++) { + if (variables(i)->is_enabled(f_cv_periodic)) { cvm::error("Error: at least one variable is periodic, " - "both walls must be provided .\n", INPUT_ERROR); + "both walls must be provided.\n", INPUT_ERROR); return INPUT_ERROR; } } } if ((lower_walls.size() > 0) && (upper_walls.size() > 0)) { - for (i = 0; i < colvars.size(); i++) { + for (i = 0; i < num_variables(); i++) { if (lower_walls[i] >= upper_walls[i]) { cvm::error("Error: one upper wall, "+ cvm::to_str(upper_walls[i])+ @@ -909,13 +912,24 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf) INPUT_ERROR); } } + if (lower_wall_k * upper_wall_k == 0.0) { + cvm::error("Error: lowerWallConstant and upperWallConstant, " + "when defined, must both be positive.\n", + INPUT_ERROR); + return INPUT_ERROR; + } + force_k = lower_wall_k * upper_wall_k; + // transform the two constants to relative values + // (allow changing both via force_k) + lower_wall_k /= force_k; + upper_wall_k /= force_k; } - for (i = 0; i < colvars.size(); i++) { - if (colvars[i]->width != 1.0) - cvm::log("The force constant for colvar \""+colvars[i]->name+ + for (i = 0; i < num_variables(); i++) { + if (variables(i)->width != 1.0) + cvm::log("The force constant for colvar \""+variables(i)->name+ "\" will be rescaled to "+ - cvm::to_str(force_k / (colvars[i]->width * colvars[i]->width))+ + cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+ " according to the specified width.\n"); } @@ -935,20 +949,20 @@ int colvarbias_restraint_harmonic_walls::update() void colvarbias_restraint_harmonic_walls::communicate_forces() { - for (size_t i = 0; i < colvars.size(); i++) { + for (size_t i = 0; i < num_variables(); i++) { if (cvm::debug()) { cvm::log("Communicating a force to colvar \""+ - colvars[i]->name+"\".\n"); + variables(i)->name+"\".\n"); } - colvars[i]->add_bias_force_actual_value(colvar_forces[i]); + variables(i)->add_bias_force_actual_value(colvar_forces[i]); } } cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const { - colvar *cv = colvars[i]; - colvarvalue const &cvv = colvars[i]->actual_value(); + colvar *cv = variables(i); + colvarvalue const &cvv = variables(i)->actual_value(); // For a periodic colvar, both walls may be applicable at the same time // in which case we pick the closer one @@ -958,21 +972,21 @@ cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const cvm::real const upper_wall_dist2 = cv->dist2(cvv, upper_walls[i]); if (lower_wall_dist2 < upper_wall_dist2) { cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]); - if (grad < 0.0) { return grad; } + if (grad < 0.0) { return 0.5 * grad; } } else { cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]); - if (grad > 0.0) { return grad; } + if (grad > 0.0) { return 0.5 * grad; } } return 0.0; } if (lower_walls.size() > 0) { cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]); - if (grad < 0.0) { return grad; } + if (grad < 0.0) { return 0.5 * grad; } } if (upper_walls.size() > 0) { cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]); - if (grad > 0.0) { return grad; } + if (grad > 0.0) { return 0.5 * grad; } } return 0.0; } @@ -981,7 +995,8 @@ cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const cvm::real colvarbias_restraint_harmonic_walls::restraint_potential(size_t i) const { cvm::real const dist = colvar_distance(i); - return 0.5 * force_k / (colvars[i]->width * colvars[i]->width) * + cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k; + return 0.5 * force_k * scale / (variables(i)->width * variables(i)->width) * dist * dist; } @@ -989,15 +1004,16 @@ cvm::real colvarbias_restraint_harmonic_walls::restraint_potential(size_t i) con colvarvalue const colvarbias_restraint_harmonic_walls::restraint_force(size_t i) const { cvm::real const dist = colvar_distance(i); - return -0.5 * force_k / (colvars[i]->width * colvars[i]->width) * - dist; + cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k; + return - force_k * scale / (variables(i)->width * variables(i)->width) * dist; } cvm::real colvarbias_restraint_harmonic_walls::d_restraint_potential_dk(size_t i) const { cvm::real const dist = colvar_distance(i); - return 0.5 / (colvars[i]->width * colvars[i]->width) * + cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k; + return 0.5 * scale / (variables(i)->width * variables(i)->width) * dist * dist; } @@ -1054,16 +1070,16 @@ int colvarbias_restraint_linear::init(std::string const &conf) colvarbias_restraint_centers_moving::init(conf); colvarbias_restraint_k_moving::init(conf); - for (size_t i = 0; i < colvars.size(); i++) { - if (colvars[i]->is_enabled(f_cv_periodic)) { + for (size_t i = 0; i < num_variables(); i++) { + if (variables(i)->is_enabled(f_cv_periodic)) { cvm::error("Error: linear biases cannot be applied to periodic variables.\n", INPUT_ERROR); return INPUT_ERROR; } - if (colvars[i]->width != 1.0) - cvm::log("The force constant for colvar \""+colvars[i]->name+ + if (variables(i)->width != 1.0) + cvm::log("The force constant for colvar \""+variables(i)->name+ "\" will be rescaled to "+ - cvm::to_str(force_k / colvars[i]->width)+ + cvm::to_str(force_k / variables(i)->width)+ " according to the specified width.\n"); } @@ -1113,19 +1129,19 @@ cvm::real colvarbias_restraint_linear::energy_difference(std::string const &conf cvm::real colvarbias_restraint_linear::restraint_potential(size_t i) const { - return force_k / colvars[i]->width * (colvars[i]->value() - colvar_centers[i]); + return force_k / variables(i)->width * (variables(i)->value() - colvar_centers[i]); } colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const { - return -1.0 * force_k / colvars[i]->width; + return -1.0 * force_k / variables(i)->width; } cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const { - return 1.0 / colvars[i]->width * (colvars[i]->value() - colvar_centers[i]); + return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]); } @@ -1279,16 +1295,16 @@ int colvarbias_restraint_histogram::update() size_t vector_size = 0; size_t icv; - for (icv = 0; icv < colvars.size(); icv++) { - vector_size += colvars[icv]->value().size(); + for (icv = 0; icv < num_variables(); icv++) { + vector_size += variables(icv)->value().size(); } cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size); // calculate the histogram p.reset(); - for (icv = 0; icv < colvars.size(); icv++) { - colvarvalue const &cv = colvars[icv]->value(); + for (icv = 0; icv < num_variables(); icv++) { + colvarvalue const &cv = variables(icv)->value(); if (cv.type() == colvarvalue::type_scalar) { cvm::real const cv_value = cv.real_value; size_t igrid; @@ -1309,7 +1325,9 @@ int colvarbias_restraint_histogram::update() } } } else { - // TODO + cvm::error("Error: unsupported type for variable "+variables(icv)->name+".\n", + COLVARS_NOT_IMPLEMENTED); + return COLVARS_NOT_IMPLEMENTED; } } @@ -1320,8 +1338,8 @@ int colvarbias_restraint_histogram::update() bias_energy = 0.5 * force_k_cv * p_diff * p_diff; // calculate the forces - for (icv = 0; icv < colvars.size(); icv++) { - colvarvalue const &cv = colvars[icv]->value(); + for (icv = 0; icv < num_variables(); icv++) { + colvarvalue const &cv = variables(icv)->value(); colvarvalue &cv_force = colvar_forces[icv]; cv_force.type(cv); cv_force.reset(); @@ -1363,10 +1381,10 @@ int colvarbias_restraint_histogram::update() std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os) { if (b_write_histogram) { - std::string file_name(cvm::output_prefix+"."+this->name+".hist.dat"); + std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat"); std::ofstream os(file_name.c_str()); - os << "# " << cvm::wrap_string(colvars[0]->name, cvm::cv_width) - << " " << "p(" << cvm::wrap_string(colvars[0]->name, cvm::cv_width-3) + os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width) + << " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3) << ")\n"; size_t igrid; for (igrid = 0; igrid < p.size(); igrid++) { diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h index cbdd9c44d1..98b967abdb 100644 --- a/lib/colvars/colvarbias_restraint.h +++ b/lib/colvars/colvarbias_restraint.h @@ -260,6 +260,12 @@ protected: /// \brief Location of the upper walls std::vector upper_walls; + /// \brief If both walls are defined, use this k for the lower + cvm::real lower_wall_k; + + /// \brief If both walls are defined, use this k for the upper + cvm::real upper_wall_k; + virtual cvm::real colvar_distance(size_t i) const; virtual cvm::real restraint_potential(size_t i) const; virtual colvarvalue const restraint_force(size_t i) const; diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index d99da56386..786bc032d2 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -48,8 +48,6 @@ colvar::cvc::cvc(std::string const &conf) get_keyval(conf, "period", period, 0.0); get_keyval(conf, "wrapAround", wrap_center, 0.0); - // All cvcs implement this - provide(f_cvc_debug_gradient); get_keyval_feature((colvarparse *)this, conf, "debugGradients", f_cvc_debug_gradient, false, parse_silent); @@ -63,6 +61,8 @@ colvar::cvc::cvc(std::string const &conf) int colvar::cvc::init_total_force_params(std::string const &conf) { + if (cvm::get_error()) return COLVARS_ERROR; + if (get_keyval_feature(this, conf, "oneSiteSystemForce", f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) { cvm::log("Warning: keyword \"oneSiteSystemForce\" is deprecated: " @@ -72,6 +72,19 @@ int colvar::cvc::init_total_force_params(std::string const &conf) f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) { cvm::log("Computing total force on group 1 only"); } + + if (! is_enabled(f_cvc_one_site_total_force)) { + // check whether any of the other atom groups is dummy + std::vector::iterator agi = atom_groups.begin(); + agi++; + for ( ; agi != atom_groups.end(); agi++) { + if ((*agi)->b_dummy) { + provide(f_cvc_inv_gradient, false); + provide(f_cvc_Jacobian, false); + } + } + } + return COLVARS_OK; } @@ -87,8 +100,7 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf, group->key = group_key; if (b_try_scalable) { - // TODO rewrite this logic in terms of dependencies - if (is_available(f_cvc_scalable_com) && is_available(f_cvc_com_based)) { + if (is_available(f_cvc_scalable_com) && is_enabled(f_cvc_com_based)) { enable(f_cvc_scalable_com); enable(f_cvc_scalable); // The CVC makes the feature available; diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index a230cae8a9..ec215cbad1 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -343,6 +343,15 @@ public: virtual void calc_value(); virtual void calc_gradients(); virtual void apply_force(colvarvalue const &force); + /// Redefined to override the distance ones + virtual cvm::real dist2(colvarvalue const &x1, + colvarvalue const &x2) const; + /// Redefined to override the distance ones + virtual colvarvalue dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const; + /// Redefined to override the distance ones + virtual colvarvalue dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const; }; diff --git a/lib/colvars/colvarcomp_angles.cpp b/lib/colvars/colvarcomp_angles.cpp index 4c3390a8bd..0204f3b4b1 100644 --- a/lib/colvars/colvarcomp_angles.cpp +++ b/lib/colvars/colvarcomp_angles.cpp @@ -21,7 +21,7 @@ colvar::angle::angle(std::string const &conf) function_type = "angle"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); group1 = parse_group(conf, "group1"); group2 = parse_group(conf, "group2"); @@ -40,7 +40,7 @@ colvar::angle::angle(cvm::atom const &a1, function_type = "angle"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); group1 = new cvm::atom_group(std::vector(1, a1)); group2 = new cvm::atom_group(std::vector(1, a2)); @@ -259,7 +259,7 @@ colvar::dihedral::dihedral(std::string const &conf) b_periodic = true; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); group1 = parse_group(conf, "group1"); group2 = parse_group(conf, "group2"); @@ -285,7 +285,7 @@ colvar::dihedral::dihedral(cvm::atom const &a1, b_periodic = true; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); b_1site_force = false; diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index 7481dd360b..f46270246f 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -23,7 +23,7 @@ colvar::distance::distance(std::string const &conf) function_type = "distance"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); group1 = parse_group(conf, "group1"); group2 = parse_group(conf, "group2"); @@ -44,7 +44,7 @@ colvar::distance::distance() function_type = "distance"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); b_no_PBC = false; x.type(colvarvalue::type_scalar); } @@ -106,7 +106,7 @@ colvar::distance_vec::distance_vec(std::string const &conf) : distance(conf) { function_type = "distance_vec"; - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_3vector); } @@ -115,7 +115,7 @@ colvar::distance_vec::distance_vec() : distance() { function_type = "distance_vec"; - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_3vector); } @@ -176,7 +176,7 @@ colvar::distance_z::distance_z(std::string const &conf) function_type = "distance_z"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_scalar); // TODO detect PBC from MD engine (in simple cases) @@ -228,7 +228,7 @@ colvar::distance_z::distance_z() function_type = "distance_z"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_scalar); } @@ -372,7 +372,7 @@ colvar::distance_xy::distance_xy(std::string const &conf) function_type = "distance_xy"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_scalar); } @@ -383,7 +383,7 @@ colvar::distance_xy::distance_xy() function_type = "distance_xy"; provide(f_cvc_inv_gradient); provide(f_cvc_Jacobian); - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_scalar); } @@ -479,7 +479,7 @@ colvar::distance_dir::distance_dir(std::string const &conf) : distance(conf) { function_type = "distance_dir"; - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_unit3vector); } @@ -488,7 +488,7 @@ colvar::distance_dir::distance_dir() : distance() { function_type = "distance_dir"; - provide(f_cvc_com_based); + enable(f_cvc_com_based); x.type(colvarvalue::type_unit3vector); } @@ -529,6 +529,27 @@ void colvar::distance_dir::apply_force(colvarvalue const &force) } +cvm::real colvar::distance_dir::dist2(colvarvalue const &x1, + colvarvalue const &x2) const +{ + return (x1.rvector_value - x2.rvector_value).norm2(); +} + + +colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + return colvarvalue((x1.rvector_value - x2.rvector_value), colvarvalue::type_unit3vector); +} + + +colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1, + colvarvalue const &x2) const +{ + return colvarvalue((x2.rvector_value - x1.rvector_value), colvarvalue::type_unit3vector); +} + + colvar::distance_inv::distance_inv(std::string const &conf) : distance(conf) diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index e3ccd4ecf5..8252f77e62 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -14,9 +14,6 @@ colvardeps::~colvardeps() { size_t i; - for (i=0; iavailable = true; +void colvardeps::provide(int feature_id, bool truefalse) { + feature_states[feature_id].available = truefalse; +} + + +void colvardeps::set_enabled(int feature_id, bool truefalse) { +// if (!is_static(feature_id)) { +// cvm::error("Cannot set feature " + features()[feature_id]->description + " statically in " + description + ".\n"); +// return; +// } + if (truefalse) { + // Resolve dependencies too + enable(feature_id); + } else { + feature_states[feature_id].enabled = false; + } } bool colvardeps::get_keyval_feature(colvarparse *cvp, - std::string const &conf, char const *key, - int feature_id, bool const &def_value, - colvarparse::Parse_Mode const parse_mode) + std::string const &conf, char const *key, + int feature_id, bool const &def_value, + colvarparse::Parse_Mode const parse_mode) { + if (!is_user(feature_id)) { + cvm::error("Cannot set feature " + features()[feature_id]->description + " from user input in " + description + ".\n"); + return false; + } bool value; bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode); if (value) enable(feature_id); @@ -52,19 +67,19 @@ bool colvardeps::get_keyval_feature(colvarparse *cvp, int colvardeps::enable(int feature_id, - bool dry_run /* default: false */, - // dry_run: fail silently, do not enable if available - // flag is passed recursively to deps of this feature - bool toplevel /* default: true */) - // toplevel: false if this is called as part of a chain of dependency resolution - // this is used to diagnose failed dependencies by displaying the full stack - // only the toplevel dependency will throw a fatal error + bool dry_run /* default: false */, + // dry_run: fail silently, do not enable if available + // flag is passed recursively to deps of this feature + bool toplevel /* default: true */) +// toplevel: false if this is called as part of a chain of dependency resolution +// this is used to diagnose failed dependencies by displaying the full stack +// only the toplevel dependency will throw a fatal error { int res; size_t i, j; bool ok; feature *f = features()[feature_id]; - feature_state *fs = feature_states[feature_id]; + feature_state *fs = &feature_states[feature_id]; if (cvm::debug()) { cvm::log("DEPS: " + description + @@ -88,6 +103,14 @@ int colvardeps::enable(int feature_id, return COLVARS_ERROR; } + if (!toplevel && !is_dynamic(feature_id)) { + if (!dry_run) { + cvm::log("Non-dynamic feature : \"" + f->description + + "\" in " + description + " may not be enabled as a dependency.\n"); + } + return COLVARS_ERROR; + } + // 1) enforce exclusions for (i=0; irequires_exclude.size(); i++) { feature *g = features()[f->requires_exclude[i]]; @@ -168,9 +191,9 @@ int colvardeps::enable(int feature_id, if (res != COLVARS_OK) { if (!dry_run) { cvm::log("...required by \"" + f->description + "\" in " + description); - } - if (toplevel) { - cvm::error("Error: Failed dependency in " + description + "."); + if (toplevel) { + cvm::error("Error: Failed dependency in " + description + "."); + } } return res; } @@ -194,9 +217,12 @@ int colvardeps::enable(int feature_id, // // we need refs to parents to walk up the deps tree! // // or refresh // } +void colvardeps::init_feature(int feature_id, const char *description, feature_type type) { + features()[feature_id]->description = description; + features()[feature_id]->type = type; +} - // Shorthand macros for describing dependencies -#define f_description(f, d) features()[f]->description = d +// Shorthand macros for describing dependencies #define f_req_self(f, g) features()[f]->requires_self.push_back(g) // This macro ensures that exclusions are symmetric #define f_req_exclude(f, g) features()[f]->requires_exclude.push_back(g); \ @@ -216,35 +242,31 @@ void colvardeps::init_cvb_requires() { for (i = 0; i < f_cvb_ntot; i++) { features().push_back(new feature); } + + init_feature(f_cvb_active, "active", f_type_dynamic); + f_req_children(f_cvb_active, f_cv_active); + + init_feature(f_cvb_apply_force, "apply force", f_type_user); + f_req_children(f_cvb_apply_force, f_cv_gradient); + + init_feature(f_cvb_get_total_force, "obtain total force"); + f_req_children(f_cvb_get_total_force, f_cv_total_force); + + init_feature(f_cvb_history_dependent, "history-dependent", f_type_static); + + init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static); + f_req_children(f_cvb_scalar_variables, f_cv_scalar); + + init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static); } - f_description(f_cvb_active, "active"); - f_req_children(f_cvb_active, f_cv_active); - - f_description(f_cvb_apply_force, "apply force"); - f_req_children(f_cvb_apply_force, f_cv_gradient); - - f_description(f_cvb_get_total_force, "obtain total force"); - f_req_children(f_cvb_get_total_force, f_cv_total_force); - - f_description(f_cvb_history_dependent, "history-dependent"); - - f_description(f_cvb_scalar_variables, "require scalar variables"); - f_req_children(f_cvb_scalar_variables, f_cv_scalar); - // Initialize feature_states for each instance feature_states.reserve(f_cvb_ntot); for (i = 0; i < f_cvb_ntot; i++) { - feature_states.push_back(new feature_state(true, false)); + feature_states.push_back(feature_state(true, false)); // Most features are available, so we set them so // and list exceptions below } - - // some biases are not history-dependent - feature_states[f_cvb_history_dependent]->available = false; - - // by default, biases should work with vector variables, too - feature_states[f_cvb_scalar_variables]->available = false; } @@ -255,117 +277,111 @@ void colvardeps::init_cv_requires() { features().push_back(new feature); } - f_description(f_cv_active, "active"); + init_feature(f_cv_active, "active", f_type_dynamic); f_req_children(f_cv_active, f_cvc_active); // Colvars must be either a linear combination, or scalar (and polynomial) or scripted f_req_alt3(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted); - f_description(f_cv_gradient, "gradient"); + init_feature(f_cv_gradient, "gradient", f_type_dynamic); f_req_children(f_cv_gradient, f_cvc_gradient); - f_description(f_cv_collect_gradient, "collect gradient"); + init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic); f_req_self(f_cv_collect_gradient, f_cv_gradient); f_req_self(f_cv_collect_gradient, f_cv_scalar); - f_description(f_cv_fdiff_velocity, "fdiff_velocity"); + init_feature(f_cv_fdiff_velocity, "fdiff_velocity", f_type_dynamic); // System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly - f_description(f_cv_total_force, "total force"); + init_feature(f_cv_total_force, "total force", f_type_dynamic); f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc); // Deps for explicit total force calculation - f_description(f_cv_total_force_calc, "total force calculation"); + init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic); f_req_self(f_cv_total_force_calc, f_cv_scalar); f_req_self(f_cv_total_force_calc, f_cv_linear); f_req_children(f_cv_total_force_calc, f_cvc_inv_gradient); f_req_self(f_cv_total_force_calc, f_cv_Jacobian); - f_description(f_cv_Jacobian, "Jacobian derivative"); + init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic); f_req_self(f_cv_Jacobian, f_cv_scalar); f_req_self(f_cv_Jacobian, f_cv_linear); f_req_children(f_cv_Jacobian, f_cvc_Jacobian); - f_description(f_cv_hide_Jacobian, "hide Jacobian force"); + init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user); f_req_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated - f_description(f_cv_extended_Lagrangian, "extended Lagrangian"); + init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user); + f_req_self(f_cv_extended_Lagrangian, f_cv_scalar); + f_req_self(f_cv_extended_Lagrangian, f_cv_gradient); - f_description(f_cv_Langevin, "Langevin dynamics"); + init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user); f_req_self(f_cv_Langevin, f_cv_extended_Lagrangian); - f_description(f_cv_linear, "linear"); + init_feature(f_cv_linear, "linear", f_type_static); - f_description(f_cv_scalar, "scalar"); + init_feature(f_cv_scalar, "scalar", f_type_static); - f_description(f_cv_output_energy, "output energy"); + init_feature(f_cv_output_energy, "output energy", f_type_user); - f_description(f_cv_output_value, "output value"); + init_feature(f_cv_output_value, "output value", f_type_user); - f_description(f_cv_output_velocity, "output velocity"); + init_feature(f_cv_output_velocity, "output velocity", f_type_user); f_req_self(f_cv_output_velocity, f_cv_fdiff_velocity); - f_description(f_cv_output_applied_force, "output applied force"); + init_feature(f_cv_output_applied_force, "output applied force", f_type_user); - f_description(f_cv_output_total_force, "output total force"); + init_feature(f_cv_output_total_force, "output total force", f_type_user); f_req_self(f_cv_output_total_force, f_cv_total_force); - f_description(f_cv_subtract_applied_force, "subtract applied force from total force"); + init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user); f_req_self(f_cv_subtract_applied_force, f_cv_total_force); - f_description(f_cv_lower_boundary, "lower boundary"); + init_feature(f_cv_lower_boundary, "lower boundary", f_type_user); f_req_self(f_cv_lower_boundary, f_cv_scalar); - f_description(f_cv_upper_boundary, "upper boundary"); + init_feature(f_cv_upper_boundary, "upper boundary", f_type_user); f_req_self(f_cv_upper_boundary, f_cv_scalar); - f_description(f_cv_grid, "grid"); + init_feature(f_cv_grid, "grid", f_type_user); f_req_self(f_cv_grid, f_cv_lower_boundary); f_req_self(f_cv_grid, f_cv_upper_boundary); - f_description(f_cv_lower_wall, "lower wall"); - f_req_self(f_cv_lower_wall, f_cv_lower_boundary); - f_req_self(f_cv_lower_wall, f_cv_gradient); + init_feature(f_cv_runave, "running average", f_type_user); - f_description(f_cv_upper_wall, "upper wall"); - f_req_self(f_cv_upper_wall, f_cv_upper_boundary); - f_req_self(f_cv_upper_wall, f_cv_gradient); + init_feature(f_cv_corrfunc, "correlation function", f_type_user); - f_description(f_cv_runave, "running average"); - - f_description(f_cv_corrfunc, "correlation function"); - - // The features below are set programmatically - f_description(f_cv_scripted, "scripted"); - f_description(f_cv_periodic, "periodic"); + init_feature(f_cv_scripted, "scripted", f_type_static); + init_feature(f_cv_periodic, "periodic", f_type_static); f_req_self(f_cv_periodic, f_cv_homogeneous); - f_description(f_cv_scalar, "scalar"); - f_description(f_cv_linear, "linear"); - f_description(f_cv_homogeneous, "homogeneous"); + init_feature(f_cv_scalar, "scalar", f_type_static); + init_feature(f_cv_linear, "linear", f_type_static); + init_feature(f_cv_homogeneous, "homogeneous", f_type_static); } // Initialize feature_states for each instance feature_states.reserve(f_cv_ntot); for (i = 0; i < f_cv_ntot; i++) { - feature_states.push_back(new feature_state(true, false)); + feature_states.push_back(feature_state(true, false)); // Most features are available, so we set them so // and list exceptions below } - // properties that may NOT be enabled as a dependency - int unavailable_deps[] = { - f_cv_lower_boundary, - f_cv_upper_boundary, - f_cv_extended_Lagrangian, - f_cv_Langevin, - f_cv_scripted, - f_cv_periodic, - f_cv_scalar, - f_cv_linear, - f_cv_homogeneous - }; - for (i = 0; i < sizeof(unavailable_deps) / sizeof(unavailable_deps[0]); i++) { - feature_states[unavailable_deps[i]]->available = false; - } +// // properties that may NOT be enabled as a dependency +// // This will be deprecated by feature types +// int unavailable_deps[] = { +// f_cv_lower_boundary, +// f_cv_upper_boundary, +// f_cv_extended_Lagrangian, +// f_cv_Langevin, +// f_cv_scripted, +// f_cv_periodic, +// f_cv_scalar, +// f_cv_linear, +// f_cv_homogeneous +// }; +// for (i = 0; i < sizeof(unavailable_deps) / sizeof(unavailable_deps[0]); i++) { +// feature_states[unavailable_deps[i]].available = false; +// } } @@ -377,34 +393,34 @@ void colvardeps::init_cvc_requires() { features().push_back(new feature); } - f_description(f_cvc_active, "active"); + init_feature(f_cvc_active, "active", f_type_dynamic); // The dependency below may become useful if we use dynamic atom groups // f_req_children(f_cvc_active, f_ag_active); - f_description(f_cvc_scalar, "scalar"); + init_feature(f_cvc_scalar, "scalar", f_type_static); - f_description(f_cvc_gradient, "gradient"); + init_feature(f_cvc_gradient, "gradient", f_type_dynamic); - f_description(f_cvc_inv_gradient, "inverse gradient"); + init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic); f_req_self(f_cvc_inv_gradient, f_cvc_gradient); - f_description(f_cvc_debug_gradient, "debug gradient"); + init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user); f_req_self(f_cvc_debug_gradient, f_cvc_gradient); - f_description(f_cvc_Jacobian, "Jacobian derivative"); + init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic); f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient); - f_description(f_cvc_com_based, "depends on group centers of mass"); + init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static); // Compute total force on first site only to avoid unwanted // coupling to other colvars (see e.g. Ciccotti et al., 2005) - f_description(f_cvc_one_site_total_force, "compute total collective force only from one group center"); + init_feature(f_cvc_one_site_total_force, "compute total collective force only from one group center", f_type_user); f_req_self(f_cvc_one_site_total_force, f_cvc_com_based); - f_description(f_cvc_scalable, "scalable calculation"); + init_feature(f_cvc_scalable, "scalable calculation", f_type_static); f_req_self(f_cvc_scalable, f_cvc_scalable_com); - f_description(f_cvc_scalable_com, "scalable calculation of centers of mass"); + init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static); f_req_self(f_cvc_scalable_com, f_cvc_com_based); @@ -414,23 +430,25 @@ void colvardeps::init_cvc_requires() { } // Initialize feature_states for each instance - // default as unavailable, not enabled + // default as available, not enabled + // except dynamic features which default as unavailable feature_states.reserve(f_cvc_ntot); for (i = 0; i < colvardeps::f_cvc_ntot; i++) { - feature_states.push_back(new feature_state(false, false)); + bool avail = is_dynamic(i) ? false : true; + feature_states.push_back(feature_state(avail, false)); } // Features that are implemented by all cvcs by default // Each cvc specifies what other features are available - feature_states[f_cvc_active]->available = true; - feature_states[f_cvc_gradient]->available = true; + feature_states[f_cvc_active].available = true; + feature_states[f_cvc_gradient].available = true; // Features that are implemented by default if their requirements are - feature_states[f_cvc_one_site_total_force]->available = true; + feature_states[f_cvc_one_site_total_force].available = true; // Features That are implemented only for certain simulation engine configurations - feature_states[f_cvc_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK); - feature_states[f_cvc_scalable]->available = feature_states[f_cvc_scalable_com]->available; + feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK); + feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available; } @@ -442,21 +460,21 @@ void colvardeps::init_ag_requires() { features().push_back(new feature); } - f_description(f_ag_active, "active"); - f_description(f_ag_center, "translational fit"); - f_description(f_ag_rotate, "rotational fit"); - f_description(f_ag_fitting_group, "reference positions group"); - f_description(f_ag_fit_gradient_group, "fit gradient for main group"); - f_description(f_ag_fit_gradient_ref, "fit gradient for reference group"); - f_description(f_ag_atom_forces, "atomic forces"); + init_feature(f_ag_active, "active", f_type_dynamic); + init_feature(f_ag_center, "translational fit", f_type_static); + init_feature(f_ag_rotate, "rotational fit", f_type_static); + init_feature(f_ag_fitting_group, "reference positions group", f_type_static); + init_feature(f_ag_fit_gradient_group, "fit gradient for main group", f_type_static); + init_feature(f_ag_fit_gradient_ref, "fit gradient for reference group", f_type_static); + init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic); // parallel calculation implies that we have at least a scalable center of mass, // but f_ag_scalable is kept as a separate feature to deal with future dependencies - f_description(f_ag_scalable, "scalable group calculation"); - f_description(f_ag_scalable_com, "scalable group center of mass calculation"); + init_feature(f_ag_scalable, "scalable group calculation", f_type_static); + init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static); f_req_self(f_ag_scalable, f_ag_scalable_com); -// f_description(f_ag_min_msd_fit, "minimum MSD fit") +// init_feature(f_ag_min_msd_fit, "minimum MSD fit") // f_req_self(f_ag_min_msd_fit, f_ag_center) // f_req_self(f_ag_min_msd_fit, f_ag_rotate) // f_req_exclude(f_ag_min_msd_fit, f_ag_fitting_group) @@ -466,15 +484,15 @@ void colvardeps::init_ag_requires() { // default as unavailable, not enabled feature_states.reserve(f_ag_ntot); for (i = 0; i < colvardeps::f_ag_ntot; i++) { - feature_states.push_back(new feature_state(false, false)); + feature_states.push_back(feature_state(false, false)); } // Features that are implemented (or not) by all atom groups - feature_states[f_ag_active]->available = true; + feature_states[f_ag_active].available = true; // f_ag_scalable_com is provided by the CVC iff it is COM-based - feature_states[f_ag_scalable_com]->available = false; + feature_states[f_ag_scalable_com].available = false; // TODO make f_ag_scalable depend on f_ag_scalable_com (or something else) - feature_states[f_ag_scalable]->available = true; + feature_states[f_ag_scalable].available = true; } @@ -482,7 +500,7 @@ void colvardeps::print_state() { size_t i; cvm::log("Enabled features of " + description); for (i = 0; i < feature_states.size(); i++) { - if (feature_states[i]->enabled) + if (feature_states[i].enabled) cvm::log("- " + features()[i]->description); } for (i=0; i feature_states; + +private: + /// List of the states of all features + std::vector feature_states; + + /// Enum of possible feature types + enum feature_type { + f_type_not_set, + f_type_dynamic, + f_type_user, + f_type_static + }; + +public: + /// Pair a numerical feature ID with a description and type + void init_feature(int feature_id, const char *description, feature_type type = f_type_not_set); /// Describes a feature and its dependecies /// used in a static array within each subclass @@ -83,8 +91,18 @@ public: // features that this feature requires in children std::vector requires_children; + + inline bool is_dynamic() { return type == f_type_dynamic; } + inline bool is_static() { return type == f_type_static; } + inline bool is_user() { return type == f_type_user; } + /// Type of this feature, from the enum feature_type + feature_type type; }; + inline bool is_dynamic(int id) { return features()[id]->type == f_type_dynamic; } + inline bool is_static(int id) { return features()[id]->type == f_type_static; } + inline bool is_user(int id) { return features()[id]->type == f_type_user; } + // Accessor to array of all features with deps, static in most derived classes // Subclasses with dynamic dependency trees may override this // with a non-static array @@ -100,9 +118,8 @@ public: /// (useful for cvcs because their children are member objects) void remove_all_children(); - - private: + // pointers to objects this object depends on // list should be maintained by any code that modifies the object // this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions @@ -130,16 +147,28 @@ public: // Checks whether given feature is enabled // Defaults to querying f_*_active inline bool is_enabled(int f = f_cv_active) const { - return feature_states[f]->enabled; + return feature_states[f].enabled; } // Checks whether given feature is available // Defaults to querying f_*_active inline bool is_available(int f = f_cv_active) const { - return feature_states[f]->available; + return feature_states[f].available; } - void provide(int feature_id); // set the feature's flag to available in local object + /// Set the feature's available flag, without checking + /// To be used for dynamic properties + /// dependencies will be checked by enable() + void provide(int feature_id, bool truefalse = true); + + /// Set the feature's enabled flag, without dependency check or resolution + /// To be used for static properties only + /// Checking for availability is up to the caller + void set_enabled(int feature_id, bool truefalse = true); + +protected: + + /// Parse a keyword and enable a feature accordingly bool get_keyval_feature(colvarparse *cvp, @@ -147,6 +176,8 @@ public: int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal); +public: + int enable(int f, bool dry_run = false, bool toplevel = true); // enable a feature and recursively solve its dependencies // dry_run is set to true to recursively test if a feature is available, without enabling it // int disable(int f); @@ -165,6 +196,7 @@ public: f_cvb_get_total_force, // requires total forces f_cvb_history_dependent, // depends on simulation history f_cvb_scalar_variables, // requires scalar colvars + f_cvb_calc_pmf, // whether this bias will compute a PMF f_cvb_ntot }; @@ -216,12 +248,6 @@ public: /// be used by the biases or in analysis (needs lower and upper /// boundary) f_cv_grid, - /// \brief Apply a restraining potential (|x-xb|^2) to the colvar - /// when it goes below the lower wall - f_cv_lower_wall, - /// \brief Apply a restraining potential (|x-xb|^2) to the colvar - /// when it goes above the upper wall - f_cv_upper_wall, /// \brief Compute running average f_cv_runave, /// \brief Compute time correlation function diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index b9a435152b..10cd3c0e47 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -36,6 +36,9 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) "variable module twice.\n"); return; } + + depth_s = 0; + cvm::log(cvm::line_marker); cvm::log("Initializing the collective variables module, version "+ cvm::to_str(COLVARS_VERSION)+".\n"); @@ -71,6 +74,48 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) } +colvarmodule * colvarmodule::main() +{ + return proxy->colvars; +} + + +std::vector *colvarmodule::variables() +{ + return &colvars; +} + + +std::vector *colvarmodule::variables_active() +{ + return &colvars_active; +} + + +std::vector *colvarmodule::variables_active_smp() +{ + return &colvars_smp; +} + + +std::vector *colvarmodule::variables_active_smp_items() +{ + return &colvars_smp_items; +} + + +std::vector *colvarmodule::biases_active() +{ + return &(biases_active_); +} + + +size_t colvarmodule::size() const +{ + return colvars.size() + biases.size(); +} + + int colvarmodule::read_config_file(char const *config_filename) { cvm::log(cvm::line_marker); @@ -118,8 +163,29 @@ int colvarmodule::read_config_string(std::string const &config_str) } +std::istream & colvarmodule::getline(std::istream &is, std::string &line) +{ + std::string l; + if (std::getline(is, l)) { + size_t const sz = l.size(); + if (sz > 0) { + if (l[sz-1] == '\r' ) { + line = l.substr(0, sz-1); + } else { + line = l; + } + } else { + line.clear(); + } + } + return is; +} + + int colvarmodule::parse_config(std::string &conf) { + extra_conf.clear(); + // parse global options if (catch_input_errors(parse_global_params(conf))) { return get_error(); @@ -140,6 +206,15 @@ int colvarmodule::parse_config(std::string &conf) return get_error(); } + if (extra_conf.size()) { + catch_input_errors(parse_global_params(extra_conf)); + catch_input_errors(parse_colvars(extra_conf)); + catch_input_errors(parse_biases(extra_conf)); + parse->check_keywords(extra_conf, "colvarmodule"); + extra_conf.clear(); + if (get_error() != COLVARS_OK) return get_error(); + } + cvm::log(cvm::line_marker); cvm::log("Collective variables module (re)initialized.\n"); cvm::log(cvm::line_marker); @@ -156,11 +231,20 @@ int colvarmodule::parse_config(std::string &conf) } +int colvarmodule::append_new_config(std::string const &new_conf) +{ + extra_conf += new_conf; + return COLVARS_OK; +} + + int colvarmodule::parse_global_params(std::string const &conf) { + colvarmodule *cvm = cvm::main(); + std::string index_file_name; if (parse->get_keyval(conf, "indexFile", index_file_name)) { - read_index_file(index_file_name.c_str()); + cvm->read_index_file(index_file_name.c_str()); } if (parse->get_keyval(conf, "smp", proxy->b_smp_active, proxy->b_smp_active)) { @@ -216,8 +300,8 @@ int colvarmodule::parse_colvars(std::string const &conf) if (colvar_conf.size()) { cvm::log(cvm::line_marker); cvm::increase_depth(); - colvars.push_back(new colvar(colvar_conf)); - if (cvm::get_error() || + colvars.push_back(new colvar()); + if (((colvars.back())->init(colvar_conf) != COLVARS_OK) || ((colvars.back())->check_keywords(colvar_conf, "colvar") != COLVARS_OK)) { cvm::log("Error while constructing colvar number " + cvm::to_str(colvars.size()) + " : deleting."); @@ -262,8 +346,7 @@ bool colvarmodule::check_new_bias(std::string &conf, char const *key) template int colvarmodule::parse_biases_type(std::string const &conf, - char const *keyword, - size_t &bias_count) + char const *keyword) { std::string bias_conf = ""; size_t conf_saved_pos = 0; @@ -277,7 +360,6 @@ int colvarmodule::parse_biases_type(std::string const &conf, return COLVARS_ERROR; } cvm::decrease_depth(); - bias_count++; } else { cvm::error("Error: keyword \""+std::string(keyword)+"\" found without configuration.\n", INPUT_ERROR); @@ -295,28 +377,28 @@ int colvarmodule::parse_biases(std::string const &conf) cvm::log("Initializing the collective variables biases.\n"); /// initialize ABF instances - parse_biases_type(conf, "abf", n_abf_biases); + parse_biases_type(conf, "abf"); /// initialize adaptive linear biases - parse_biases_type(conf, "ALB", n_rest_biases); + parse_biases_type(conf, "ALB"); /// initialize harmonic restraints - parse_biases_type(conf, "harmonic", n_rest_biases); + parse_biases_type(conf, "harmonic"); /// initialize harmonic walls restraints - parse_biases_type(conf, "harmonicWalls", n_rest_biases); + parse_biases_type(conf, "harmonicWalls"); /// initialize histograms - parse_biases_type(conf, "histogram", n_histo_biases); + parse_biases_type(conf, "histogram"); /// initialize histogram restraints - parse_biases_type(conf, "histogramRestraint", n_rest_biases); + parse_biases_type(conf, "histogramRestraint"); /// initialize linear restraints - parse_biases_type(conf, "linear", n_rest_biases); + parse_biases_type(conf, "linear"); /// initialize metadynamics instances - parse_biases_type(conf, "metadynamics", n_meta_biases); + parse_biases_type(conf, "metadynamics"); if (use_scripted_forces) { cvm::log(cvm::line_marker); @@ -363,6 +445,36 @@ int colvarmodule::parse_biases(std::string const &conf) } +int colvarmodule::num_biases_feature(int feature_id) +{ + colvarmodule *cv = cvm::main(); + size_t n = 0; + for (std::vector::iterator bi = cv->biases.begin(); + bi != cv->biases.end(); + bi++) { + if ((*bi)->is_enabled(feature_id)) { + n++; + } + } + return n; +} + + +int colvarmodule::num_biases_type(std::string const &type) +{ + colvarmodule *cv = cvm::main(); + size_t n = 0; + for (std::vector::iterator bi = cv->biases.begin(); + bi != cv->biases.end(); + bi++) { + if ((*bi)->bias_type == type) { + n++; + } + } + return n; +} + + int colvarmodule::catch_input_errors(int result) { if (result != COLVARS_OK || get_error()) { @@ -376,8 +488,9 @@ int colvarmodule::catch_input_errors(int result) colvarbias * colvarmodule::bias_by_name(std::string const &name) { - for (std::vector::iterator bi = biases.begin(); - bi != biases.end(); + colvarmodule *cv = cvm::main(); + for (std::vector::iterator bi = cv->biases.begin(); + bi != cv->biases.end(); bi++) { if ((*bi)->name == name) { return (*bi); @@ -388,8 +501,9 @@ colvarbias * colvarmodule::bias_by_name(std::string const &name) { colvar *colvarmodule::colvar_by_name(std::string const &name) { - for (std::vector::iterator cvi = colvars.begin(); - cvi != colvars.end(); + colvarmodule *cv = cvm::main(); + for (std::vector::iterator cvi = cv->colvars.begin(); + cvi != cv->colvars.end(); cvi++) { if ((*cvi)->name == name) { return (*cvi); @@ -555,9 +669,15 @@ int colvarmodule::calc_colvars() int error_code = COLVARS_OK; std::vector::iterator cvi; - // Determine which colvars are active at this time step - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { - (*cvi)->feature_states[colvardeps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0); + // Determine which colvars are active at this iteration + variables_active()->resize(0); + variables_active()->reserve(variables()->size()); + for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) { + // This is a dynamic feature - the next call should be to enable() + // or disable() when dynamic dependency resolution is fully implemented + (*cvi)->set_enabled(colvardeps::f_cv_active, + step_absolute() % (*cvi)->get_time_step_factor() == 0); + variables_active()->push_back(*cvi); } // if SMP support is available, split up the work @@ -565,25 +685,24 @@ int colvarmodule::calc_colvars() // first, calculate how much work (currently, how many active CVCs) each colvar has - colvars_smp.resize(0); - colvars_smp_items.resize(0); + variables_active_smp()->resize(0); + variables_active_smp_items()->resize(0); - colvars_smp.reserve(colvars.size()); - colvars_smp_items.reserve(colvars.size()); + variables_active_smp()->reserve(variables_active()->size()); + variables_active_smp_items()->reserve(variables_active()->size()); // set up a vector containing all components cvm::increase_depth(); - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) { - if (!(*cvi)->is_enabled()) continue; error_code |= (*cvi)->update_cvc_flags(); size_t num_items = (*cvi)->num_active_cvcs(); - colvars_smp.reserve(colvars_smp.size() + num_items); - colvars_smp_items.reserve(colvars_smp_items.size() + num_items); + variables_active_smp()->reserve(variables_active_smp()->size() + num_items); + variables_active_smp_items()->reserve(variables_active_smp_items()->size() + num_items); for (size_t icvc = 0; icvc < num_items; icvc++) { - colvars_smp.push_back(*cvi); - colvars_smp_items.push_back(icvc); + variables_active_smp()->push_back(*cvi); + variables_active_smp_items()->push_back(icvc); } } cvm::decrease_depth(); @@ -592,8 +711,7 @@ int colvarmodule::calc_colvars() error_code |= proxy->smp_colvars_loop(); cvm::increase_depth(); - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { - if (!(*cvi)->is_enabled()) continue; + for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) { error_code |= (*cvi)->collect_cvc_data(); } cvm::decrease_depth(); @@ -602,8 +720,7 @@ int colvarmodule::calc_colvars() // calculate colvars one at a time cvm::increase_depth(); - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { - if (!(*cvi)->is_enabled()) continue; + for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) { error_code |= (*cvi)->calc(); if (cvm::get_error()) { return COLVARS_ERROR; @@ -627,6 +744,18 @@ int colvarmodule::calc_biases() std::vector::iterator bi; int error_code = COLVARS_OK; + // Total bias energy is reset before calling scripted biases + total_bias_energy = 0.0; + + // update the list of active biases + biases_active()->resize(0); + biases_active()->reserve(biases.size()); + for (bi = biases.begin(); bi != biases.end(); bi++) { + if ((*bi)->is_enabled()) { + biases_active()->push_back(*bi); + } + } + // if SMP support is available, split up the work if (proxy->smp_enabled() == COLVARS_OK) { @@ -645,7 +774,7 @@ int colvarmodule::calc_biases() } cvm::increase_depth(); - for (bi = biases.begin(); bi != biases.end(); bi++) { + for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) { error_code |= (*bi)->update(); if (cvm::get_error()) { return error_code; @@ -654,12 +783,10 @@ int colvarmodule::calc_biases() cvm::decrease_depth(); } - cvm::real total_bias_energy = 0.0; - for (bi = biases.begin(); bi != biases.end(); bi++) { + for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) { total_bias_energy += (*bi)->get_energy(); } - proxy->add_energy(total_bias_energy); return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } @@ -675,7 +802,7 @@ int colvarmodule::update_colvar_forces() if (cvm::debug() && biases.size()) cvm::log("Collecting forces from all biases.\n"); cvm::increase_depth(); - for (bi = biases.begin(); bi != biases.end(); bi++) { + for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) { (*bi)->communicate_forces(); if (cvm::get_error()) { return COLVARS_ERROR; @@ -687,6 +814,11 @@ int colvarmodule::update_colvar_forces() error_code |= calc_scripted_forces(); } + // Now we have collected energies from both built-in and scripted biases + if (cvm::debug()) + cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n"); + proxy->add_energy(total_bias_energy); + cvm::real total_colvar_energy = 0.0; // sum up the forces for each colvar, including wall forces // and integrate any internal @@ -695,7 +827,7 @@ int colvarmodule::update_colvar_forces() cvm::log("Updating the internal degrees of freedom " "of colvars (if they have any).\n"); cvm::increase_depth(); - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) { // Here we call even inactive colvars, so they accumulate biasing forces // as well as update their extended-system dynamics total_colvar_energy += (*cvi)->update_forces_energy(); @@ -704,6 +836,8 @@ int colvarmodule::update_colvar_forces() } } cvm::decrease_depth(); + if (cvm::debug()) + cvm::log("Adding total colvar energy: " + cvm::to_str(total_colvar_energy) + "\n"); proxy->add_energy(total_colvar_energy); // make collective variables communicate their forces to their @@ -711,9 +845,8 @@ int colvarmodule::update_colvar_forces() if (cvm::debug()) cvm::log("Communicating forces from the colvars to the atoms.\n"); cvm::increase_depth(); - for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) { + for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) { if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) { - if (!(*cvi)->is_enabled()) continue; (*cvi)->communicate_forces(); if (cvm::get_error()) { return COLVARS_ERROR; @@ -800,8 +933,8 @@ int colvarmodule::analyze() cvm::log("Performing analysis.\n"); // perform colvar-specific analysis - for (std::vector::iterator cvi = colvars.begin(); - cvi != colvars.end(); + for (std::vector::iterator cvi = variables_active()->begin(); + cvi != variables_active()->end(); cvi++) { cvm::increase_depth(); (*cvi)->analyze(); @@ -825,8 +958,8 @@ int colvarmodule::setup() { if (this->size() == 0) return cvm::get_error(); // loop over all components of all colvars to reset masses of all groups - for (std::vector::iterator cvi = colvars.begin(); - cvi != colvars.end(); cvi++) { + for (std::vector::iterator cvi = variables()->begin(); + cvi != variables()->end(); cvi++) { (*cvi)->setup(); } return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); @@ -934,18 +1067,18 @@ int colvarmodule::setup_output() cvm::log("The restart output state file will be \""+restart_out_name+"\".\n"); } - output_prefix = proxy->output_prefix(); - if (output_prefix.size()) { + output_prefix() = proxy->output_prefix(); + if (output_prefix().size()) { cvm::log("The final output state file will be \""+ - (output_prefix.size() ? - std::string(output_prefix+".colvars.state") : + (output_prefix().size() ? + std::string(output_prefix()+".colvars.state") : std::string("colvars.state"))+"\".\n"); // cvm::log (cvm::line_marker); } cv_traj_name = - (output_prefix.size() ? - std::string(output_prefix+".colvars.traj") : + (output_prefix().size() ? + std::string(output_prefix()+".colvars.traj") : std::string("")); if (cv_traj_freq && cv_traj_name.size()) { @@ -1077,14 +1210,14 @@ continue the previous simulation.\n\n"); cvm::log(cvm::line_marker); // update this ahead of time in this special case - output_prefix = proxy->input_prefix(); - cvm::log("All output files will now be saved with the prefix \""+output_prefix+".tmp.*\".\n"); + output_prefix() = proxy->input_prefix(); + cvm::log("All output files will now be saved with the prefix \""+output_prefix()+".tmp.*\".\n"); cvm::log(cvm::line_marker); cvm::log("Please review the important warning above. After that, you may rename:\n\ -\""+output_prefix+".tmp.colvars.state\"\n\ +\""+output_prefix()+".tmp.colvars.state\"\n\ to:\n\ \""+ proxy->input_prefix()+".colvars.state\"\n"); - output_prefix = output_prefix+".tmp"; + output_prefix() = output_prefix()+".tmp"; write_output_files(); cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR); } @@ -1104,8 +1237,8 @@ int colvarmodule::write_output_files() // if this is a simulation run (i.e. not a postprocessing), output data // must be written to be able to restart the simulation std::string const out_name = - (output_prefix.size() ? - std::string(output_prefix+".colvars.state") : + (output_prefix().size() ? + std::string(output_prefix()+".colvars.state") : std::string("colvars.state")); cvm::log("Saving collective variables state to \""+out_name+"\".\n"); @@ -1340,7 +1473,8 @@ std::ostream & colvarmodule::write_traj(std::ostream &os) void cvm::log(std::string const &message) { - size_t const d = depth(); + // allow logging when the module is not fully initialized + size_t const d = (cvm::main() != NULL) ? depth() : 0; if (d > 0) proxy->log((std::string(2*d, ' '))+message); else @@ -1365,19 +1499,20 @@ void cvm::decrease_depth() size_t & cvm::depth() { // NOTE: do not call log() or error() here, to avoid recursion - size_t const nt = proxy->smp_num_threads(); + colvarmodule *cv = cvm::main(); if (proxy->smp_enabled() == COLVARS_OK) { - if (depth_v.size() != nt) { - // update array of depths + int const nt = proxy->smp_num_threads(); + if (int(cv->depth_v.size()) != nt) { proxy->smp_lock(); - if (depth_v.size() > 0) { depth_s = depth_v[0]; } - depth_v.clear(); - depth_v.assign(nt, depth_s); + // update array of depths + if (cv->depth_v.size() > 0) { cv->depth_s = cv->depth_v[0]; } + cv->depth_v.clear(); + cv->depth_v.assign(nt, cv->depth_s); proxy->smp_unlock(); } - return depth_v[proxy->smp_thread_id()]; + return cv->depth_v[proxy->smp_thread_id()]; } - return depth_s; + return cv->depth_s; } @@ -1451,8 +1586,8 @@ int cvm::read_index_file(char const *filename) FILE_ERROR); } } - cvm::index_group_names.push_back(group_name); - cvm::index_groups.push_back(std::vector ()); + index_group_names.push_back(group_name); + index_groups.push_back(std::vector()); } else { cvm::error("Error: in parsing index file \""+ std::string(filename)+"\".\n", @@ -1462,7 +1597,7 @@ int cvm::read_index_file(char const *filename) int atom_number = 1; size_t pos = is.tellg(); while ( (is >> atom_number) && (atom_number > 0) ) { - (cvm::index_groups.back()).push_back(atom_number); + (index_groups.back()).push_back(atom_number); pos = is.tellg(); } is.clear(); @@ -1532,8 +1667,8 @@ int cvm::load_coords_xyz(char const *filename, + std::string(filename) + ".\n", INPUT_ERROR); } // skip comment line - std::getline(xyz_is, line); - std::getline(xyz_is, line); + cvm::getline(xyz_is, line); + cvm::getline(xyz_is, line); xyz_is.width(255); std::vector::iterator pos_i = pos.begin(); @@ -1543,7 +1678,7 @@ int cvm::load_coords_xyz(char const *filename, for ( ; pos_i != pos.end() ; pos_i++, index++) { while ( next < *index ) { - std::getline(xyz_is, line); + cvm::getline(xyz_is, line); next++; } xyz_is >> symbol; @@ -1558,15 +1693,9 @@ int cvm::load_coords_xyz(char const *filename, return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } -// static pointers -std::vector colvarmodule::colvars; -std::vector colvarmodule::biases; -size_t colvarmodule::n_abf_biases = 0; -size_t colvarmodule::n_rest_biases = 0; -size_t colvarmodule::n_histo_biases = 0; -size_t colvarmodule::n_meta_biases = 0; -colvarproxy *colvarmodule::proxy = NULL; +// shared pointer to the proxy object +colvarproxy *colvarmodule::proxy = NULL; // static runtime data cvm::real colvarmodule::debug_gradients_step_size = 1.0e-07; @@ -1575,14 +1704,9 @@ long colvarmodule::it = 0; long colvarmodule::it_restart = 0; size_t colvarmodule::restart_out_freq = 0; size_t colvarmodule::cv_traj_freq = 0; -size_t colvarmodule::depth_s = 0; -std::vector colvarmodule::depth_v(0); bool colvarmodule::b_analysis = false; -std::list colvarmodule::index_group_names; -std::list > colvarmodule::index_groups; -bool colvarmodule::use_scripted_forces = false; -bool colvarmodule::scripting_after_biases = true; -std::string colvarmodule::output_prefix = ""; +bool colvarmodule::use_scripted_forces = false; +bool colvarmodule::scripting_after_biases = true; // i/o constants size_t const colvarmodule::it_width = 12; diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 0e98709adb..b4f80e0b5e 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -11,7 +11,7 @@ #define COLVARMODULE_H #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2016-12-27" +#define COLVARS_VERSION "2017-03-09" #endif #ifndef COLVARS_DEBUG @@ -161,12 +161,37 @@ public: /// dt) static real debug_gradients_step_size; - /// Prefix for all output files for this run - static std::string output_prefix; +private: + /// Prefix for all output files for this run + std::string cvm_output_prefix; + +public: + /// Accessor for the above + static inline std::string &output_prefix() + { + colvarmodule *cv = colvarmodule::main(); + return cv->cvm_output_prefix; + } + +private: /// Array of collective variables - static std::vector colvars; + std::vector colvars; + + /// Array of collective variables + std::vector colvars_active; + + /// Collective variables to be calculated on different threads; + /// colvars with multple items (e.g. multiple active CVCs) are duplicated + std::vector colvars_smp; + /// Indexes of the items to calculate for each colvar + std::vector colvars_smp_items; + +public: + + /// Array of collective variables + std::vector *variables(); /* TODO: implement named CVCs /// Array of named (reusable) collective variable components @@ -177,26 +202,31 @@ public: } */ + /// Collective variables with the active flag on + std::vector *variables_active(); + /// Collective variables to be calculated on different threads; /// colvars with multple items (e.g. multiple active CVCs) are duplicated - std::vector colvars_smp; + std::vector *variables_active_smp(); + /// Indexes of the items to calculate for each colvar - std::vector colvars_smp_items; + std::vector *variables_active_smp_items(); /// Array of collective variable biases - static std::vector biases; - /// \brief Number of ABF biases initialized (in normal conditions - /// should be 1) - static size_t n_abf_biases; - /// \brief Number of metadynamics biases initialized (in normal - /// conditions should be 1) - static size_t n_meta_biases; - /// \brief Number of restraint biases initialized (no limit on the - /// number) - static size_t n_rest_biases; - /// \brief Number of histograms initialized (no limit on the - /// number) - static size_t n_histo_biases; + std::vector biases; + + /// Energy of built-in and scripted biases, summed per time-step + real total_bias_energy; + +private: + + /// Array of active collective variable biases + std::vector biases_active_; + +public: + + /// Array of active collective variable biases + std::vector *biases_active(); /// \brief Whether debug output should be enabled (compile-time option) static inline bool debug() @@ -205,10 +235,7 @@ public: } /// \brief How many objects are configured yet? - inline size_t size() const - { - return colvars.size() + biases.size(); - } + size_t size() const; /// \brief Constructor \param config_name Configuration file name /// \param restart_name (optional) Restart file name @@ -230,9 +257,12 @@ public: /// \brief Parse a "clean" config string (no comments) int parse_config(std::string &conf); - // Parse functions (setup internal data based on a string) + /// Allow reading from Windows text files using using std::getline + /// (which can still be used when the text is produced by Colvars itself) + static std::istream & getline(std::istream &is, std::string &line); + /// Parse the few module's global parameters int parse_global_params(std::string const &conf); @@ -242,14 +272,33 @@ public: /// Parse and initialize collective variable biases int parse_biases(std::string const &conf); + /// \brief Add new configuration during parsing (e.g. to implement + /// back-compatibility); cannot be nested, i.e. conf should not contain + /// anything that triggers another call + int append_new_config(std::string const &conf); + +private: + + /// Auto-generated configuration during parsing (e.g. to implement + /// back-compatibility) + std::string extra_conf; + /// Parse and initialize collective variable biases of a specific type template - int parse_biases_type(std::string const &conf, char const *keyword, size_t &bias_count); + int parse_biases_type(std::string const &conf, char const *keyword); /// Test error condition and keyword parsing /// on error, delete new bias bool check_new_bias(std::string &conf, char const *key); +public: + + /// Return how many biases have this feature enabled + static int num_biases_feature(int feature_id); + + /// Return how many biases are defined with this type + static int num_biases_type(std::string const &type); + private: /// Useful wrapper to interrupt parsing if any error occurs int catch_input_errors(int result); @@ -449,13 +498,13 @@ public: /// \brief Names of groups from a Gromacs .ndx file to be read at startup - static std::list index_group_names; + std::list index_group_names; /// \brief Groups from a Gromacs .ndx file read at startup - static std::list > index_groups; + std::list > index_groups; /// \brief Read a Gromacs .ndx file - static int read_index_file(char const *filename); + int read_index_file(char const *filename); /// \brief Create atoms from a file \param filename name of the file @@ -515,13 +564,13 @@ protected: /// Output restart file colvarmodule::ofstream restart_out_os; -protected: +private: /// Counter for the current depth in the object hierarchy (useg e.g. in output) - static size_t depth_s; + size_t depth_s; /// Thread-specific depth - static std::vector depth_v; + std::vector depth_v; public: @@ -552,6 +601,10 @@ public: /// from the hosting program; it is static in order to be accessible /// from static functions in the colvarmodule class static colvarproxy *proxy; + + /// \brief Accessor for the above + static colvarmodule *main(); + }; diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp index 4d2e17f098..8055d925db 100644 --- a/lib/colvars/colvarparse.cpp +++ b/lib/colvars/colvarparse.cpp @@ -503,7 +503,7 @@ int colvarparse::check_keywords(std::string &conf, char const *key) std::string line; std::istringstream is(conf); - while (std::getline(is, line)) { + while (cvm::getline(is, line)) { if (line.size() == 0) continue; if (line.find_first_not_of(white_space) == @@ -539,10 +539,9 @@ int colvarparse::check_keywords(std::string &conf, char const *key) std::istream & colvarparse::getline_nocomments(std::istream &is, - std::string &line, - char const delim) + std::string &line) { - std::getline(is, line, delim); + cvm::getline(is, line); size_t const comment = line.find('#'); if (comment != std::string::npos) { line.erase(comment); diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h index acdc46ddc9..9f116caafd 100644 --- a/lib/colvars/colvarparse.h +++ b/lib/colvars/colvarparse.h @@ -304,8 +304,7 @@ public: /// \brief Works as std::getline() but also removes everything /// between a comment character and the following newline static std::istream & getline_nocomments(std::istream &is, - std::string &s, - char const delim = '\n'); + std::string &s); /// Check if the content of the file has matching braces bool brace_check(std::string const &conf, diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index bdf65c0b1f..5b216c9d41 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -336,8 +336,6 @@ public: /// Are total forces being used? virtual bool total_forces_enabled() const { - cvm::error("Error: total forces are currently not implemented.\n", - COLVARS_NOT_IMPLEMENTED); return false; } diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index ffb83e9780..f192dcb7c0 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -12,6 +12,7 @@ #include #include "colvarscript.h" +#include "colvardeps.h" colvarscript::colvarscript(colvarproxy *p) @@ -221,6 +222,16 @@ int colvarscript::run(int argc, char const *argv[]) { } } + if (cmd == "addenergy") { + if (argc == 3) { + colvars->total_bias_energy += strtod(argv[2], NULL); + return COLVARS_OK; + } else { + result = "Wrong arguments to command \"addenergy\"\n" + help_string(); + return COLVARSCRIPT_ERROR; + } + } + result = "Syntax error\n" + help_string(); return COLVARSCRIPT_ERROR; } @@ -263,10 +274,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) { } if (subcmd == "delete") { - if (cv->biases.size() > 0) { - result = "Cannot delete a colvar currently used by biases, delete those biases first"; - return COLVARSCRIPT_ERROR; + size_t i; + for (i = 0; i < cv->biases.size(); i++) { + delete cv->biases[i]; } + cv->biases.resize(0); // colvar destructor is tasked with the cleanup delete cv; // TODO this could be done by the destructors @@ -338,9 +350,8 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) { return COLVARS_OK; } - if (subcmd == "state") { - cv->print_state(); - return COLVARS_OK; + if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) { + return proc_features(cv, argc, argv); } result = "Syntax error\n" + help_string(); @@ -379,11 +390,6 @@ int colvarscript::proc_bias(int argc, char const *argv[]) { return COLVARS_OK; } - if (subcmd == "state") { - b->print_state(); - return COLVARS_OK; - } - // Subcommands for MW ABF if (subcmd == "bin") { int r = b->current_bin(); @@ -420,6 +426,10 @@ int colvarscript::proc_bias(int argc, char const *argv[]) { return COLVARS_OK; } + if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) { + return proc_features(b, argc, argv); + } + if (argc >= 4) { std::string param = argv[3]; if (subcmd == "count") { @@ -441,6 +451,83 @@ int colvarscript::proc_bias(int argc, char const *argv[]) { } +int colvarscript::proc_features(colvardeps *obj, + int argc, char const *argv[]) { + // size was already checked before calling + std::string subcmd = argv[2]; + + if (argc == 3) { + if (subcmd == "state") { + // TODO make this returned as result? + obj->print_state(); + return COLVARS_OK; + } + + // get and set commands require more arguments + result = "Syntax error\n" + help_string(); + return COLVARSCRIPT_ERROR; + } + + if ((subcmd == "get") || (subcmd == "set")) { + std::vector &features = obj->features(); + std::string const req_feature(argv[3]); + colvardeps::feature *f = NULL; + int fid = 0; + for (fid = 0; fid < int(features.size()); fid++) { + if (features[fid]->description == + colvarparse::to_lower_cppstr(req_feature)) { + f = features[fid]; + break; + } + } + + if (f == NULL) { + + result = "Error: feature \""+req_feature+"\" does not exist.\n"; + return COLVARSCRIPT_ERROR; + + } else { + + if (! obj->is_available(fid)) { + result = "Error: feature \""+req_feature+"\" is unavailable.\n"; + return COLVARSCRIPT_ERROR; + } + + if (subcmd == "get") { + result = cvm::to_str(obj->is_enabled(fid) ? 1 : 0); + return COLVARS_OK; + } + + if (subcmd == "set") { + if (argc == 5) { + std::string const yesno = + colvarparse::to_lower_cppstr(std::string(argv[4])); + if ((yesno == std::string("yes")) || + (yesno == std::string("on")) || + (yesno == std::string("1"))) { + obj->enable(fid); + return COLVARS_OK; + } else if ((yesno == std::string("no")) || + (yesno == std::string("off")) || + (yesno == std::string("0"))) { + // TODO disable() function does not exist yet, + // dependencies will not be resolved + // obj->disable(fid); + obj->set_enabled(fid, false); + return COLVARS_OK; + } + } + result = "Syntax error\n" + help_string(); + return COLVARSCRIPT_ERROR; + } + } + } + + result = "Syntax error\n" + help_string(); + return COLVARSCRIPT_ERROR; +} + + std::string colvarscript::help_string() { std::string buf; @@ -459,6 +546,7 @@ Input and output:\n\ load -- load a state file (requires configuration)\n\ save -- save a state file (requires configuration)\n\ update -- recalculate colvars and biases\n\ + addenergy -- add to the total bias energy\n\ printframe -- return a summary of the current frame\n\ printframelabels -- return labels to annotate printframe's output\n"; @@ -478,12 +566,17 @@ Accessing collective variables:\n\ colvar addforce -- apply given force on colvar \n\ colvar getconfig -- return config string of colvar \n\ colvar cvcflags -- enable or disable cvcs according to 0/1 flags\n\ + colvar get -- get the value of the colvar feature \n\ + colvar set -- set the value of the colvar feature \n\ \n\ Accessing biases:\n\ bias energy -- return the current energy of bias \n\ bias update -- recalculate bias \n\ bias delete -- delete bias \n\ - bias getconfig -- return config string of bias \n"; + bias getconfig -- return config string of bias \n\ + bias get -- get the value of the bias feature \n\ + bias set -- set the value of the bias feature \n\ +"; return buf; } diff --git a/lib/colvars/colvarscript.h b/lib/colvars/colvarscript.h index bfb8381e3b..46b1ddd203 100644 --- a/lib/colvars/colvarscript.h +++ b/lib/colvars/colvarscript.h @@ -51,6 +51,10 @@ private: /// Run subcommands on bias int proc_bias(int argc, char const *argv[]); + /// Run subcommands on base colvardeps object (colvar, bias, ...) + int proc_features(colvardeps *obj, + int argc, char const *argv[]); + /// Builds and return a short help std::string help_string(void); }; diff --git a/potentials/Al_jpc.agni b/potentials/Al_jpc.agni new file mode 100644 index 0000000000..0a82a3c8f4 --- /dev/null +++ b/potentials/Al_jpc.agni @@ -0,0 +1,3020 @@ +# DATE: 2017-02-24 CONTRIBUTOR: Venkatesh Botu CITATION: Botu, V., Batra, R., Chapman, J., and Ramprasad, R., J. 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a191b22220..1fca89f25f 100644 --- a/potentials/Al_prb.agni +++ b/potentials/Al_prb.agni @@ -1,4 +1,5 @@ # DATE: 2016-11-11 CONTRIBUTOR: Venkatesh Botu CITATION: Botu, V. and Ramprasad, R., Phys. Rev. B, 92, 094306 (2015) +# This potential is deprecated. Please use Al_jpc.agni instead. # This potential file is parameterized for metal units generation 1 diff --git a/potentials/CC.KC b/potentials/CC.KC new file mode 100644 index 0000000000..6559eb4120 --- /dev/null +++ b/potentials/CC.KC @@ -0,0 +1,8 @@ +# Kolmogorov-Crespi Potential +# +# Cite as A.N. Kolmogorov & V. H. Crespi, +# Registry-dependent interlayer potential for graphitic systems +# Physical Review B 71, 235415 (2005) +# +# z0 C0 C2 C4 C delta lambda A S +C C 3.34 15.71 12.29 4.933 3.030 0.578 3.629 10.238 1.0 diff --git a/examples/snap/Ta06A_pot.snap b/potentials/Ta06A.snap similarity index 86% rename from examples/snap/Ta06A_pot.snap rename to potentials/Ta06A.snap index 7c86c24641..edcc002524 100644 --- a/examples/snap/Ta06A_pot.snap +++ b/potentials/Ta06A.snap @@ -9,9 +9,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap & -zbl ${zblcutinner} ${zblcutouter} - +pair_style hybrid/overlay & +zbl ${zblcutinner} ${zblcutouter} & +snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta diff --git a/examples/snap/W_2940_2017_2.pot.snap b/potentials/W_2940_2017_2.snap similarity index 77% rename from examples/snap/W_2940_2017_2.pot.snap rename to potentials/W_2940_2017_2.snap index ea98d65c9e..51eee41a0a 100644 --- a/examples/snap/W_2940_2017_2.pot.snap +++ b/potentials/W_2940_2017_2.snap @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 diff --git a/potentials/W_2940_2017_2.snapcoeff b/potentials/W_2940_2017_2.snapcoeff index 98a5c50635..dcfea3feaf 100644 --- a/potentials/W_2940_2017_2.snapcoeff +++ b/potentials/W_2940_2017_2.snapcoeff @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # LAMMPS SNAP coefficients for W diff --git a/potentials/W_2940_2017_2.snapparam b/potentials/W_2940_2017_2.snapparam index 7ff57c905d..e0b20005e6 100644 --- a/potentials/W_2940_2017_2.snapparam +++ b/potentials/W_2940_2017_2.snapparam @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # required rcutfac 4.73442 diff --git a/potentials/W.SNAP_HePair.pot b/potentials/W_2940_2017_2_He_JW2013.snap similarity index 82% rename from potentials/W.SNAP_HePair.pot rename to potentials/W_2940_2017_2_He_JW2013.snap index eb5ee4dfbe..45a31955b3 100644 --- a/potentials/W.SNAP_HePair.pot +++ b/potentials/W_2940_2017_2_He_JW2013.snap @@ -1,4 +1,4 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 diff --git a/python/README b/python/README index f0e95d3c45..6b13959f4d 100644 --- a/python/README +++ b/python/README @@ -23,7 +23,7 @@ of LAMMPS: >>> from lammps import lammps >>> lmp = lammps() -If that gives no errors, you have succesfully wrapped LAMMPS with +If that gives no errors, you have successfully wrapped LAMMPS with Python. See doc/Section_python.html#py_7 for tests you can then use to run LAMMPS both in serial or parallel thru Python. @@ -43,7 +43,7 @@ simple.py parallel example, mimicing examples/COUPLE/simple/simple.cpp split.py parallel example mc.py Monte Carlo energy relaxation wrapper on LAMMPS gui.py GUI go/stop/temperature-slider to control LAMMPS -plot.py real-time temeperature plot with GnuPlot via Pizza.py +plot.py real-time temperature plot with GnuPlot via Pizza.py viz_tool.py real-time viz via some viz package vizplotgui_tool.py combination of viz.py and plot.py and gui.py diff --git a/python/examples/demo.py b/python/examples/demo.py index 958ebcd04b..5d2b62fee3 100755 --- a/python/examples/demo.py +++ b/python/examples/demo.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # demo.py # Purpose: illustrate use of many library interface commands diff --git a/python/examples/gui.py b/python/examples/gui.py index 3fc1d7e36c..ac96448b43 100755 --- a/python/examples/gui.py +++ b/python/examples/gui.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # gui.py # Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI diff --git a/python/examples/mc.py b/python/examples/mc.py index 9e7317218b..fb2bfabab9 100755 --- a/python/examples/mc.py +++ b/python/examples/mc.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # mc.py # Purpose: mimic operation of example/MC/in.mc via Python diff --git a/python/examples/plot.py b/python/examples/plot.py index efb9ecaa68..c67509f650 100755 --- a/python/examples/plot.py +++ b/python/examples/plot.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # plot.py # Purpose: plot Temp of running LAMMPS simulation via GnuPlot in Pizza.py diff --git a/python/examples/simple.py b/python/examples/simple.py index 6336c89de3..da07a69997 100755 --- a/python/examples/simple.py +++ b/python/examples/simple.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # simple.py # Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python diff --git a/python/examples/split.py b/python/examples/split.py index 719877d826..77e605092e 100755 --- a/python/examples/split.py +++ b/python/examples/split.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # split.py # Purpose: similar to simple.py, but first the world communicator diff --git a/python/examples/trivial.py b/python/examples/trivial.py index 0e3d6b91af..e52f1745e0 100755 --- a/python/examples/trivial.py +++ b/python/examples/trivial.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # trivial.py # Purpose: run a LAMMPS input script via Python diff --git a/python/examples/viz_atomeye.py b/python/examples/viz_atomeye.py index 3803b2e79c..d9cf4dcef2 100755 --- a/python/examples/viz_atomeye.py +++ b/python/examples/viz_atomeye.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_atomeye.py # Purpose: viz running LAMMPS simulation via AtomEye diff --git a/python/examples/viz_gl.py b/python/examples/viz_gl.py index 476509ad43..5878b68502 100755 --- a/python/examples/viz_gl.py +++ b/python/examples/viz_gl.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_gl.py # Purpose: viz running LAMMPS simulation via GL tool in Pizza.py diff --git a/python/examples/viz_pymol.py b/python/examples/viz_pymol.py index 02178a0fb0..0950b3668b 100755 --- a/python/examples/viz_pymol.py +++ b/python/examples/viz_pymol.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_pymol.py # Purpose: viz running LAMMPS simulation via PyMol diff --git a/python/examples/viz_vmd.py b/python/examples/viz_vmd.py index 807a8c9d55..f592857566 100755 --- a/python/examples/viz_vmd.py +++ b/python/examples/viz_vmd.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # viz_vmd.py # Purpose: viz running LAMMPS simulation via VMD diff --git a/python/examples/vizplotgui_atomeye.py b/python/examples/vizplotgui_atomeye.py index 71730974df..02f119b726 100755 --- a/python/examples/vizplotgui_atomeye.py +++ b/python/examples/vizplotgui_atomeye.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_atomeye.py # Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI diff --git a/python/examples/vizplotgui_gl.py b/python/examples/vizplotgui_gl.py index 937670e511..c4847667fd 100755 --- a/python/examples/vizplotgui_gl.py +++ b/python/examples/vizplotgui_gl.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_gl.py # Purpose: viz running LAMMPS simulation via GL tool with plot and GUI diff --git a/python/examples/vizplotgui_pymol.py b/python/examples/vizplotgui_pymol.py index c7a8a00c6d..11be498741 100755 --- a/python/examples/vizplotgui_pymol.py +++ b/python/examples/vizplotgui_pymol.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_pymol.py # Purpose: viz running LAMMPS simulation via PyMol with plot and GUI diff --git a/python/examples/vizplotgui_vmd.py b/python/examples/vizplotgui_vmd.py index 9eab0865e2..0003ebc929 100755 --- a/python/examples/vizplotgui_vmd.py +++ b/python/examples/vizplotgui_vmd.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -i -# preceeding line should have path for Python on your machine +# preceding line should have path for Python on your machine # vizplotgui_vmd.py # Purpose: viz running LAMMPS simulation via VMD with plot and GUI diff --git a/src/ASPHERE/compute_erotate_asphere.h b/src/ASPHERE/compute_erotate_asphere.h index be1c534923..23e30d7c93 100644 --- a/src/ASPHERE/compute_erotate_asphere.h +++ b/src/ASPHERE/compute_erotate_asphere.h @@ -56,6 +56,6 @@ Self-explanatory. E: Compute erotate/asphere requires extended particles -This compute cannot be used with point paritlces. +This compute cannot be used with point particles. */ diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h index 4688a5612d..d1cce38025 100644 --- a/src/ASPHERE/compute_temp_asphere.h +++ b/src/ASPHERE/compute_temp_asphere.h @@ -65,7 +65,7 @@ Self-explanatory. E: Compute temp/asphere requires extended particles -This compute cannot be used with point paritlces. +This compute cannot be used with point particles. E: Could not find compute ID for temperature bias diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index eafa57973c..a50473a194 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -153,7 +153,7 @@ void PairLubricateU::compute(int eflag, int vflag) } // Stage one of Midpoint method - // Solve for velocities based on intial positions + // Solve for velocities based on initial positions stage_one(); @@ -651,7 +651,7 @@ void PairLubricateU::compute_Fh(double **x) jnum = numneigh[i]; // Find the contribution to stress from isotropic RS0 - // Set psuedo force to obtain the required contribution + // Set pseudo force to obtain the required contribution // need to set delx and fy only fx = 0.0; delx = radi; diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 30ad42ea60..29e192cd94 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -122,7 +122,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag) } // Stage one of Midpoint method - // Solve for velocities based on intial positions + // Solve for velocities based on initial positions iterate(atom->x,1); @@ -421,7 +421,7 @@ void PairLubricateUPoly::compute_Fh(double **x) pre[0] *= 6.0; // Find the contribution to stress from isotropic RS0 - // Set psuedo force to obtain the required contribution + // Set pseudo force to obtain the required contribution // need to set delx and fy only fx = 0.0; delx = radi; diff --git a/src/COLLOID/pair_yukawa_colloid.h b/src/COLLOID/pair_yukawa_colloid.h index f22c9654be..ac15d535b3 100644 --- a/src/COLLOID/pair_yukawa_colloid.h +++ b/src/COLLOID/pair_yukawa_colloid.h @@ -43,10 +43,10 @@ class PairYukawaColloid : public PairYukawa { E: Pair yukawa/colloid requires atom style sphere -Self-explantory. +Self-explanatory. E: Pair yukawa/colloid requires atoms with same type have same radius -Self-explantory. +Self-explanatory. */ diff --git a/src/DEPEND/fastdep.c b/src/DEPEND/fastdep.c index 2f4927abce..3a6d3a0173 100644 --- a/src/DEPEND/fastdep.c +++ b/src/DEPEND/fastdep.c @@ -178,7 +178,7 @@ typedef struct { * linked list functions ************************************************************************/ -/* allocate and intitialize linked list */ +/* allocate and initialize linked list */ static llist_t *llist_init() { llist_t *ll; diff --git a/src/GPU/README b/src/GPU/README index ea1fa70285..792fc1a8b9 100644 --- a/src/GPU/README +++ b/src/GPU/README @@ -1,11 +1,16 @@ This package implements GPU optimizations of various LAMMPS styles. -This package uses an external library in lib/gpu which must be -compiled before making LAMMPS. See the lib/gpu/README file and the +Section 5.3.1 on the manual gives details of what hardware and Cuda +software is required on your system, and full details on how to build +and use this package. See the KOKKOS package, which also has +GPU-enabled styles. + +This package uses an external library provided in lib/gpu which must +be compiled before making LAMMPS. See the lib/gpu/README file and the LAMMPS manual for information on building LAMMPS with external libraries. The settings in the Makefile.lammps file in that directory must be correct for LAMMPS to build correctly with this package installed. -The people who created this package are Mike Brown (while at Sandia -and ORNL) and Trung Nguyen (while at ORNL). +The GPU package and its associated library was created by Mike Brown +while at Sandia and ORNL, and by Trung Nguyen while at ORNL. diff --git a/src/GPU/pair_born_gpu.h b/src/GPU/pair_born_gpu.h index 49c76fadf6..d8ccbe0029 100644 --- a/src/GPU/pair_born_gpu.h +++ b/src/GPU/pair_born_gpu.h @@ -54,6 +54,6 @@ package E: Cannot use newton pair with born/gpu pair style -Self-explantory. +Self-explanatory. */ diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h index 0939dafaaa..950fe952dd 100644 --- a/src/GPU/pair_zbl_gpu.h +++ b/src/GPU/pair_zbl_gpu.h @@ -53,6 +53,6 @@ package E: Cannot use newton pair with zbl/gpu pair style -Self-explantory. +Self-explanatory. */ diff --git a/src/KIM/README b/src/KIM/README index e450d7dfd1..496db92cf2 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -1,5 +1,3 @@ --*- fill-column: 70; -*- - This package provides a pair_style kim command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, so that they can be used by LAMMPS scripts. diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 843fb6db2a..07947f9d18 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -126,7 +126,7 @@ namespace LAMMPS_NS { int lmps_maxalloc; // max allocated memory value int* kim_particleSpecies; // array of KIM particle species double** lmps_force_tmp; // temp storage for f, when running in - // hybrid mode needed to avoid reseting + // hybrid mode needed to avoid resetting // f to zero in each object int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS // is in molecular mode diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index e2a605b802..346077e071 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -64,7 +64,7 @@ void AngleCharmmKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 0232571bcc..e851e9d500 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -64,7 +64,7 @@ void AngleClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index 0d3110f904..9fd237ddb3 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -64,7 +64,7 @@ void AngleHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 82dc3f382a..b01af92b5f 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -60,7 +60,7 @@ void BondClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index b10469b45e..cfc37bfa9f 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -69,7 +69,7 @@ void BondFENEKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index aead602747..408f59c563 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -61,7 +61,7 @@ void BondHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 3ec22c42fa..f38a6c21c9 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -71,6 +71,10 @@ CommKokkos::CommKokkos(LAMMPS *lmp) : CommBrick(lmp) maxsendlist[i] = BUFMIN; } memory->create_kokkos(k_sendlist,sendlist,maxswap,BUFMIN,"comm:sendlist"); + + max_buf_pair = 0; + k_buf_send_pair = DAT::tdual_xfloat_1d("comm:k_buf_send_pair",1); + k_buf_recv_pair = DAT::tdual_xfloat_1d("comm:k_recv_send_pair",1); } /* ---------------------------------------------------------------------- */ @@ -89,6 +93,9 @@ CommKokkos::~CommKokkos() void CommKokkos::init() { + maxsend = BUFMIN; + maxrecv = BUFMIN; + grow_send_kokkos(maxsend+bufextra,0,Host); grow_recv_kokkos(maxrecv,Host); @@ -300,9 +307,13 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) int nsize = pair->comm_forward; for (iswap = 0; iswap < nswap; iswap++) { + int n = MAX(max_buf_pair,nsize*sendnum[iswap]); + n = MAX(n,nsize*recvnum[iswap]); + if (n > max_buf_pair) + grow_buf_pair(n); + } - DAT::tdual_xfloat_1d k_buf_send_pair = DAT::tdual_xfloat_1d("comm:k_buf_send_pair",nsize*sendnum[iswap]); - DAT::tdual_xfloat_1d k_buf_recv_pair = DAT::tdual_xfloat_1d("comm:k_recv_send_pair",nsize*recvnum[iswap]); + for (iswap = 0; iswap < nswap; iswap++) { // pack buffer @@ -327,6 +338,12 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) } } +void CommKokkos::grow_buf_pair(int n) { + max_buf_pair = n * BUFFACTOR; + k_buf_send_pair.resize(max_buf_pair); + k_buf_recv_pair.resize(max_buf_pair); +} + void CommKokkos::reverse_comm_pair(Pair *pair) { k_sendlist.sync(); diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h index 587b030595..71d5e59595 100644 --- a/src/KOKKOS/comm_kokkos.h +++ b/src/KOKKOS/comm_kokkos.h @@ -59,6 +59,11 @@ class CommKokkos : public CommBrick { //double *buf_send; // send buffer for all comm //double *buf_recv; // recv buffer for all comm + int max_buf_pair; + DAT::tdual_xfloat_1d k_buf_send_pair; + DAT::tdual_xfloat_1d k_buf_recv_pair; + void grow_buf_pair(int); + void grow_send(int, int); void grow_recv(int); void grow_send_kokkos(int, int, ExecutionSpace space = Host); diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 0af9fc4e83..ee9e3d1244 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -69,7 +69,7 @@ void DihedralCharmmKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 9f7ef52cb0..edfd1b3395 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -69,7 +69,7 @@ void DihedralClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 5406a6daaf..8e222ad860 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -69,7 +69,7 @@ void DihedralOPLSKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index 60e2133984..25bd2c732f 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -71,7 +71,7 @@ void ImproperClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index cde7d60e8e..9c99b35bd9 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -71,7 +71,7 @@ void ImproperHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index 2a85255e12..e40e6a238c 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -64,6 +64,7 @@ NeighborKokkos::~NeighborKokkos() memory->destroy_kokkos(k_ex1_bit,ex1_bit); memory->destroy_kokkos(k_ex2_bit,ex2_bit); memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit); + memory->destroy_kokkos(k_ex_mol_intra,ex_mol_intra); memory->destroy_kokkos(k_bondlist,bondlist); memory->destroy_kokkos(k_anglelist,anglelist); @@ -133,6 +134,14 @@ void NeighborKokkos::init_ex_mol_bit_kokkos() k_ex_mol_bit.modify(); } +/* ---------------------------------------------------------------------- */ + +void NeighborKokkos::grow_ex_mol_intra_kokkos() +{ + memory->grow_kokkos(k_ex_mol_intra, ex_mol_intra, maxex_mol, "neigh:ex_mol_intra"); + k_ex_mol_intra.modify(); +} + /* ---------------------------------------------------------------------- if any atom moved trigger distance (half of neighbor skin) return 1 shrink trigger distance if box size has changed @@ -348,6 +357,12 @@ void NeighborKokkos::modify_mol_group_grow_kokkos(){ k_ex_mol_group.modify(); } +/* ---------------------------------------------------------------------- */ +void NeighborKokkos::modify_mol_intra_grow_kokkos(){ + memory->grow_kokkos(k_ex_mol_intra,ex_mol_intra,maxex_mol,"neigh:ex_mol_intra"); + k_ex_mol_intra.modify(); +} + /* ---------------------------------------------------------------------- */ void NeighborKokkos::init_topology() { diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 244de19dce..137c071e87 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -54,6 +54,7 @@ class NeighborKokkos : public Neighbor { DAT::tdual_int_1d k_ex1_bit,k_ex2_bit; DAT::tdual_int_1d k_ex_mol_group; DAT::tdual_int_1d k_ex_mol_bit; + DAT::tdual_int_1d k_ex_mol_intra; NeighBondKokkos neighbond_host; NeighBondKokkos neighbond_device; @@ -76,6 +77,7 @@ class NeighborKokkos : public Neighbor { void init_ex_type_kokkos(int); void init_ex_bit_kokkos(); void init_ex_mol_bit_kokkos(); + void grow_ex_mol_intra_kokkos(); virtual int check_distance(); template int check_distance_kokkos(); virtual void build(int); @@ -84,6 +86,7 @@ class NeighborKokkos : public Neighbor { void modify_ex_type_grow_kokkos(); void modify_ex_group_grow_kokkos(); void modify_mol_group_grow_kokkos(); + void modify_mol_intra_grow_kokkos(); }; } diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index f49e44c352..3614a82cfe 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -56,6 +56,7 @@ void NPairKokkos::copy_neighbor_info() k_ex2_bit = neighborKK->k_ex2_bit; k_ex_mol_group = neighborKK->k_ex_mol_group; k_ex_mol_bit = neighborKK->k_ex_mol_bit; + k_ex_mol_intra = neighborKK->k_ex_mol_intra; } /* ---------------------------------------------------------------------- @@ -147,6 +148,7 @@ void NPairKokkos::build(NeighList *list_) nex_mol, k_ex_mol_group.view(), k_ex_mol_bit.view(), + k_ex_mol_intra.view(), bboxhi,bboxlo, domain->xperiodic,domain->yperiodic,domain->zperiodic, domain->xprd_half,domain->yprd_half,domain->zprd_half); @@ -161,6 +163,7 @@ void NPairKokkos::build(NeighList *list_) k_ex2_bit.sync(); k_ex_mol_group.sync(); k_ex_mol_bit.sync(); + k_ex_mol_intra.sync(); k_bincount.sync(), k_bins.sync(), atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK); @@ -284,8 +287,12 @@ int NeighborKokkosExecute::exclusion(const int &i,const int &j, if (nex_mol) { for (m = 0; m < nex_mol; m++) - if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) && - molecule(i) == molecule(j)) return 1; + if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule + if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] && + molecule[i] == molecule[j]) return 1; + } else // exclude i-j pair if on different molecules + if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] && + molecule[i] != molecule[j]) return 1; } return 0; diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 54726cb971..52cdfe0d53 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -98,6 +98,7 @@ class NPairKokkos : public NPair { DAT::tdual_int_1d k_ex1_bit,k_ex2_bit; DAT::tdual_int_1d k_ex_mol_group; DAT::tdual_int_1d k_ex_mol_bit; + DAT::tdual_int_1d k_ex_mol_intra; // data from NBin class @@ -139,6 +140,7 @@ class NeighborKokkosExecute const int nex_mol; const typename AT::t_int_1d_const ex_mol_group; const typename AT::t_int_1d_const ex_mol_bit; + const typename AT::t_int_1d_const ex_mol_intra; // data from NBin class @@ -216,6 +218,7 @@ class NeighborKokkosExecute const int & _nex_mol, const typename AT::t_int_1d_const & _ex_mol_group, const typename AT::t_int_1d_const & _ex_mol_bit, + const typename AT::t_int_1d_const & _ex_mol_intra, const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo, const int & _xperiodic, const int & _yperiodic, const int & _zperiodic, const int & _xprd_half, const int & _yprd_half, const int & _zprd_half): @@ -235,6 +238,7 @@ class NeighborKokkosExecute ex1_group(_ex1_group),ex2_group(_ex2_group), ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol), ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit), + ex_mol_intra(_ex_mol_intra), xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic), xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) { diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index afe2d14fcc..34fd427226 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -92,7 +92,7 @@ void PairBuckCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index fa05c99995..243bac5ab7 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -111,7 +111,7 @@ void PairBuckCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 02f767fa03..d8534f7900 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -81,7 +81,7 @@ void PairBuckKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index a770d55be9..80ab01d91a 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -80,7 +80,7 @@ void PairCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index e9314c2a0a..dc85c39832 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -87,7 +87,7 @@ void PairCoulDebyeKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index 948a234a4a..f2063bdc08 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -80,7 +80,7 @@ void PairCoulDSFKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index dcf4943104..7dbadf4834 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -104,7 +104,7 @@ void PairCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 55b19958a3..8049ba0031 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -75,7 +75,7 @@ void PairCoulWolfKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 491ec10f66..45c320bc51 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -74,7 +74,7 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 006db6abc2..b9fa82740a 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -74,7 +74,7 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 656dd11c62..e4128de722 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -69,7 +69,7 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index a4e0fa963d..c00b1fbae4 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -112,7 +112,7 @@ void PairLJCharmmCoulCharmmImplicitKokkos::compute(int eflag_in, int if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 1e5509c39c..c88c7db2e3 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -112,7 +112,7 @@ void PairLJCharmmCoulCharmmKokkos::compute(int eflag_in, int vflag_i if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 2f94c47bae..8ebc5f87f3 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -112,7 +112,7 @@ void PairLJCharmmCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 4283cfa981..936eae79d5 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -89,7 +89,7 @@ void PairLJClass2CoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index adbffff50f..268213cdbc 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -97,7 +97,7 @@ void PairLJClass2CoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index c26aa4f467..c899327d7c 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -89,7 +89,7 @@ void PairLJClass2Kokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index e9f587d0cc..f4de48f176 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -89,7 +89,7 @@ void PairLJCutCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 0af781affd..ad51dd0a88 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -93,7 +93,7 @@ void PairLJCutCoulDebyeKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index 5ddf035b62..89f263113e 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -101,7 +101,7 @@ void PairLJCutCoulDSFKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index e3754cdb5d..4de51ca8d2 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -101,7 +101,7 @@ void PairLJCutCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 9a2a7e23a9..ea78b73711 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -89,7 +89,7 @@ void PairLJCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index cdede8bd52..6b62150632 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -88,7 +88,7 @@ void PairLJExpandKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 0ca8375657..0c492131dd 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -103,7 +103,7 @@ void PairLJGromacsCoulGromacsKokkos::compute(int eflag_in, int vflag if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index e6606d30cf..76d7abbe28 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -100,7 +100,7 @@ void PairLJGromacsKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index 2d74e37192..41561c2988 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -88,7 +88,7 @@ void PairLJSDKKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index e0685f1376..3201fad215 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -93,7 +93,7 @@ void PairMorseKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_reax_c_kokkos.cpp b/src/KOKKOS/pair_reax_c_kokkos.cpp index 5490268e56..acf9c754cd 100644 --- a/src/KOKKOS/pair_reax_c_kokkos.cpp +++ b/src/KOKKOS/pair_reax_c_kokkos.cpp @@ -633,7 +633,7 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ } if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // innner wall + { // inner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); lr->e_vdW += Tap * e_core; diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 6b2c1ca04b..a8950a0c79 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -80,7 +80,7 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 93556635c2..7f763baae6 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -86,7 +86,7 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 0f5e939794..75280c8f7c 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -164,7 +164,7 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 1f66da409d..d16a7fc4d7 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -164,7 +164,7 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 264b769df3..e9bae49fb7 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -178,7 +178,7 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 0e972d2464..f81af0b149 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -79,7 +79,7 @@ void PairVashishtaKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = vflag_fdotr = 0; // reallocate per-atom arrays if necessary diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 7b88563cbb..c59bd89e51 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -615,7 +615,7 @@ void PPPMKokkos::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); + if (eflag || vflag) ev_setup(eflag,vflag,0); else evflag = evflag_atom = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; diff --git a/src/KSPACE/pair_buck_long_coul_long.h b/src/KSPACE/pair_buck_long_coul_long.h index 736742a77a..cf752a09b0 100644 --- a/src/KSPACE/pair_buck_long_coul_long.h +++ b/src/KSPACE/pair_buck_long_coul_long.h @@ -80,15 +80,15 @@ command-line option when running LAMMPS to see the offending line. W: Using largest cutoff for buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: Cutoffs missing in pair_style buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: LJ6 off not supported in pair_style buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: Coulomb cut not supported in pair_style buck/long/coul/coul diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index ae07ea9e07..6993ad6c91 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -513,7 +513,7 @@ E: Cannot compute initial g_ewald_disp LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 factor that partitions the computation between real space and k-space -for Disptersion interactions. +for Dispersion interactions. E: Could not compute grid size for Dispersion diff --git a/src/MAKE/OPTIONS/Makefile.omp b/src/MAKE/OPTIONS/Makefile.omp index 5c25c8e41c..fd485d5416 100644 --- a/src/MAKE/OPTIONS/Makefile.omp +++ b/src/MAKE/OPTIONS/Makefile.omp @@ -7,7 +7,7 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler CC = mpicxx -CCFLAGS = -g -O3 -fopenmp +CCFLAGS = -g -O3 -restrict -fopenmp SHFLAGS = -fPIC DEPFLAGS = -M diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 51cf221668..cacc8b3416 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -753,7 +753,7 @@ void PairAIREBO::FLJ(int eflag, int vflag) tee = drij / swidth; tee2 = tee*tee; slw = 1.0 - tee2 * (3.0 - 2.0 * tee); - dslw = 6.0 * tee * (1.0 - tee) / rij / swidth; + dslw = -6.0 * tee * (1.0 - tee) / swidth; } else { slw = 1.0; dslw = 0.0; @@ -2104,6 +2104,9 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, double F12[3],F23[3],F34[3],F31[3],F24[3]; double fi[3],fj[3],fk[3],fl[3],f1[3],f2[3],f3[3],f4[4]; double rji[3],rki[3],rlj[3],r13[3],r43[3]; + double realrij[3], realrijmag; + double rjkmag, rilmag, dctdjk, dctdik, dctdil, dctdjl; + double fjk[3], fil[3], rijmbr; double **x = atom->x; int *type = atom->type; @@ -2130,6 +2133,12 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, Stb = 0.0; dStb = 0.0; + realrij[0] = x[atomi][0] - x[atomj][0]; + realrij[1] = x[atomi][1] - x[atomj][1]; + realrij[2] = x[atomi][2] - x[atomj][2]; + realrijmag = sqrt(realrij[0] * realrij[0] + realrij[1] * realrij[1] + + realrij[2] * realrij[2]); + REBO_neighs = REBO_firstneigh[i]; for (k = 0; k < REBO_numneigh[i]; k++) { atomk = REBO_neighs[k]; @@ -2319,50 +2328,53 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, lamdajik = 4.0*kronecker(itype,1) * ((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag)); wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik); - cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) / - (rijmag*rikmag); + rjk[0] = rik[0] - rij[0]; + rjk[1] = rik[1] - rij[1]; + rjk[2] = rik[2] - rij[2]; + rjkmag = sqrt(rjk[0] * rjk[0] + rjk[1] * rjk[1] + rjk[2] * rjk[2]); + rijrik = 2 * rijmag * rikmag; + rr = rijmag * rijmag - rikmag * rikmag; + cosjik = (rijmag * rijmag + rikmag * rikmag - rjkmag * rjkmag) / rijrik; cosjik = MIN(cosjik,1.0); cosjik = MAX(cosjik,-1.0); - - dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) - - (cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag)))); - dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) - - (cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag)))); - dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) - - (cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag)))); - dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) + - (cosjik*(rik[0]/(rikmag*rikmag))); - dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) + - (cosjik*(rik[1]/(rikmag*rikmag))); - dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) + - (cosjik*(rik[2]/(rikmag*rikmag))); - dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) + - (cosjik*(rij[0]/(rijmag*rijmag))); - dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) + - (cosjik*(rij[1]/(rijmag*rijmag))); - dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) + - (cosjik*(rij[2]/(rijmag*rijmag))); + dctdjk = -2 / rijrik; + dctdik = (-rr + rjkmag * rjkmag) / (rijrik * rikmag * rikmag); + // evaluate splines g and derivatives dg g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN); tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik)); - fj[0] = -tmp2*dcosjikdrj[0]; - fj[1] = -tmp2*dcosjikdrj[1]; - fj[2] = -tmp2*dcosjikdrj[2]; - fi[0] = -tmp2*dcosjikdri[0]; - fi[1] = -tmp2*dcosjikdri[1]; - fi[2] = -tmp2*dcosjikdri[2]; - fk[0] = -tmp2*dcosjikdrk[0]; - fk[1] = -tmp2*dcosjikdrk[1]; - fk[2] = -tmp2*dcosjikdrk[2]; + + fi[0] = -tmp2 * dctdik * rik[0]; + fi[1] = -tmp2 * dctdik * rik[1]; + fi[2] = -tmp2 * dctdik * rik[2]; + fk[0] = tmp2 * dctdik * rik[0]; + fk[1] = tmp2 * dctdik * rik[1]; + fk[2] = tmp2 * dctdik * rik[2]; + fj[0] = 0; + fj[1] = 0; + fj[2] = 0; + fjk[0] = -tmp2 * dctdjk * rjk[0]; + fjk[1] = -tmp2 * dctdjk * rjk[1]; + fjk[2] = -tmp2 * dctdjk * rjk[2]; + fi[0] += fjk[0]; + fi[1] += fjk[1]; + fi[2] += fjk[2]; + fk[0] -= fjk[0]; + fk[1] -= fjk[1]; + fk[2] -= fjk[2]; + rijmbr = rcmin[itype][jtype] / realrijmag; + fj[0] += rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); + fj[1] += rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); + fj[2] += rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); + fi[0] -= rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); + fi[1] -= rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); + fi[2] -= rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag)); tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1)); - fj[0] -= tmp2*(-rij[0]/rijmag); - fj[1] -= tmp2*(-rij[1]/rijmag); - fj[2] -= tmp2*(-rij[2]/rijmag); - fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]/rijmag)); - fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]/rijmag)); - fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]/rijmag)); + fi[0] += tmp2*(rik[0]/rikmag); + fi[1] += tmp2*(rik[1]/rikmag); + fi[2] += tmp2*(rik[2]/rikmag); fk[0] -= tmp2*(rik[0]/rikmag); fk[1] -= tmp2*(rik[1]/rikmag); fk[2] -= tmp2*(rik[2]/rikmag); @@ -2427,51 +2439,53 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, lamdaijl = 4.0*kronecker(jtype,1) * ((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag)); wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl); - cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) / - (rijmag*rjlmag); + ril[0] = rij[0] + rjl[0]; + ril[1] = rij[1] + rjl[1]; + ril[2] = rij[2] + rjl[2]; + rilmag = sqrt(ril[0] * ril[0] + ril[1] * ril[1] + ril[2] * ril[2]); + rijrjl = 2 * rijmag * rjlmag; + rr = rijmag * rijmag - rjlmag * rjlmag; + cosijl = (rijmag * rijmag + rjlmag * rjlmag - rilmag * rilmag) / rijrjl; cosijl = MIN(cosijl,1.0); cosijl = MAX(cosijl,-1.0); - - dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) - - (cosijl*rij[0]/(rijmag*rijmag)); - dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) - - (cosijl*rij[1]/(rijmag*rijmag)); - dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) - - (cosijl*rij[2]/(rijmag*rijmag)); - dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) + - (cosijl*((rij[0]/square(rijmag))-(rjl[0]/(rjlmag*rjlmag)))); - dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) + - (cosijl*((rij[1]/square(rijmag))-(rjl[1]/(rjlmag*rjlmag)))); - dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) + - (cosijl*((rij[2]/square(rijmag))-(rjl[2]/(rjlmag*rjlmag)))); - dcosijldrl[0] = (rij[0]/(rijmag*rjlmag)) + - (cosijl*rjl[0]/(rjlmag*rjlmag)); - dcosijldrl[1] = (rij[1]/(rijmag*rjlmag)) + - (cosijl*rjl[1]/(rjlmag*rjlmag)); - dcosijldrl[2] = (rij[2]/(rijmag*rjlmag)) + - (cosijl*rjl[2]/(rjlmag*rjlmag)); + dctdil = -2 / rijrjl; + dctdjl = (-rr + rilmag * rilmag) / (rijrjl * rjlmag * rjlmag); // evaluate splines g and derivatives dg g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN); tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl)); - fi[0] = -tmp2*dcosijldri[0]; - fi[1] = -tmp2*dcosijldri[1]; - fi[2] = -tmp2*dcosijldri[2]; - fj[0] = -tmp2*dcosijldrj[0]; - fj[1] = -tmp2*dcosijldrj[1]; - fj[2] = -tmp2*dcosijldrj[2]; - fl[0] = -tmp2*dcosijldrl[0]; - fl[1] = -tmp2*dcosijldrl[1]; - fl[2] = -tmp2*dcosijldrl[2]; + fj[0] = -tmp2 * dctdjl * rjl[0]; + fj[1] = -tmp2 * dctdjl * rjl[1]; + fj[2] = -tmp2 * dctdjl * rjl[2]; + fl[0] = tmp2 * dctdjl * rjl[0]; + fl[1] = tmp2 * dctdjl * rjl[1]; + fl[2] = tmp2 * dctdjl * rjl[2]; + fi[0] = 0; + fi[1] = 0; + fi[2] = 0; + fil[0] = -tmp2 * dctdil * ril[0]; + fil[1] = -tmp2 * dctdil * ril[1]; + fil[2] = -tmp2 * dctdil * ril[2]; + fj[0] += fil[0]; + fj[1] += fil[1]; + fj[2] += fil[2]; + fl[0] -= fil[0]; + fl[1] -= fil[1]; + fl[2] -= fil[2]; + rijmbr = rcmin[itype][jtype] / realrijmag; + fi[0] += rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + fi[1] += rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + fi[2] += rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + fj[0] -= rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + fj[1] -= rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + fj[2] -= rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag)); + tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1)); - fi[0] -= tmp2*(rij[0]/rijmag); - fi[1] -= tmp2*(rij[1]/rijmag); - fi[2] -= tmp2*(rij[2]/rijmag); - fj[0] -= tmp2*((-rjl[0]/rjlmag)-(rij[0]/rijmag)); - fj[1] -= tmp2*((-rjl[1]/rjlmag)-(rij[1]/rijmag)); - fj[2] -= tmp2*((-rjl[2]/rjlmag)-(rij[2]/rijmag)); + fj[0] += tmp2*(rjl[0]/rjlmag); + fj[1] += tmp2*(rjl[1]/rjlmag); + fj[2] += tmp2*(rjl[2]/rjlmag); fl[0] -= tmp2*(rjl[0]/rjlmag); fl[1] -= tmp2*(rjl[1]/rjlmag); fl[2] -= tmp2*(rjl[2]/rjlmag); @@ -2654,14 +2668,14 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, dN3[2] = dN3Tij[2]; atom2 = atomi; atom3 = atomj; - r32[0] = x[atom3][0]-x[atom2][0]; - r32[1] = x[atom3][1]-x[atom2][1]; - r32[2] = x[atom3][2]-x[atom2][2]; - r32mag = sqrt((r32[0]*r32[0])+(r32[1]*r32[1])+(r32[2]*r32[2])); - r23[0] = -r32[0]; - r23[1] = -r32[1]; - r23[2] = -r32[2]; - r23mag = r32mag; + r32[0] = -rij[0]; + r32[1] = -rij[1]; + r32[2] = -rij[2]; + r23[0] = rij[0]; + r23[1] = rij[1]; + r23[2] = rij[2]; + r32mag = rijmag; + r23mag = rijmag; REBO_neighs_i = REBO_firstneigh[i]; for (k = 0; k < REBO_numneigh[i]; k++) { @@ -2690,7 +2704,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, rijrik = 2.0*rijmag*r21mag; rik2 = r21mag*r21mag; dctik = (-rr+rjk2)/(rijrik*rik2); - dctij = (rr+rjk2)/(rijrik*rijmag*rijmag); dctjk = -2.0/rijrik; w21 = Sp(r21mag,rcmin[itype][ktype],rcmaxp[itype][ktype],dw21); rikmag = r21mag; @@ -2729,7 +2742,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, rijrjl = 2.0*r23mag*r34mag; rjl2 = r34mag*r34mag; dctjl = (-rr+ril2)/(rijrjl*rjl2); - dctji = (rr+ril2)/(rijrjl*r23mag*r23mag); dctil = -2.0/rijrjl; rjlmag = r34mag; rjl2 = r34mag*r34mag; @@ -2750,15 +2762,11 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, cwnom = r21mag*r34mag*r23mag*r23mag*sin321*sin234; om1234 = cwnum/cwnom; cw = om1234; - Etmp += ((1.0-square(om1234))*w21*w34) * - (1.0-tspjik)*(1.0-tspijl); dt1dik = (rik2i)-(dctik*sink2i*cos321); dt1djk = (-dctjk*sink2i*cos321); dt1djl = (rjl2i)-(dctjl*sinl2i*cos234); dt1dil = (-dctil*sinl2i*cos234); - dt1dij = (2.0/(r23mag*r23mag)) - - (dctij*sink2i*cos321)-(dctji*sinl2i*cos234); dt2dik[0] = (-r23[2]*cross234[1])+(r23[1]*cross234[2]); dt2dik[1] = (-r23[0]*cross234[2])+(r23[2]*cross234[0]); @@ -2768,16 +2776,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, dt2djl[1] = (-r23[2]*cross321[0])+(r23[0]*cross321[2]); dt2djl[2] = (-r23[0]*cross321[1])+(r23[1]*cross321[0]); - dt2dij[0] = (r21[2]*cross234[1]) - - (r34[2]*cross321[1])-(r21[1]*cross234[2]) + - (r34[1]*cross321[2]); - dt2dij[1] = (r21[0]*cross234[2]) - - (r34[0]*cross321[2])-(r21[2]*cross234[0]) + - (r34[2]*cross321[0]); - dt2dij[2] = (r21[1]*cross234[0]) - - (r34[1]*cross321[0])-(r21[0]*cross234[1]) + - (r34[0]*cross321[1]); - aa = (prefactor*2.0*cw/cwnom)*w21*w34 * (1.0-tspjik)*(1.0-tspijl); aaa1 = -prefactor*(1.0-square(om1234)) * @@ -2785,17 +2783,11 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, aaa2 = aaa1*w21*w34; at2 = aa*cwnum; - fcijpc = (-dt1dij*at2)+(aaa2*dtsjik*dctij*(1.0-tspijl)) + - (aaa2*dtsijl*dctji*(1.0-tspjik)); fcikpc = (-dt1dik*at2)+(aaa2*dtsjik*dctik*(1.0-tspijl)); fcjlpc = (-dt1djl*at2)+(aaa2*dtsijl*dctjl*(1.0-tspjik)); fcjkpc = (-dt1djk*at2)+(aaa2*dtsjik*dctjk*(1.0-tspijl)); fcilpc = (-dt1dil*at2)+(aaa2*dtsijl*dctil*(1.0-tspjik)); - F23[0] = (fcijpc*r23[0])+(aa*dt2dij[0]); - F23[1] = (fcijpc*r23[1])+(aa*dt2dij[1]); - F23[2] = (fcijpc*r23[2])+(aa*dt2dij[2]); - F12[0] = (fcikpc*r21[0])+(aa*dt2dik[0]); F12[1] = (fcikpc*r21[1])+(aa*dt2dik[1]); F12[2] = (fcikpc*r21[2])+(aa*dt2dik[2]); @@ -2815,16 +2807,31 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag, f1[0] = -F12[0]-F31[0]; f1[1] = -F12[1]-F31[1]; f1[2] = -F12[2]-F31[2]; - f2[0] = F23[0]+F12[0]+F24[0]; - f2[1] = F23[1]+F12[1]+F24[1]; - f2[2] = F23[2]+F12[2]+F24[2]; - f3[0] = -F23[0]+F34[0]+F31[0]; - f3[1] = -F23[1]+F34[1]+F31[1]; - f3[2] = -F23[2]+F34[2]+F31[2]; + f2[0] = F12[0]+F31[0]; + f2[1] = F12[1]+F31[1]; + f2[2] = F12[2]+F31[2]; + f3[0] = F34[0]+F24[0]; + f3[1] = F34[1]+F24[1]; + f3[2] = F34[2]+F24[2]; f4[0] = -F34[0]-F24[0]; f4[1] = -F34[1]-F24[1]; f4[2] = -F34[2]-F24[2]; + rijmbr = rcmin[itype][jtype] / realrijmag; + f2[0] += rijmbr * (F24[0] - (realrij[0] * realrij[0] * F24[0] + realrij[0] * realrij[1] * F24[1] + realrij[0] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + f2[1] += rijmbr * (F24[1] - (realrij[1] * realrij[0] * F24[0] + realrij[1] * realrij[1] * F24[1] + realrij[1] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + f2[2] += rijmbr * (F24[2] - (realrij[2] * realrij[0] * F24[0] + realrij[2] * realrij[1] * F24[1] + realrij[2] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + f3[0] -= rijmbr * (F24[0] - (realrij[0] * realrij[0] * F24[0] + realrij[0] * realrij[1] * F24[1] + realrij[0] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + f3[1] -= rijmbr * (F24[1] - (realrij[1] * realrij[0] * F24[0] + realrij[1] * realrij[1] * F24[1] + realrij[1] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + f3[2] -= rijmbr * (F24[2] - (realrij[2] * realrij[0] * F24[0] + realrij[2] * realrij[1] * F24[1] + realrij[2] * realrij[2] * F24[2]) / (realrijmag * realrijmag)); + + f2[0] -= rijmbr * (F31[0] - (realrij[0] * realrij[0] * F31[0] + realrij[0] * realrij[1] * F31[1] + realrij[0] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + f2[1] -= rijmbr * (F31[1] - (realrij[1] * realrij[0] * F31[0] + realrij[1] * realrij[1] * F31[1] + realrij[1] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + f2[2] -= rijmbr * (F31[2] - (realrij[2] * realrij[0] * F31[0] + realrij[2] * realrij[1] * F31[1] + realrij[2] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + f3[0] += rijmbr * (F31[0] - (realrij[0] * realrij[0] * F31[0] + realrij[0] * realrij[1] * F31[1] + realrij[0] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + f3[1] += rijmbr * (F31[1] - (realrij[1] * realrij[0] * F31[0] + realrij[1] * realrij[1] * F31[1] + realrij[1] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + f3[2] += rijmbr * (F31[2] - (realrij[2] * realrij[0] * F31[0] + realrij[2] * realrij[1] * F31[1] + realrij[2] * realrij[2] * F31[2]) / (realrijmag * realrijmag)); + // coordination forces tmp2 = VA*Tij*((1.0-(om1234*om1234))) * diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index a0408d55dd..d55d9a79a4 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -274,7 +274,7 @@ atomic structure to ensure that it is realistic. E: Too many atom triplets for pair bop The number of three atom groups for angle determinations exceeds the -expected number. Check your atomic structrure to ensure that it is +expected number. Check your atomic structure to ensure that it is realistic. E: Cannot open BOP potential file %s diff --git a/src/MISC/fix_ttm.h b/src/MISC/fix_ttm.h index 34629fb538..57d18bcb3a 100644 --- a/src/MISC/fix_ttm.h +++ b/src/MISC/fix_ttm.h @@ -148,7 +148,7 @@ Self-explanatory. E: Initial temperatures not all set in fix ttm -Self-explantory. +Self-explanatory. W: Too many inner timesteps in fix ttm diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python.cpp index 6c89be6922..11bb848b33 100644 --- a/src/PYTHON/python.cpp +++ b/src/PYTHON/python.cpp @@ -146,7 +146,7 @@ void Python::command(int narg, char **arg) int ifunc = create_entry(arg[0]); - // one-time intitialization of Python interpreter + // one-time initialization of Python interpreter // Py_SetArgv() enables finding of *.py module files in current dir // only needed for module load, not for direct file read into __main__ // pymain stores pointer to main module diff --git a/src/PYTHON/python.h b/src/PYTHON/python.h index 61e5f015e2..5f65e3970b 100644 --- a/src/PYTHON/python.h +++ b/src/PYTHON/python.h @@ -94,12 +94,12 @@ path and name are correct. E: Could not process Python file -The Python code in the specified file was not run sucessfully by +The Python code in the specified file was not run successfully by Python, probably due to errors in the Python code. E: Could not process Python string -The Python code in the here string was not run sucessfully by Python, +The Python code in the here string was not run successfully by Python, probably due to errors in the Python code. E: Could not find Python function @@ -123,7 +123,7 @@ Self-explanatory. E: Python function evaluation failed -The Python function did not run succesfully and/or did not return a +The Python function did not run successfully and/or did not return a value (if it is supposed to return a value). This is probably due to some error condition in the function. diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h index dc7c6d389e..99237d8397 100644 --- a/src/REAX/fix_reax_bonds.h +++ b/src/REAX/fix_reax_bonds.h @@ -63,7 +63,7 @@ Check that the path and name are correct. E: Cannot use fix reax/bonds without pair_style reax -Self-explantory. +Self-explanatory. E: Fix reax/bonds numbonds > nsbmax_most diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 00719dcc95..afedf0cdc5 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -106,7 +106,7 @@ for NEB. E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. E: Unexpected end of neb file diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index cc866007d2..be09af4965 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -122,7 +122,7 @@ after the PRD simulation. E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. E: Cannot use PRD with a changing box diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index 8b8b22552a..d44b226643 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -145,7 +145,7 @@ after the PRD simulation. E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. E: Too many iterations diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index 832e36e491..3d24fdbc69 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -96,7 +96,7 @@ temperature (nvt or langevin). E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. E: Tempering could not find thermo_pe compute diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 4358793a33..2d8e736a1e 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2488,7 +2488,7 @@ void FixRigidSmall::write_restart_file(char *file) { FILE *fp; - // do not write file if bodies have not yet been intialized + // do not write file if bodies have not yet been initialized if (!setupflag) return; diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 5907a69b1f..6d5d470545 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -447,7 +447,6 @@ void FixShake::setup(int vflag) next_output = (ntimestep/output_every)*output_every + output_every; } else next_output = -1; - // set respa to 0 if verlet is used and to 1 otherwise if (strstr(update->integrate_style,"verlet")) @@ -476,7 +475,6 @@ void FixShake::setup(int vflag) // precalculate constraining forces for first integration step shake_end_of_step(vflag); - } /* ---------------------------------------------------------------------- @@ -592,6 +590,7 @@ void FixShake::post_force(int vflag) } // store vflag for coordinate_constraints_end_of_step() + vflag_post_force = vflag; } diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h index afd3868cb4..ff12b9e120 100644 --- a/src/RIGID/fix_shake.h +++ b/src/RIGID/fix_shake.h @@ -184,7 +184,7 @@ Self-explanatory. W: Molecule template for fix shake has multiple molecules -The fix shake command will only recoginze molecules of a single +The fix shake command will only recognize molecules of a single type, i.e. the first molecule in the template. E: Fix shake molecule template must have shake info diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h index d9885998be..cc26acc8b8 100644 --- a/src/SHOCK/fix_append_atoms.h +++ b/src/SHOCK/fix_append_atoms.h @@ -94,7 +94,7 @@ type p (periodic). E: Cannot append atoms to a triclinic box -The simulation box must be defined with edges alligned with the +The simulation box must be defined with edges aligned with the Cartesian axes. E: Fix ID for fix ave/spatial does not exist diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index d3f132bd04..dc84b0be05 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -700,7 +700,7 @@ double PairSNAP::extra_cutoff() // Note that at most one atom is exchanged per processor pair. -// Also note that the local atom assignement +// Also note that the local atom assignment // doesn't change. This load balancer will cause // some ghost atoms to have full neighborlists // which are unique to PairSNAP. diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index ef93ce9ff6..8b16b89336 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -815,7 +815,7 @@ void SNA::compute_dbidrj() // for mb1 = 0,...,j1mid // for ma1 = 0,...,j1 // zdb += - // Conj(dudr(j1,ma1,mb1))*z(j1,j2,j,ma1,mb1) + // Conj(dudr(j1,ma1,mb1))*z(j,j2,j1,ma1,mb1) // dbdr(j1,j2,j) += 2*zdb*(j+1)/(j1+1) // zdb = 0 // for mb2 = 0,...,j2mid diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 736b10d83f..7e43901dc9 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -811,7 +811,7 @@ void FixSRD::post_force(int vflag) } // if wall has moved too far, trigger reneigh on next step - // analagous to neighbor check for big particle moving 1/2 of skin distance + // analogous to neighbor check for big particle moving 1/2 of skin distance if (wallexist) { for (m = 0; m < nwall; m++) diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h index fae9780b89..e14652e526 100644 --- a/src/SRD/fix_srd.h +++ b/src/SRD/fix_srd.h @@ -361,11 +361,11 @@ warning. E: Bad quadratic solve for particle/line collision -This is an internal error. It should nornally not occur. +This is an internal error. It should normally not occur. E: Bad quadratic solve for particle/tri collision -This is an internal error. It should nornally not occur. +This is an internal error. It should normally not occur. W: Fix srd particle moved outside valid domain @@ -377,7 +377,7 @@ Big particles must be extended spheriods or ellipsoids. E: Cannot use lines with fix srd unless overlap is set -This is because line segements are connected to each other. +This is because line segments are connected to each other. E: Cannot use tris with fix srd unless overlap is set diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h index e43c093ca3..d1a0c7c7f2 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.h +++ b/src/USER-AWPMD/atom_vec_wavepacket.h @@ -95,9 +95,9 @@ private: // AWPMD- specific: ///\en electron tag: must be the same for the WPs belonging to the same electron int *etag; - ///\en wavepacket split coeffcients: cre, cim, size is 2*N + ///\en wavepacket split coefficients: cre, cim, size is 2*N double *cs; - ///\en force on wavepacket split coeffcients: re, im, size is 2*N + ///\en force on wavepacket split coefficients: re, im, size is 2*N double *csforce; ///\en (generalized) force on velocity, size is 3*N double *vforce; diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index 7320263ba7..89453ded9b 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -352,12 +352,17 @@ int colvarproxy_lammps::smp_enabled() int colvarproxy_lammps::smp_colvars_loop() { colvarmodule *cv = this->colvars; + colvarproxy_lammps *proxy = (colvarproxy_lammps *) cv->proxy; #pragma omp parallel for - for (size_t i = 0; i < cv->colvars_smp.size(); i++) { + for (size_t i = 0; i < cv->variables_active_smp()->size(); i++) { + colvar *x = (*(cv->variables_active_smp()))[i]; + int x_item = (*(cv->variables_active_smp_items()))[i]; if (cvm::debug()) { - cvm::log("Calculating colvar \""+cv->colvars_smp[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n"); + cvm::log("["+cvm::to_str(proxy->smp_thread_id())+"/"+cvm::to_str(proxy->smp_num_threads())+ + "]: calc_colvars_items_smp(), i = "+cvm::to_str(i)+", cv = "+ + x->name+", cvc = "+cvm::to_str(x_item)+"\n"); } - cv->colvars_smp[i]->calc_cvcs(cv->colvars_smp_items[i], 1); + x->calc_cvcs(x_item, 1); } return cvm::get_error(); } @@ -367,11 +372,13 @@ int colvarproxy_lammps::smp_biases_loop() { colvarmodule *cv = this->colvars; #pragma omp parallel for - for (size_t i = 0; i < cv->biases.size(); i++) { + for (size_t i = 0; i < cv->biases_active()->size(); i++) { + colvarbias *b = (*(cv->biases_active()))[i]; if (cvm::debug()) { - cvm::log("Calculating bias \""+cv->biases[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n"); + cvm::log("Calculating bias \""+b->name+"\" on thread "+ + cvm::to_str(smp_thread_id())+"\n"); } - cv->biases[i]->update(); + b->update(); } return cvm::get_error(); } diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index c0b4ea20fe..ad63eb2f9e 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -29,7 +29,7 @@ #endif #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2016-12-27" +#define COLVARPROXY_VERSION "2017-01-09" #endif /* struct for packed data communication of coordinates and forces. */ diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index b8cee21c35..294b003b0c 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -106,15 +106,15 @@ Self-explanatory. E: Invalid fix ave/time off column -Self-explantory. +Self-explanatory. E: Fix ave/time compute does not calculate a scalar -Self-explantory. +Self-explanatory. E: Fix ave/time compute does not calculate a vector -Self-explantory. +Self-explanatory. E: Fix ave/time compute vector is accessed out-of-range diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 399383ec18..477ed05e3f 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -488,8 +488,6 @@ int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf) buf[m++] = uCond[j]; buf[m++] = uMech[j]; buf[m++] = uChem[j]; - buf[m++] = uCG[j]; - buf[m++] = uCGnew[j]; } return m; } @@ -589,8 +587,6 @@ int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf) uCond[i] = buf[m++]; uMech[i] = buf[m++]; uChem[i] = buf[m++]; - uCG[i] = buf[m++]; - uCGnew[i] = buf[m++]; } return m; } diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/USER-DPD/fix_eos_table_rx.h index 8c26d133a5..9de7c5fbc7 100644 --- a/src/USER-DPD/fix_eos_table_rx.h +++ b/src/USER-DPD/fix_eos_table_rx.h @@ -157,6 +157,6 @@ Self-explanatory. E: Maxit exceeded in secant solver -The maximum number of interations was exceeded in the secant solver +The maximum number of iterations was exceeded in the secant solver */ diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 1a07fb9d38..deff0d34e9 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -1098,7 +1098,7 @@ void PairExp6rx::getMixingWeights(int id,double &epsilon1,double &alpha1,double fraction2 = atom->dvector[ispecies][id]/nTotal; } - // If Site1 or Site2 matches is a fluid, then compute the paramters + // If Site1 or Site2 matches is a fluid, then compute the parameters if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) { if (isite1 == params[iparam].ispecies || isite2 == params[iparam].ispecies) continue; rmi = params[iparam].rm; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 6e20f206d5..43d4114741 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -385,11 +385,11 @@ void PairMultiLucyRX::coeff(int narg, char **arg) nspecies = atom->nspecies_dpd; int n; - n = strlen(arg[3]) + 1; + n = strlen(arg[4]) + 1; site1 = new char[n]; strcpy(site1,arg[4]); - n = strlen(arg[4]) + 1; + n = strlen(arg[5]) + 1; site2 = new char[n]; strcpy(site2,arg[5]); @@ -923,15 +923,15 @@ void PairMultiLucyRX::computeLocalDensity() rho_i += factor; if (newton_pair || j < nlocal) rho[j] += factor; - } else if (rsq < cutsq[itype][jtype]) { - const double rcut = sqrt(cutsq[itype][jtype]); - const double tmpFactor = 1.0-sqrt(rsq)/rcut; - const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor; - const double factor = (84.0/(5.0*pi*rcut*rcut*rcut))*(1.0+3.0*sqrt(rsq)/(2.0*rcut))*tmpFactor4; - rho_i += factor; - if (newton_pair || j < nlocal) - rho[j] += factor; } + } else if (rsq < cutsq[itype][jtype]) { + const double rcut = sqrt(cutsq[itype][jtype]); + const double tmpFactor = 1.0-sqrt(rsq)/rcut; + const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor; + const double factor = (84.0/(5.0*pi*rcut*rcut*rcut))*(1.0+3.0*sqrt(rsq)/(2.0*rcut))*tmpFactor4; + rho_i += factor; + if (newton_pair || j < nlocal) + rho[j] += factor; } } diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 8498d752e3..2529d33f91 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -351,7 +351,7 @@ void PairTableRX::coeff(int narg, char **arg) nspecies = atom->nspecies_dpd; if(nspecies==0) error->all(FLERR,"There are no rx species specified."); int n; - n = strlen(arg[3]) + 1; + n = strlen(arg[4]) + 1; site1 = new char[n]; strcpy(site1,arg[4]); @@ -362,7 +362,7 @@ void PairTableRX::coeff(int narg, char **arg) if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) error->all(FLERR,"Site1 name not recognized in pair coefficients"); - n = strlen(arg[4]) + 1; + n = strlen(arg[5]) + 1; site2 = new char[n]; strcpy(site2,arg[5]); diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 5b4463631f..d6c3e23ab4 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -50,7 +50,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) : // where: nevery: call this fix every nevery timesteps. // (keep this set to 1 for now). // typeLB: there are two different integrators - // in the code labelled "1" and "2". + // in the code labeled "1" and "2". // viscosity: the viscosity of the fluid. // densityinit_real: the density of the fluid. // diff --git a/src/USER-MANIFOLD/README b/src/USER-MANIFOLD/README index 3656391641..f55a9bb8e3 100644 --- a/src/USER-MANIFOLD/README +++ b/src/USER-MANIFOLD/README @@ -31,7 +31,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory: e. The header file has to contain somewhere the macro ManifoldStyle with as first argument the name of the manifold and as second argument the name of the class implementing this manifold. The macro expands into some code - that registers the manifold during static initialisation, before main is + that registers the manifold during static initialization, before main is entered. 2. In the source file, make sure you implement the following (of course, @@ -51,7 +51,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory: | | manifold in LAMMPS input scripts. | | const char *id() | Should return whatever type() returns. | | static int expected_argc() | Returns the number of arguments needed | -| | for the construction/initialisation of | +| | for the construction/initialization of | | | your manifold. Example: Sphere only | | | needs a radius, so it returns 1. The | | | spine needs 5 parameters, so it | diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index c3bbc935af..2fac8e40df 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -104,7 +104,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : } - // Perform any further initialisation for the manifold that depends on params: + // Perform any further initialization for the manifold that depends on params: ptr_m->post_param_init(); } diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index 82a565af38..85692a8b6b 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -65,7 +65,7 @@ namespace user_manifold { virtual int nparams() = 0; double **get_params(){ return ¶ms; }; - // Overload if any initialisation depends on params: + // Overload if any initialization depends on params: virtual void post_param_init(){} virtual void checkup(){} // Some diagnostics... protected: diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 8aed797235..52ee6cad94 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -63,6 +63,7 @@ pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 +pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16 diff --git a/src/USER-MISC/fix_grem.h b/src/USER-MISC/fix_grem.h index 5e828a8b9f..4806505f61 100644 --- a/src/USER-MISC/fix_grem.h +++ b/src/USER-MISC/fix_grem.h @@ -77,7 +77,7 @@ in energy directly. E: Must use variable energy with fix grem -Must define an energy vartiable when applyting a dynamic +Must define an energy variable when applying a dynamic force during minimization. */ diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 5b5341f506..5a7937e4ee 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -26,7 +26,7 @@ (2002) This potential does not affect small amplitude vibrations but is used in an ad hoc way to prevent the onset of - accidentially large amplitude fluctuations leading to + accidentally large amplitude fluctuations leading to the occurrence of a planar conformation of the three bonds i, i + 1 and i', an intermediate conformation toward the chiral inversion of a methine carbon. diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 03bb22c713..9cd2cf57b8 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -60,6 +60,14 @@ static const char cite_pair_agni[] = " pages = {094306},\n" " year = {2015},\n" " publisher = {APS}\n" + "}\n\n" + "@article{botu2017jpc,\n" + " author = {Botu, V. and Batra, R. and Chapman, J. and Ramprasad, Rampi},\n" + " journal = {J. Phys. Chem. C},\n" + " volume = {121},\n" + " number = {1},\n" + " pages = {511},\n" + " year = {2017},\n" "}\n\n"; #define AGNI_VERSION 1 diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index f3a599dbdb..6ce84ab767 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -1034,7 +1034,7 @@ void PairEDIP::setup_params() if (rtmp > cutmax) cutmax = rtmp; } - // this should be removed for multi species parametrizations + // this should be removed for multi species parameterization A = params[0].A; B = params[0].B; diff --git a/src/USER-MISC/pair_edip.h b/src/USER-MISC/pair_edip.h index 6a55992f1f..6c4a37d795 100644 --- a/src/USER-MISC/pair_edip.h +++ b/src/USER-MISC/pair_edip.h @@ -64,7 +64,7 @@ class PairEDIP : public Pair { double *tauFunctionGrid; double *tauFunctionDerivedGrid; - // this should be removed for multi species parametrizations + // this should be removed for multi species parameterization // since these parameters should be addressed through indexes // see also the PairEDIP::setup() diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp new file mode 100644 index 0000000000..ddb39f6870 --- /dev/null +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -0,0 +1,441 @@ +/* ---------------------------------------------------------------------- + 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: Jaap Kroes (Radboud Universiteit) + e-mail: jaapkroes at gmail dot com + based on previous versions by Merel van Wijk and by Marco Raguzzoni + + This is a simplified version of the potential described in + [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] + The simplification is that all normals are taken along the z-direction +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_kolmogorov_crespi_z.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; + + // initialize element to parameter maps + nelements = 0; + elements = NULL; + nparams = maxparam = 0; + params = NULL; + elem2param = NULL; + map = NULL; + + // always compute energy offset + offset_flag = true; +} + +/* ---------------------------------------------------------------------- */ + +PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(offset); + } + + if (elements) + for (int i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + memory->destroy(params); + memory->destroy(elem2param); + if (allocated) delete [] map; +} + +/* ---------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpair1; + double rsq,r,rhosq,exp1,exp2,r6,r8; + double frho,sumC,sumC2,sumCff,fsum,rdsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + 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; + int newton_pair = force->newton_pair; + + 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]; + 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]; + // rho^2 = r^2 - (n,r) = r^2 - z^2 + rhosq = delx*delx + dely*dely; + rsq = rhosq + delz*delz; + + if (rsq < cutsq[itype][jtype]) { + + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; + + r = sqrt(rsq); + r6 = rsq*rsq*rsq; + r8 = r6*rsq; + rdsq = rhosq*p.delta2inv; // (rho/delta)^2 + + // store exponents + exp1 = exp(-p.lambda*(r-p.z0)); + exp2 = exp(-rdsq); + + // note that f(rho_ij) equals f(rho_ji) as normals are all along z + sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq; + sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv; + frho = exp2*sumC; + sumCff = p.C + 2*frho; + + // derivatives + fpair = -6.0*p.A*p.z06/r8+p.lambda*exp1/r*sumCff; + fpair1 = exp1*exp2*(4.0*p.delta2inv*sumC-2.0*sumC2); + fsum = fpair + fpair1; + + f[i][0] += delx*fsum; + f[i][1] += dely*fsum; + // fi_z does not contain contributions from df/dr + // because rho_ij does not depend on z_i or z_j + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fsum; + f[j][1] -= dely*fsum; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = -p.A*p.z06/r6+ exp1*sumCff - offset[itype][jtype]; + } + + if (evflag){ + ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0, + fsum,fsum,fpair,delx,dely,delz); + } + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::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"); + memory->create(offset,n+1,n+1,"pair:offset"); + map = new int[atom->ntypes+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + + cut_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + 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; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::coeff(int narg, char **arg) +{ + int i,j,n; + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + + read_file(arg[2]); + + double cut_one = cut_global; + + 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 PairKolmogorovCrespiZ::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + if (offset_flag) { + int iparam_ij = elem2param[map[i]][map[j]]; + Param& p = params[iparam_ij]; + offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); + } else offset[i][j] = 0.0; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + read Kolmogorov-Crespi potential file +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::read_file(char *filename) +{ + int params_per_line = 11; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; + + // open file on proc 0 + + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open KC potential file %s",filename); + error->one(FLERR,str); + } + } + + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + int i,j,n,m,nwords,ielement,jelement; + 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,"Insufficient format in KC 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; + + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) + + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) 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].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].z0 = atof(words[2]); + params[nparams].C0 = atof(words[3]); + params[nparams].C2 = atof(words[4]); + params[nparams].C4 = atof(words[5]); + params[nparams].C = atof(words[6]); + params[nparams].delta = atof(words[7]); + params[nparams].lambda = atof(words[8]); + params[nparams].A = atof(words[9]); + // S provides a convenient scaling of all energies + params[nparams].S = atof(words[10]); + + // energies in meV further scaled by S + double meV = 1.0e-3*params[nparams].S; + params[nparams].C *= meV; + params[nparams].A *= meV; + params[nparams].C0 *= meV; + params[nparams].C2 *= meV; + params[nparams].C4 *= meV; + + // precompute some quantities + params[nparams].delta2inv = pow(params[nparams].delta,-2); + params[nparams].z06 = pow(params[nparams].z0,6); + + nparams++; + if(nparams >= pow(atom->ntypes,3)) break; + } + memory->destroy(elem2param); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + } + } + delete [] words; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h new file mode 100644 index 0000000000..3a81e571ef --- /dev/null +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h @@ -0,0 +1,83 @@ +/* ---------------------------------------------------------------------- + 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(kolmogorov/crespi/z,PairKolmogorovCrespiZ) + +#else + +#ifndef LMP_PAIR_KolmogorovCrespiZ_H +#define LMP_PAIR_KolmogorovCrespiZ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairKolmogorovCrespiZ : public Pair { + public: + PairKolmogorovCrespiZ(class LAMMPS *); + virtual ~PairKolmogorovCrespiZ(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + + protected: + int me; + + struct Param { + double z0,C0,C2,C4,C,delta,lambda,A,S; + double delta2inv,z06; + int ielement,jelement; + }; + Param *params; // parameter set for I-J interactions + char **elements; // names of unique elements + int **elem2param; // mapping from element pairs to parameters + int *map; // mapping from atom types to elements + int nelements; // # of unique elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + + double cut_global; + double **cut; + double **offset; + void read_file( char * ); + void allocate(); +}; + +} + +#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: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +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. + +*/ + diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index 53b8a91446..f379814c61 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -101,7 +101,7 @@ temperature (nvt or npt). E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. E: Grem could not find thermo_pe compute diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index b9ee2238a9..37f343736d 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -464,7 +464,7 @@ int MolfileInterface::load_plugin(const char *filename) return E_SYMBOL; } - // intialize plugin. skip plugin if it fails. + // initialize plugin. skip plugin if it fails. if (((initfunc)(ifunc))()) { my_dlclose(dso); return E_SYMBOL; diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.h b/src/USER-OMP/pair_buck_long_coul_long_omp.h index 2dc017d8fb..f874dd9b68 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.h +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.h @@ -70,15 +70,15 @@ Self-explanatory. W: Using largest cutoff for buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: Cutoffs missing in pair_style buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: LJ6 off not supported in pair_style buck/long/coul/long -Self-exlanatory. +Self-explanatory. E: Coulomb cut not supported in pair_style buck/long/coul/coul diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp index 0e9eafb2f5..28fd27f9b8 100644 --- a/src/USER-OMP/thr_data.cpp +++ b/src/USER-OMP/thr_data.cpp @@ -312,7 +312,7 @@ void LAMMPS_NS::data_reduce_thr(double *dall, int nall, int nthreads, int ndim, int m = 0; // for architectures that have L1 D-cache line sizes of 64 bytes - // (8 doubles) wide, explictly unroll this loop to compute 8 + // (8 doubles) wide, explicitly unroll this loop to compute 8 // contiguous values in the array at a time // -- modify this code based on the size of the cache line double t0, t1, t2, t3, t4, t5, t6, t7; diff --git a/src/USER-QTB/fix_qbmsst.h b/src/USER-QTB/fix_qbmsst.h index 0ed210c995..3484076abf 100644 --- a/src/USER-QTB/fix_qbmsst.h +++ b/src/USER-QTB/fix_qbmsst.h @@ -89,7 +89,7 @@ class FixQBMSST : public Fix { int seed; // seed for the random number generator double f_max; // frequency cutoff int N_f; // number of frequency grid - double eta; // coupling coefficient bewteen shock and the qtb + double eta; // coupling coefficient between shock and the qtb int beta; // average beta steps before updating the qtb temperature double t_init; // initial qtb temperature int qtb_set; // 1 if its a restarting qbmsst, 0 if not diff --git a/src/USER-REAXC/README b/src/USER-REAXC/README index cdcfb17603..86803957b8 100644 --- a/src/USER-REAXC/README +++ b/src/USER-REAXC/README @@ -14,7 +14,7 @@ particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. -For technical details about this implemention of ReaxFF, see +For technical details about this implementation of ReaxFF, see this paper: Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index fff046ba7c..cb24e2dc37 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -139,7 +139,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, } if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // innner wall + { // inner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); data->my_en.e_vdW += Tap * e_core; @@ -398,7 +398,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace, } if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) - { // innner wall + { // inner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); lr->e_vdW += Tap * e_core; diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index e4a7ea1c12..eec9e517ea 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -249,7 +249,7 @@ void PairTriSurf::compute(int eflag, int vflag) { } /* - * if particle comes too close to triangle, reflect its velocity and explicitely move it away + * if particle comes too close to triangle, reflect its velocity and explicitly move it away */ touch_distance = 1.0 * radius[particle]; diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index 5ab12aed6b..5e24ced35c 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -548,7 +548,7 @@ void PairSMTBQ::read_file(char *file) // --------------------------------- m += 1; - // Ligne 5 - parametre des potentiels + // Ligne 5 - parametre des potentials fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr); // Lecture des protagonistes @@ -615,7 +615,7 @@ void PairSMTBQ::read_file(char *file) if (verbose) printf (" %s %f %f %f %f\n",words[0], intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q); - // Ligne 6 - rayon de coupure potentiel SM + // Ligne 6 - rayon de coupure potential SM fgets( ptr, MAXLINE, fp); Tokenize( ptr, &words ); @@ -1724,7 +1724,7 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng) { /* =================================================================== - Coulombian potentiel energy calcul between i and j atoms + Coulombian potential energy calcul between i and j atoms with fafb table make in sm_table(). fafb[i][j] : i is the table's step (r) j is the interaction's # (in intype[itype][jtype]) @@ -2655,7 +2655,7 @@ void PairSMTBQ::Charge() forward(q) ; // reverse(q); - // Calcul des potentiel + // Calcul des potential // ---------------------- QForce_charge(iloop); @@ -2736,7 +2736,7 @@ void PairSMTBQ::Charge() //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: // ========================================== - // Ecriture des potentiels dans un fichier + // Ecriture des potentials dans un fichier // ========================================== if (strcmp(writepot,"true") == 0 && fmod(static_cast(step), Neverypot) == 0.0) { diff --git a/src/USER-VTK/dump_custom_vtk.h b/src/USER-VTK/dump_custom_vtk.h index 189e96aa99..f3b4a8b63e 100644 --- a/src/USER-VTK/dump_custom_vtk.h +++ b/src/USER-VTK/dump_custom_vtk.h @@ -147,7 +147,7 @@ output to dump file. E: Invalid attribute in dump custom command -Self-explantory. +Self-explanatory. E: Dump_modify format string is too short @@ -186,7 +186,7 @@ cannot be used in a dump between runs. E: Threshhold for an atom property that isn't allocated -A dump threshhold has been requested on a quantity that is +A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. E: Dumping an atom property that isn't allocated @@ -255,7 +255,7 @@ Number of element names must equal number of atom types. E: Invalid attribute in dump modify command -Self-explantory. +Self-explanatory. E: Could not find dump modify compute ID @@ -313,7 +313,7 @@ E: Could not find dump modify custom atom integer property ID Self-explanatory. -E: Invalid dump_modify threshhold operator +E: Invalid dump_modify threshold operator Operator keyword used for threshold specification in not recognized. diff --git a/src/angle.cpp b/src/angle.cpp index 14433fc44d..1366c48865 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -76,7 +76,7 @@ void Angle::init() see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void Angle::ev_setup(int eflag, int vflag) +void Angle::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -94,25 +94,29 @@ void Angle::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); + } } // zero accumulators if (eflag_global) energy = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) { diff --git a/src/angle.h b/src/angle.h index 119f206c36..000c3fe916 100644 --- a/src/angle.h +++ b/src/angle.h @@ -27,7 +27,7 @@ class Angle : protected Pointers { int *setflag; int writedata; // 1 if writes coeffs to data file double energy; // accumulated energies - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial // KOKKOS host/device flag and data masks @@ -58,7 +58,7 @@ class Angle : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; - void ev_setup(int, int); + void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, double, double *, double *, double, double, double, double, double, double); }; diff --git a/src/atom.cpp b/src/atom.cpp index 6b3427c04e..4df2bc2194 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1634,7 +1634,7 @@ int Atom::find_molecule(char *id) /* ---------------------------------------------------------------------- add info to current atom ilocal from molecule template onemol and its iatom - offset = atom ID preceeding IDs of atoms in this molecule + offset = atom ID preceding IDs of atoms in this molecule called by fixes and commands that add molecules ------------------------------------------------------------------------- */ diff --git a/src/atom.h b/src/atom.h index 9abbb49569..0f84c8242f 100644 --- a/src/atom.h +++ b/src/atom.h @@ -97,7 +97,7 @@ class Atom : protected Pointers { // molecular info - int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs + int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom int maxspecial; // special[nlocal][maxspecial] diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 54bd78a83c..40c744afc5 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -82,7 +82,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) delete [] allstyles; // hybrid settings are MAX or MIN of sub-style settings - // hybrid sizes are minimial values plus extra values for each sub-style + // hybrid sizes are minimal values plus extra values for each sub-style molecular = 0; comm_x_only = comm_f_only = 1; diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index b5dc2cfde0..390efc7c10 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -140,7 +140,7 @@ the atom coordinate. E: Insufficient Jacobi rotations for triangle -The calculation of the intertia tensor of the triangle failed. This +The calculation of the inertia tensor of the triangle failed. This should not happen if it is a reasonably shaped triangle. */ diff --git a/src/balance.cpp b/src/balance.cpp index 7780b5207c..52f6072a6c 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -276,7 +276,7 @@ void Balance::command(int narg, char **arg) set_weights(); double imbinit = imbalance_factor(maxinit); - // no load-balance if imbalance doesn't exceed threshhold + // no load-balance if imbalance doesn't exceed threshold // unless switching from tiled to non tiled layout, then force rebalance if (comm->layout == LAYOUT_TILED && style != BISECTION) { @@ -456,6 +456,7 @@ void Balance::options(int iarg, int narg, char **arg) wtflag = 0; varflag = 0; + oldrcb = 0; outflag = 0; int outarg = 0; fp = NULL; @@ -491,6 +492,9 @@ void Balance::options(int iarg, int narg, char **arg) } iarg += 2+nopt; + } else if (strcmp(arg[iarg],"old") == 0) { + oldrcb = 1; + iarg++; } else if (strcmp(arg[iarg],"out") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal (fix) balance command"); outflag = 1; @@ -640,13 +644,22 @@ int *Balance::bisection(int sortflag) double *shrinkhi = &shrinkall[3]; // invoke RCB - // then invert() to create list of proc assignements for my atoms - - if (wtflag) { - weight = fixstore->vstore; - rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi); - } else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi); + // then invert() to create list of proc assignments for my atoms + // NOTE: (3/2017) can remove undocumented "old" option at some point + // ditto in rcb.cpp + if (oldrcb) { + if (wtflag) { + weight = fixstore->vstore; + rcb->compute_old(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi); + } else rcb->compute_old(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi); + } else { + if (wtflag) { + weight = fixstore->vstore; + rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi); + } else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi); + } + rcb->invert(sortflag); // reset RCB lo/hi bounding box to full simulation box as needed @@ -776,7 +789,7 @@ int Balance::shift() bigint natoms = atom->natoms; if (natoms == 0) return 0; - // set delta for 1d balancing = root of threshhold + // set delta for 1d balancing = root of threshold // root = # of dimensions being balanced on double delta = pow(stopthresh,1.0/ndim) - 1.0; @@ -865,7 +878,7 @@ int Balance::shift() // stop if all split sums are within delta of targets // this is a 1d test of particle count per slice // assumption is that this is sufficient accuracy - // for 3d imbalance factor to reach threshhold + // for 3d imbalance factor to reach threshold doneflag = 1; for (i = 1; i < np; i++) @@ -918,7 +931,7 @@ int Balance::shift() } */ - // stop at this point in bstr if imbalance factor < threshhold + // stop at this point in bstr if imbalance factor < threshold // this is a true 3d test of particle count per processor double imbfactor = imbalance_splits(max); @@ -937,7 +950,7 @@ int Balance::shift() N = # of slices split = N+1 cuts between N slices return updated count = particles per slice - return updated sum = cummulative count below each of N+1 splits + return updated sum = cumulative count below each of N+1 splits use binary search to find which slice each atom is in ------------------------------------------------------------------------- */ @@ -972,8 +985,8 @@ void Balance::tally(int dim, int n, double *split) /* ---------------------------------------------------------------------- adjust cuts between N slices in a dim via recursive multisectioning method split = current N+1 cuts, with 0.0 and 1.0 at end points - sum = cummulative count up to each split - target = desired cummulative count up to each split + sum = cumulative count up to each split + target = desired cumulative count up to each split lo/hi = split values that bound current split update lo/hi to reflect sums at current split values overwrite split with new cuts diff --git a/src/balance.h b/src/balance.h index 7ca0354023..0f2f79bb15 100644 --- a/src/balance.h +++ b/src/balance.h @@ -49,10 +49,11 @@ class Balance : protected Pointers { private: int me,nprocs; - double thresh; // threshhold to perform LB + double thresh; // threshold to perform LB int style; // style of LB int xflag,yflag,zflag; // xyz LB flags double *user_xsplit,*user_ysplit,*user_zsplit; // params for xyz LB + int oldrcb; // use old-style RCB compute int nitermax; // params for shift LB double stopthresh; @@ -63,10 +64,10 @@ class Balance : protected Pointers { int *bdim; // XYZ for each character in bstr double *onecost; // work vector of counts in one dim double *allcost; // counts for slices in one dim - double *sum; // cummulative count for slices in one dim + double *sum; // cumulative count for slices in one dim double *target; // target sum for slices in one dim double *lo,*hi; // lo/hi split coords that bound each target - double *losum,*hisum; // cummulative counts at lo/hi coords + double *losum,*hisum; // cumulative counts at lo/hi coords int rho; // 0 for geometric recursion // 1 for density weighted recursion diff --git a/src/bond.cpp b/src/bond.cpp index 8074d97677..5a33f107cf 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -79,7 +79,7 @@ void Bond::init() see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void Bond::ev_setup(int eflag, int vflag) +void Bond::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -97,25 +97,29 @@ void Bond::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); + } } // zero accumulators if (eflag_global) energy = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) { diff --git a/src/bond.h b/src/bond.h index 06e05a7265..41604387a3 100644 --- a/src/bond.h +++ b/src/bond.h @@ -27,7 +27,7 @@ class Bond : protected Pointers { int *setflag; int writedata; // 1 if writes coeffs to data file double energy; // accumulated energies - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial // KOKKOS host/device flag and data masks @@ -60,7 +60,7 @@ class Bond : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; - void ev_setup(int, int); + void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, double, double, double, double, double); }; diff --git a/src/citeme.h b/src/citeme.h index 80b642ab6d..18e9a712db 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -42,7 +42,7 @@ E: Cannot open log.cite file This file is created when you use some LAMMPS features, to indicate what paper you should cite on behalf of those who implemented -the feature. Check that you have write priveleges into the directory +the feature. Check that you have write privileges into the directory you are running in. */ diff --git a/src/compute_angle.h b/src/compute_angle.h index d50e3e21d7..c39a2c3d27 100644 --- a/src/compute_angle.h +++ b/src/compute_angle.h @@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute bond must use group all -Bond styles accumlate energy on all atoms. +Bond styles accumulate energy on all atoms. E: Unrecognized bond style in compute bond command diff --git a/src/compute_bond.h b/src/compute_bond.h index 0f3c811218..0f6c088f1d 100644 --- a/src/compute_bond.h +++ b/src/compute_bond.h @@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute bond must use group all -Bond styles accumlate energy on all atoms. +Bond styles accumulate energy on all atoms. E: Unrecognized bond style in compute bond command diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 925c5fbf81..ac35629d08 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -616,6 +616,7 @@ void ComputeChunkAtom::setup() { if (nchunkflag == ONCE) setup_chunks(); if (idsflag == ONCE) compute_ichunk(); + else invoked_ichunk = -1; } /* ---------------------------------------------------------------------- @@ -1298,7 +1299,7 @@ int ComputeChunkAtom::setup_sphere_bins() } // if pbcflag set, sradmax must be < 1/2 box in any periodic dim - // treat orthongonal and triclinic the same + // treat orthogonal and triclinic the same // check every time bins are created if (pbcflag) { @@ -1363,7 +1364,7 @@ int ComputeChunkAtom::setup_cylinder_bins() } // if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim - // treat orthongonal and triclinic the same + // treat orthogonal and triclinic the same // check every time bins are created if (pbcflag) { diff --git a/src/compute_chunk_atom.h b/src/compute_chunk_atom.h index cbec221048..9c64e9bc7a 100644 --- a/src/compute_chunk_atom.h +++ b/src/compute_chunk_atom.h @@ -248,11 +248,11 @@ The lo/hi values are inconsistent. E: Compute chunk/atom bin/sphere radius is too large for periodic box -Radius cannot be bigger than 1/2 of any periodic dimention. +Radius cannot be bigger than 1/2 of any periodic dimension. E: Compute chunk/atom bin/cylinder radius is too large for periodic box -Radius cannot be bigger than 1/2 of a non-axis periodic dimention. +Radius cannot be bigger than 1/2 of a non-axis periodic dimension. E: Cannot use compute chunk/atom bin z for 2d model diff --git a/src/compute_cna_atom.h b/src/compute_cna_atom.h index 77ea5951dc..82cf8df608 100644 --- a/src/compute_cna_atom.h +++ b/src/compute_cna_atom.h @@ -57,11 +57,11 @@ command-line option when running LAMMPS to see the offending line. E: Compute cna/atom requires a pair style be defined -Self-explantory. +Self-explanatory. E: Compute cna/atom cutoff is longer than pairwise cutoff -Self-explantory. +Self-explanatory. W: Compute cna/atom cutoff may be too large to find ghost atom neighbors diff --git a/src/compute_contact_atom.h b/src/compute_contact_atom.h index bf2f1314d9..2ce7678f56 100644 --- a/src/compute_contact_atom.h +++ b/src/compute_contact_atom.h @@ -60,7 +60,7 @@ Self-explanatory. E: Compute contact/atom requires a pair style be defined -Self-explantory. +Self-explanatory. W: More than one compute contact/atom diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h index 2ad46fa854..6c60c86266 100644 --- a/src/compute_coord_atom.h +++ b/src/compute_coord_atom.h @@ -67,7 +67,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute coord/atom requires a pair style be defined -Self-explantory. +Self-explanatory. E: Compute coord/atom cutoff is longer than pairwise cutoff diff --git a/src/compute_dihedral.h b/src/compute_dihedral.h index 80b78aba98..041e1f6eae 100644 --- a/src/compute_dihedral.h +++ b/src/compute_dihedral.h @@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute bond must use group all -Bond styles accumlate energy on all atoms. +Bond styles accumulate energy on all atoms. E: Unrecognized bond style in compute bond command diff --git a/src/compute_group_group.h b/src/compute_group_group.h index 906a185cf2..c7443bda5c 100644 --- a/src/compute_group_group.h +++ b/src/compute_group_group.h @@ -72,7 +72,7 @@ Cannot calculate group interactions without a pair style defined. E: Pair style does not support compute group/group The pair_style does not have a single() function, so it cannot be -invokded by the compute group/group command. +invoked by the compute group/group command. E: No Kspace style defined for compute group/group @@ -84,6 +84,6 @@ Self-explanatory. W: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero -Self-explantory. +Self-explanatory. */ diff --git a/src/compute_hexorder_atom.h b/src/compute_hexorder_atom.h index 84c80abc57..39af576cb7 100644 --- a/src/compute_hexorder_atom.h +++ b/src/compute_hexorder_atom.h @@ -62,7 +62,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute hexorder/atom requires a pair style be defined -Self-explantory. +Self-explanatory. E: Compute hexorder/atom cutoff is longer than pairwise cutoff diff --git a/src/compute_improper.h b/src/compute_improper.h index 6f92f068e3..d3602677a6 100644 --- a/src/compute_improper.h +++ b/src/compute_improper.h @@ -52,7 +52,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute bond must use group all -Bond styles accumlate energy on all atoms. +Bond styles accumulate energy on all atoms. E: Unrecognized bond style in compute bond command diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h index 81b08dbddc..eb814e9c1c 100644 --- a/src/compute_orientorder_atom.h +++ b/src/compute_orientorder_atom.h @@ -72,7 +72,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute orientorder/atom requires a pair style be defined -Self-explantory. +Self-explanatory. E: Compute orientorder/atom cutoff is longer than pairwise cutoff diff --git a/src/compute_pair.h b/src/compute_pair.h index 37f026f1ee..91702748a6 100644 --- a/src/compute_pair.h +++ b/src/compute_pair.h @@ -54,7 +54,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute pair must use group all -Pair styles accumlate energy on all atoms. +Pair styles accumulate energy on all atoms. E: Unrecognized pair style in compute pair command diff --git a/src/compute_property_chunk.h b/src/compute_property_chunk.h index 077129a06e..48211ec91b 100644 --- a/src/compute_property_chunk.h +++ b/src/compute_property_chunk.h @@ -81,15 +81,15 @@ It will only store IDs if its compress option is enabled. E: Compute chunk/atom stores no coord1 for compute property/chunk -Only certain binning options for comptue chunk/atom store coordinates. +Only certain binning options for compute chunk/atom store coordinates. E: Compute chunk/atom stores no coord2 for compute property/chunk -Only certain binning options for comptue chunk/atom store coordinates. +Only certain binning options for compute chunk/atom store coordinates. E: Compute chunk/atom stores no coord3 for compute property/chunk -Only certain binning options for comptue chunk/atom store coordinates. +Only certain binning options for compute chunk/atom store coordinates. E: Invalid keyword in compute property/chunk command diff --git a/src/compute_property_local.h b/src/compute_property_local.h index fbc1ea3097..2b0dda5a10 100644 --- a/src/compute_property_local.h +++ b/src/compute_property_local.h @@ -99,7 +99,7 @@ command-line option when running LAMMPS to see the offending line. E: Compute property/local cannot use these inputs together Only inputs that generate the same number of datums can be used -togther. E.g. bond and angle quantities cannot be mixed. +together. E.g. bond and angle quantities cannot be mixed. E: Invalid keyword in compute property/local command diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 776a94c8b9..04a2df91f8 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -806,7 +806,7 @@ void CreateAtoms::add_molecule(double *center, double *quat_user) onemol->quat_external = quat; // create atoms in molecule with atom ID = 0 and mol ID = 0 - // reset in caller after all moleclues created by all procs + // reset in caller after all molecules created by all procs // pass add_molecule_atom an offset of 0 since don't know // max tag of atoms in previous molecules at this point diff --git a/src/create_atoms.h b/src/create_atoms.h index 721b31e8c5..56e9c65b89 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -88,7 +88,7 @@ is the number of atom types. E: Molecule template ID for create_atoms does not exist -Self-explantory. +Self-explanatory. W: Molecule template for create_atoms has multiple molecules diff --git a/src/dihedral.cpp b/src/dihedral.cpp index 4c941d7225..f5c1c6c44c 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -76,7 +76,7 @@ void Dihedral::init() see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void Dihedral::ev_setup(int eflag, int vflag) +void Dihedral::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -94,25 +94,29 @@ void Dihedral::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); + } } // zero accumulators if (eflag_global) energy = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) { diff --git a/src/dihedral.h b/src/dihedral.h index 68167eb86f..d27810c4d6 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -27,7 +27,7 @@ class Dihedral : protected Pointers { int *setflag; int writedata; // 1 if writes coeffs to data file double energy; // accumulated energy - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial // KOKKOS host/device flag and data masks @@ -56,7 +56,7 @@ class Dihedral : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; - void ev_setup(int, int); + void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, int, double, double *, double *, double *, double, double, double, double, double, double, double, double, double); diff --git a/src/domain.cpp b/src/domain.cpp index 1dede69729..31fb3b8559 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -514,7 +514,7 @@ void Domain::pbc() double *coord; int n3 = 3*nlocal; - coord = &x[0][0]; // note: x is always initialzed to at least one element. + coord = &x[0][0]; // note: x is always initialized to at least one element. int flag = 0; for (i = 0; i < n3; i++) if (!ISFINITE(*coord++)) flag = 1; diff --git a/src/dump_custom.h b/src/dump_custom.h index 38567b7523..8067415834 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -206,7 +206,7 @@ output to dump file. E: Invalid attribute in dump custom command -Self-explantory. +Self-explanatory. E: Dump_modify format string is too short @@ -314,7 +314,7 @@ Number of element names must equal number of atom types. E: Invalid attribute in dump modify command -Self-explantory. +Self-explanatory. E: Could not find dump modify compute ID diff --git a/src/dump_local.h b/src/dump_local.h index 6f8dc09f57..ffca02b381 100644 --- a/src/dump_local.h +++ b/src/dump_local.h @@ -125,7 +125,7 @@ Every column of output must be the same length. E: Invalid attribute in dump local command -Self-explantory. +Self-explanatory. E: Dump local compute does not compute local info diff --git a/src/fix.h b/src/fix.h index bd3189afe7..8005da1add 100644 --- a/src/fix.h +++ b/src/fix.h @@ -89,7 +89,7 @@ class Fix : protected Pointers { int comm_reverse; // size of reverse communication (0 if none) int comm_border; // size of border communication (0 if none) - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial int restart_reset; // 1 if restart just re-initialized fix diff --git a/src/fix_addforce.h b/src/fix_addforce.h index d19c0db0d1..f06ed5ed4c 100644 --- a/src/fix_addforce.h +++ b/src/fix_addforce.h @@ -85,7 +85,7 @@ in energy directly. E: Must use variable energy with fix addforce -Must define an energy vartiable when applyting a dynamic +Must define an energy variable when applying a dynamic force during minimization. */ diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index 18622699de..eb51043e0f 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -162,7 +162,7 @@ Self-explanatory. E: Fix ave/chunk does not use chunk/atom compute -The specified conpute is not for a compute chunk/atom command. +The specified compute is not for a compute chunk/atom command. E: Error writing file header diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 277a57a48d..37dd8c9898 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -126,7 +126,7 @@ void FixAveHistoWeight::end_of_step() modify->clearstep_compute(); - // calcualte weight factors which are 2nd value (i = 1) + // calculate weight factors which are 2nd value (i = 1) double weight = 0.0; double *weights = NULL; diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index d771036530..0357815f0c 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -101,15 +101,15 @@ Self-explanatory. E: Invalid fix ave/time off column -Self-explantory. +Self-explanatory. E: Fix ave/time compute does not calculate a scalar -Self-explantory. +Self-explanatory. E: Fix ave/time compute does not calculate a vector -Self-explantory. +Self-explanatory. E: Fix ave/time compute vector is accessed out-of-range diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 33054e0e3b..7e0aa681bb 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -189,7 +189,7 @@ void FixBalance::setup_pre_exchange() domain->reset_box(); if (domain->triclinic) domain->lamda2x(atom->nlocal); - // perform a rebalance if threshhold exceeded + // perform a rebalance if threshold exceeded balance->set_weights(); imbnow = balance->imbalance_factor(maxloadperproc); @@ -224,7 +224,7 @@ void FixBalance::pre_exchange() domain->reset_box(); if (domain->triclinic) domain->lamda2x(atom->nlocal); - // perform a rebalance if threshhold exceeded + // perform a rebalance if threshold exceeded // if weight variable is used, wrap weight setting in clear/add compute if (balance->varflag) modify->clearstep_compute(); diff --git a/src/fix_deform.h b/src/fix_deform.h index efbecfd636..cdda1b8547 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -107,7 +107,7 @@ Only one fix deform can be defined at a time. E: Variable name for fix deform does not exist -Self-explantory. +Self-explanatory. E: Variable for fix deform is invalid style diff --git a/src/fix_group.h b/src/fix_group.h index 5815d31459..6ed842578d 100644 --- a/src/fix_group.h +++ b/src/fix_group.h @@ -77,10 +77,10 @@ The variable must be an atom-style variable. W: One or more dynamic groups may not be updated at correct point in timestep -If there are other fixes that act immediately after the intitial stage +If there are other fixes that act immediately after the initial stage of time integration within a timestep (i.e. after atoms move), then the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignements are made +fixes. This will insure that dynamic group assignments are made after all atoms have moved. */ diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index ca74efa454..2a4af4dc66 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -30,9 +30,10 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{BONDMAX,VARIABLE}; +enum{BONDMAX,TLIMIT,VARIABLE}; enum{LT,LE,GT,GE,EQ,NEQ,XOR}; enum{HARD,SOFT,CONTINUE}; +enum{NOMSG,YESMSG}; /* ---------------------------------------------------------------------- */ @@ -47,7 +48,8 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : idvar = NULL; - if (strcmp(arg[4],"bondmax") == 0) attribute = BONDMAX; + if (strcmp(arg[4],"tlimit") == 0) attribute = TLIMIT; + else if (strcmp(arg[4],"bondmax") == 0) attribute = BONDMAX; else if (strncmp(arg[4],"v_",2) == 0) { attribute = VARIABLE; int n = strlen(arg[4]); @@ -73,6 +75,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : // parse optional args eflag = SOFT; + msgflag = YESMSG; int iarg = 7; while (iarg < narg) { @@ -83,6 +86,12 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg+1],"continue") == 0) eflag = CONTINUE; else error->all(FLERR,"Illegal fix halt command"); iarg += 2; + } else if (strcmp(arg[iarg],"message") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix halt command"); + if (strcmp(arg[iarg+1],"no") == 0) msgflag = NOMSG; + else if (strcmp(arg[iarg+1],"yes") == 0) msgflag = YESMSG; + else error->all(FLERR,"Illegal fix halt command"); + iarg += 2; } else error->all(FLERR,"Illegal fix halt command"); } @@ -125,6 +134,11 @@ void FixHalt::init() if (input->variable->equalstyle(ivar) == 0) error->all(FLERR,"Fix halt variable is not equal-style variable"); } + + // settings used by TLIMIT + + nextstep = (update->ntimestep/nevery)*nevery + nevery; + tratio = 0.5; } /* ---------------------------------------------------------------------- */ @@ -135,8 +149,12 @@ void FixHalt::end_of_step() double attvalue; - if (attribute == BONDMAX) attvalue = bondmax(); - else { + if (attribute == TLIMIT) { + if (update->ntimestep != nextstep) return; + attvalue = tlimit(); + } else if (attribute == BONDMAX) { + attvalue = bondmax(); + } else { modify->clearstep_compute(); attvalue = input->variable->compute_equal(ivar); modify->addstep_compute(update->ntimestep + nevery); @@ -169,9 +187,10 @@ void FixHalt::end_of_step() sprintf(str,"Fix halt %s condition met on step %ld with value %g", id,update->ntimestep,attvalue); - if (eflag == HARD) error->all(FLERR,str); - else if (eflag == SOFT || eflag == CONTINUE) { - if (comm->me == 0) error->message(FLERR,str); + if (eflag == HARD) { + error->all(FLERR,str); + } else if (eflag == SOFT || eflag == CONTINUE) { + if (comm->me == 0 && msgflag == YESMSG) error->message(FLERR,str); timer->force_timeout(); } } @@ -218,3 +237,27 @@ double FixHalt::bondmax() return sqrt(maxall); } + +/* ---------------------------------------------------------------------- + compute synced elapsed time + reset nextstep = estimate of timestep when run will end + first project to 1/2 the run time, thereafter to end of run +------------------------------------------------------------------------- */ + +double FixHalt::tlimit() +{ + double cpu = timer->elapsed(Timer::TOTAL); + MPI_Bcast(&cpu,1,MPI_DOUBLE,0,world); + + if (cpu < value) { + bigint elapsed = update->ntimestep - update->firststep; + bigint final = update->firststep + + static_cast (tratio*value/cpu * elapsed); + nextstep = (final/nevery)*nevery + nevery; + tratio = 1.0; + } + + //printf("EVAL %ld %g %d\n",update->ntimestep,cpu,nevery); + + return cpu; +} diff --git a/src/fix_halt.h b/src/fix_halt.h index 156397a4b5..52d2f95d2f 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -35,11 +35,13 @@ class FixHalt : public Fix { void post_run(); private: - int attribute,operation,eflag,ivar; - double value; + int attribute,operation,eflag,msgflag,ivar; + bigint nextstep; + double value,tratio; char *idvar; double bondmax(); + double tlimit(); }; } diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 863c0f554c..34eec63987 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -132,7 +132,7 @@ One of the particles has radius 0.0. E: Fix langevin angmom requires extended particles -This fix option cannot be used with point paritlces. +This fix option cannot be used with point particles. E: Cannot zero Langevin force of 0 atoms diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp index e885392c41..21942d753f 100644 --- a/src/fix_shear_history.cpp +++ b/src/fix_shear_history.cpp @@ -38,7 +38,7 @@ FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) : npartner(NULL), partner(NULL), shearpartner(NULL), pair(NULL), ipage(NULL), dpage(NULL) { - if (narg != 4) error->all(FLERR,"Illegal fix SHEAR_HISTORY commmand"); + if (narg != 4) error->all(FLERR,"Illegal fix SHEAR_HISTORY command"); restart_peratom = 1; create_attribute = 1; diff --git a/src/improper.cpp b/src/improper.cpp index e20d0d2666..089fc43aad 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -74,7 +74,7 @@ void Improper::init() see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void Improper::ev_setup(int eflag, int vflag) +void Improper::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -92,25 +92,29 @@ void Improper::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); + } } // zero accumulators if (eflag_global) energy = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; for (i = 0; i < n; i++) { diff --git a/src/improper.h b/src/improper.h index b20bc732df..df3c966cdc 100644 --- a/src/improper.h +++ b/src/improper.h @@ -27,7 +27,7 @@ class Improper : protected Pointers { int *setflag; int writedata; // 1 if writes coeffs to data file double energy; // accumulated energies - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial // KOKKOS host/device flag and data masks @@ -56,7 +56,7 @@ class Improper : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; - void ev_setup(int, int); + void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, int, double, double *, double *, double *, double, double, double, double, double, double, double, double, double); diff --git a/src/kspace.cpp b/src/kspace.cpp index 48626346b1..c2113cdf76 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -206,7 +206,7 @@ void KSpace::pair_check() see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void KSpace::ev_setup(int eflag, int vflag) +void KSpace::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -227,25 +227,29 @@ void KSpace::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,maxeatom,"kspace:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,maxeatom,"kspace:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,maxvatom,6,"kspace:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,maxvatom,6,"kspace:vatom"); + } } // zero accumulators if (eflag_global) energy = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (tip4pflag) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (tip4pflag) n += atom->nghost; for (i = 0; i < n; i++) { diff --git a/src/kspace.h b/src/kspace.h index 95fb6ffaf2..ad29c21472 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -33,7 +33,7 @@ class KSpace : protected Pointers { public: double energy; // accumulated energies double energy_1,energy_6; - double virial[6]; // accumlated virial + double virial[6]; // accumulated virial double *eatom,**vatom; // accumulated per-atom energy/virial double e2group; // accumulated group-group energy double f2group[3]; // accumulated group-group force @@ -62,14 +62,14 @@ class KSpace : protected Pointers { int order,order_6,order_allocated; double accuracy; // accuracy of KSpace solver (force units) - double accuracy_absolute; // user-specifed accuracy in force units + double accuracy_absolute; // user-specified accuracy in force units double accuracy_relative; // user-specified dimensionless accuracy // accurary = acc_rel * two_charge_force double accuracy_real_6; // real space accuracy for // dispersion solver (force units) double accuracy_kspace_6; // reciprocal space accuracy for // dispersion solver (force units) - int auto_disp_flag; // use automatic paramter generation for pppm/disp + int auto_disp_flag; // use automatic parameter generation for pppm/disp double two_charge_force; // force in user units of two point // charges separated by 1 Angstrom @@ -197,7 +197,7 @@ class KSpace : protected Pointers { int kx_ewald,ky_ewald,kz_ewald; // kspace settings for Ewald sum void pair_check(); - void ev_setup(int, int); + void ev_setup(int, int, int alloc = 1); double estimate_table_accuracy(double, double); }; diff --git a/src/library.cpp b/src/library.cpp index 992b8ba100..5980b135eb 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -140,7 +140,7 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr) /* ---------------------------------------------------------------------- create an instance of LAMMPS and return pointer to it caller doesn't know MPI communicator, so use MPI_COMM_WORLD - intialize MPI if needed + initialize MPI if needed ------------------------------------------------------------------------- */ void lammps_open_no_mpi(int argc, char **argv, void **ptr) @@ -646,7 +646,7 @@ void *lammps_extract_variable(void *ptr, char *name, char *group) /* ---------------------------------------------------------------------- reset simulation box parameters see domain.h for definition of these arguments - assumes domain->set_intiial_box() has been invoked previously + assumes domain->set_initial_box() has been invoked previously ------------------------------------------------------------------------- */ void lammps_reset_box(void *ptr, double *boxlo, double *boxhi, @@ -761,6 +761,10 @@ void lammps_gather_atoms(void *ptr, char *name, int i,j,offset; void *vptr = lmp->atom->extract(name); + if(vptr == NULL) { + lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name"); + return; + } // copy = Natom length vector of per-atom values // use atom ID to insert each atom's values into copy @@ -857,6 +861,10 @@ void lammps_scatter_atoms(void *ptr, char *name, int i,j,m,offset; void *vptr = lmp->atom->extract(name); + if(vptr == NULL) { + lmp->error->warning(FLERR,"lammps_scatter_atoms: unknown property name"); + return; + } // copy = Natom length vector of per-atom values // use atom ID to insert each atom's values into copy diff --git a/src/lmptype.h b/src/lmptype.h index a8c09bd2ad..253f9a7470 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -13,7 +13,7 @@ // define integer data types used by LAMMPS and associated size limits -// smallint = variables for on-procesor system (nlocal, nmax, etc) +// smallint = variables for on-processor system (nlocal, nmax, etc) // imageint = variables for atom image flags (image) // tagint = variables for atom IDs and molecule IDs (tag,molecule) // bigint = variables for total system (natoms, ntimestep, etc) diff --git a/src/molecule.cpp b/src/molecule.cpp index 2253e86af0..76b28e3d47 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1395,7 +1395,7 @@ void Molecule::check_attributes(int flag) if (atom->maxspecial < onemol->maxspecial) mismatch = 1; if (mismatch) - error->all(FLERR,"Molecule toplogy/atom exceeds system topology/atom"); + error->all(FLERR,"Molecule topology/atom exceeds system topology/atom"); } // warn if molecule topology defined but no special settings diff --git a/src/molecule.h b/src/molecule.h index 0bbe684636..bfc9da1857 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -406,7 +406,7 @@ The number of bond, angle, etc types in the molecule exceeds the system setting. See the create_box command for how to specify these values. -E: Molecule toplogy/atom exceeds system topology/atom +E: Molecule topology/atom exceeds system topology/atom The number of bonds, angles, etc per-atom in the molecule exceeds the system setting. See the create_box command for how to specify these diff --git a/src/neighbor.cpp b/src/neighbor.cpp index e0b84cc410..8da6c1b9d2 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -166,7 +166,7 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL) ex1_group = ex2_group = ex1_bit = ex2_bit = NULL; nex_mol = maxex_mol = 0; - ex_mol_group = ex_mol_bit = NULL; + ex_mol_group = ex_mol_bit = ex_mol_intra = NULL; // Kokkos setting @@ -234,6 +234,7 @@ Neighbor::~Neighbor() memory->destroy(ex_mol_group); delete [] ex_mol_bit; + memory->destroy(ex_mol_intra); } /* ---------------------------------------------------------------------- */ @@ -918,7 +919,7 @@ void Neighbor::morph_other() requests[i-1]->historylist = i; } - // if respaouter, point all asociated rRESPA lists at each other + // if respaouter, point all associated rRESPA lists at each other if (irq->respaouter) { if (requests[i-1]->respainner) { @@ -1128,6 +1129,11 @@ void Neighbor::morph_halffull() if (!irq->half) continue; + // Kokkos doesn't yet support half from full + + if (irq->kokkos_host) continue; + if (irq->kokkos_device) continue; + // these lists are created other ways, no need for halffull // do want to process skip lists @@ -1153,8 +1159,6 @@ void Neighbor::morph_halffull() // this includes custom cutoff set by requestor // no need to check respaouter b/c it stores same pairs // no need to check dnum b/c only set for history - // NOTE: need check for 2 Kokkos flags? - // Kokkos doesn't yet support half from full? if (irq->ghost != jrq->ghost) continue; if (irq->size != jrq->size) continue; @@ -2323,7 +2327,8 @@ void Neighbor::modify_params(int narg, char **arg) nex_group++; iarg += 4; - } else if (strcmp(arg[iarg+1],"molecule") == 0) { + } else if (strcmp(arg[iarg+1],"molecule/inter") == 0 || + strcmp(arg[iarg+1],"molecule/intra") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command"); if (atom->molecule_flag == 0) error->all(FLERR,"Neigh_modify exclude molecule " @@ -2331,13 +2336,21 @@ void Neighbor::modify_params(int narg, char **arg) if (nex_mol == maxex_mol) { maxex_mol += EXDELTA; memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group"); + if (lmp->kokkos) + grow_ex_mol_intra_kokkos(); + else + memory->grow(ex_mol_intra,maxex_mol,"neigh:ex_mol_intra"); } ex_mol_group[nex_mol] = group->find(arg[iarg+2]); if (ex_mol_group[nex_mol] == -1) error->all(FLERR,"Invalid group ID in neigh_modify command"); + if (strcmp(arg[iarg+1],"molecule/intra") == 0) + ex_mol_intra[nex_mol] = 1; + else + ex_mol_intra[nex_mol] = 0; nex_mol++; iarg += 3; - + } else if (strcmp(arg[iarg+1],"none") == 0) { nex_type = nex_group = nex_mol = 0; iarg += 2; diff --git a/src/neighbor.h b/src/neighbor.h index 8e2fad1f1b..16a80b5991 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -71,6 +71,8 @@ class Neighbor : protected Pointers { int nex_mol; // # of entries in molecule exclusion list int *ex_mol_group; // molecule group #'s to exclude int *ex_mol_bit; // molecule group bits to exclude + int *ex_mol_intra; // 0 = exclude if in 2 molecules (inter) + // 1 = exclude if in same molecule (intra) // special info, used by NeighPair @@ -229,6 +231,7 @@ class Neighbor : protected Pointers { virtual void init_ex_type_kokkos(int) {} virtual void init_ex_bit_kokkos() {} virtual void init_ex_mol_bit_kokkos() {} + virtual void grow_ex_mol_intra_kokkos() {} }; namespace NeighConst { diff --git a/src/npair.cpp b/src/npair.cpp index 9fe326cbd1..6c3f8ac05e 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -86,6 +86,7 @@ void NPair::copy_neighbor_info() nex_mol = neighbor->nex_mol; ex_mol_group = neighbor->ex_mol_group; ex_mol_bit = neighbor->ex_mol_bit; + ex_mol_intra = neighbor->ex_mol_intra; // special info @@ -180,8 +181,17 @@ int NPair::exclusion(int i, int j, int itype, int jtype, if (nex_mol) { for (m = 0; m < nex_mol; m++) - if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] && - molecule[i] == molecule[j]) return 1; + + // intra-chain: exclude i-j pair if in same molecule + // inter-chain: exclude i-j pair if in different molecules + + if (ex_mol_intra[m]) { + if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] && + molecule[i] == molecule[j]) return 1; + } else { + if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] && + molecule[i] != molecule[j]) return 1; + } } return 0; diff --git a/src/npair.h b/src/npair.h index cdb8b3061d..8f2bcb13bc 100644 --- a/src/npair.h +++ b/src/npair.h @@ -61,8 +61,10 @@ class NPair : protected Pointers { int *ex1_bit,*ex2_bit; // pairs of group bits to exclude int nex_mol; // # of entries in molecule exclusion list - int *ex_mol_group; // molecule group #'s to exclude int *ex_mol_bit; // molecule group bits to exclude + int *ex_mol_group; // molecule group #'s to exclude + int *ex_mol_intra; // 0 = exclude if in 2 molecules (inter) + // 1 = exclude if in same molecule (intra) // special data from Neighbor class diff --git a/src/output.h b/src/output.h index cc282cbedd..de5eaaa70b 100644 --- a/src/output.h +++ b/src/output.h @@ -172,7 +172,7 @@ W: New thermo_style command, previous thermo_modify settings will be lost If a thermo_style command is used after a thermo_modify command, the settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify commmand acts on +default values. This is because the thermo_modify command acts on the currently defined thermo style, and a thermo_style command creates a new style. diff --git a/src/pair.cpp b/src/pair.cpp index 5d73a592e8..d90ed8bb43 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -749,7 +749,7 @@ void Pair::del_tally_callback(Compute *ptr) see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) ------------------------------------------------------------------------- */ -void Pair::ev_setup(int eflag, int vflag) +void Pair::ev_setup(int eflag, int vflag, int alloc) { int i,n; @@ -767,13 +767,17 @@ void Pair::ev_setup(int eflag, int vflag) if (eflag_atom && atom->nmax > maxeatom) { maxeatom = atom->nmax; - memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); + if (alloc) { + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); + } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; - memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); + if (alloc) { + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); + } } // zero accumulators @@ -782,12 +786,12 @@ void Pair::ev_setup(int eflag, int vflag) if (eflag_global) eng_vdwl = eng_coul = 0.0; if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; - if (eflag_atom) { + if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton) n += atom->nghost; for (i = 0; i < n; i++) eatom[i] = 0.0; } - if (vflag_atom) { + if (vflag_atom && alloc) { n = atom->nlocal; if (force->newton) n += atom->nghost; for (i = 0; i < n; i++) { @@ -1534,7 +1538,7 @@ void Pair::virial_fdotr_compute() void Pair::write_file(int narg, char **arg) { - if (narg < 8) error->all(FLERR,"Illegal pair_write command"); + if (narg != 8 && narg != 10) error->all(FLERR,"Illegal pair_write command"); if (single_enable == 0) error->all(FLERR,"Pair style does not support pair_write"); diff --git a/src/pair.h b/src/pair.h index 16746a29a8..3f66c6095a 100644 --- a/src/pair.h +++ b/src/pair.h @@ -221,7 +221,7 @@ class Pair : protected Pointers { int copymode; // if set, do not deallocate during destruction // required when classes are used as functors by Kokkos - virtual void ev_setup(int, int); + virtual void ev_setup(int, int, int alloc = 1); void ev_unset(); void ev_tally_full(int, double, double, double, double, double, double); void ev_tally_xyz_full(int, double, double, diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index c7b77c3270..c8f6afdacc 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -168,7 +168,7 @@ void PairGauss::settings(int narg, char **arg) cut_global = force->numeric(FLERR,arg[0]); - // reset cutoffs that have been explicity set + // reset cutoffs that have been explicitly set if (allocated) { int i,j; diff --git a/src/procmap.cpp b/src/procmap.cpp index 088939b218..f54ac1915c 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -216,7 +216,7 @@ void ProcMap::numa_grid(int nprocs, int *user_procgrid, int *procgrid, best_factors(numapossible,numafactors,numagrid,1,1,1); - // user_nodegrid = implied user contraints on nodes + // user_nodegrid = implied user constraints on nodes int user_nodegrid[3]; user_nodegrid[0] = user_procgrid[0] / numagrid[0]; diff --git a/src/rcb.cpp b/src/rcb.cpp index 7223e4616a..1aca015daf 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -42,7 +42,7 @@ RCB::RCB(LAMMPS *lmp) : Pointers(lmp) dots = NULL; nlist = maxlist = 0; - dotlist = dotmark = NULL; + dotlist = dotmark = dotmark_select = NULL; maxbuf = 0; buf = NULL; @@ -73,6 +73,7 @@ RCB::~RCB() memory->sfree(dots); memory->destroy(dotlist); memory->destroy(dotmark); + memory->destroy(dotmark_select); memory->sfree(buf); memory->destroy(recvproc); @@ -91,6 +92,9 @@ RCB::~RCB() /* ---------------------------------------------------------------------- perform RCB balancing of N particles at coords X in bounding box LO/HI + NEW version: each RCB cut is tested in all dimensions + dimeension that produces 2 boxes with largest min size is selected + this is to prevent very narrow boxes from being produced if wt = NULL, ignore per-particle weights if wt defined, per-particle weights > 0.0 dimension = 2 or 3 @@ -103,6 +107,523 @@ RCB::~RCB() void RCB::compute(int dimension, int n, double **x, double *wt, double *bboxlo, double *bboxhi) +{ + int i,j,k; + int keep,outgoing,incoming,incoming2; + int dim,markactive; + int indexlo,indexhi; + int first_iteration,breakflag; + double wttot,wtlo,wthi,wtsum,wtok,wtupto,wtmax; + double targetlo,targethi; + double valuemin,valuemax,valuehalf,valuehalf_select,smaller; + double tolerance; + MPI_Comm comm,comm_half; + MPI_Request request,request2; + Median med,medme; + + // create list of my Dots + + ndot = nkeep = noriginal = n; + + if (ndot > maxdot) { + maxdot = ndot; + memory->sfree(dots); + dots = (Dot *) memory->smalloc(ndot*sizeof(Dot),"RCB:dots"); + } + + for (i = 0; i < ndot; i++) { + dots[i].x[0] = x[i][0]; + dots[i].x[1] = x[i][1]; + dots[i].x[2] = x[i][2]; + dots[i].proc = me; + dots[i].index = i; + } + + if (wt) + for (i = 0; i < ndot; i++) dots[i].wt = wt[i]; + else + for (i = 0; i < ndot; i++) dots[i].wt = 1.0; + + // initial bounding box = simulation box + // includes periodic or shrink-wrapped boundaries + + lo = bbox.lo; + hi = bbox.hi; + + lo[0] = bboxlo[0]; + lo[1] = bboxlo[1]; + lo[2] = bboxlo[2]; + hi[0] = bboxhi[0]; + hi[1] = bboxhi[1]; + hi[2] = bboxhi[2]; + + cut = 0.0; + cutdim = -1; + + // initialize counters + + counters[0] = 0; + counters[1] = 0; + counters[2] = 0; + counters[3] = ndot; + counters[4] = maxdot; + counters[5] = 0; + counters[6] = 0; + + // create communicator for use in recursion + + MPI_Comm_dup(world,&comm); + + // recurse until partition is a single proc = me + // proclower,procupper = lower,upper procs in partition + // procmid = 1st proc in upper half of partition + + int procpartner,procpartner2; + + int procmid; + int proclower = 0; + int procupper = nprocs - 1; + + while (proclower != procupper) { + + // if odd # of procs, lower partition gets extra one + + procmid = proclower + (procupper - proclower) / 2 + 1; + + // determine communication partner(s) + // readnumber = # of proc partners to read from + + if (me < procmid) + procpartner = me + (procmid - proclower); + else + procpartner = me - (procmid - proclower); + + int readnumber = 1; + if (procpartner > procupper) { + readnumber = 0; + procpartner--; + } + if (me == procupper && procpartner != procmid - 1) { + readnumber = 2; + procpartner2 = procpartner + 1; + } + + // wttot = summed weight of entire partition + // search tolerance = largest single weight (plus epsilon) + // targetlo = desired weight in lower half of partition + // targethi = desired weight in upper half of partition + + wtmax = wtsum = 0.0; + + if (wt) { + for (i = 0; i < ndot; i++) { + wtsum += dots[i].wt; + if (dots[i].wt > wtmax) wtmax = dots[i].wt; + } + } else { + for (i = 0; i < ndot; i++) wtsum += dots[i].wt; + wtmax = 1.0; + } + + MPI_Allreduce(&wtsum,&wttot,1,MPI_DOUBLE,MPI_SUM,comm); + if (wt) MPI_Allreduce(&wtmax,&tolerance,1,MPI_DOUBLE,MPI_MAX,comm); + else tolerance = 1.0; + + tolerance *= 1.0 + TINY; + targetlo = wttot * (procmid - proclower) / (procupper + 1 - proclower); + targethi = wttot - targetlo; + + // attempt a cut in each dimension + // each cut produces 2 boxes, each with a reduced box length in that dim + // smaller = the smaller of the 2 reduced box lengths in that dimension + // choose to cut in dimension which produces largest smaller value + // this should induce final proc sub-boxes to be as cube-ish as possible + // dim_select = selected cut dimension + // valuehalf_select = valuehalf in that dimension + // dotmark_select = dot markings in that dimension + + int dim_select = -1; + double largest = 0.0; + + for (dim = 0; dim < dimension; dim++) { + + // create active list and mark array for dots + // initialize active list to all dots + + if (ndot > maxlist) { + memory->destroy(dotlist); + memory->destroy(dotmark); + memory->destroy(dotmark_select); + maxlist = maxdot; + memory->create(dotlist,maxlist,"RCB:dotlist"); + memory->create(dotmark,maxlist,"RCB:dotmark"); + memory->create(dotmark_select,maxlist,"RCB:dotmark_select"); + } + + nlist = ndot; + for (i = 0; i < nlist; i++) dotlist[i] = i; + + // median iteration + // zoom in on bisector until correct # of dots in each half of partition + // as each iteration of median-loop begins, require: + // all non-active dots are marked with 0/1 in dotmark + // valuemin <= every active dot <= valuemax + // wtlo, wthi = total wt of non-active dots + // when leave median-loop, require only: + // valuehalf = correct cut position + // all dots <= valuehalf are marked with 0 in dotmark + // all dots >= valuehalf are marked with 1 in dotmark + // markactive = which side of cut is active = 0/1 + // indexlo,indexhi = indices of dot closest to median + + wtlo = wthi = 0.0; + valuemin = lo[dim]; + valuemax = hi[dim]; + first_iteration = 1; + indexlo = indexhi = 0; + + while (1) { + + // choose bisector value + // use old value on 1st iteration if old cut dimension is the same + // on 2nd option: could push valuehalf towards geometric center + // with "1.0-factor" to force overshoot + + if (first_iteration && reuse && dim == tree[procmid].dim) { + counters[5]++; + valuehalf = tree[procmid].cut; + if (valuehalf < valuemin || valuehalf > valuemax) + valuehalf = 0.5 * (valuemin + valuemax); + } else if (wt) + valuehalf = valuemin + (targetlo - wtlo) / + (wttot - wtlo - wthi) * (valuemax - valuemin); + else + valuehalf = 0.5 * (valuemin + valuemax); + + first_iteration = 0; + + // initialize local median data structure + + medme.totallo = medme.totalhi = 0.0; + medme.valuelo = -MYHUGE; + medme.valuehi = MYHUGE; + medme.wtlo = medme.wthi = 0.0; + medme.countlo = medme.counthi = 0; + medme.proclo = medme.prochi = me; + + // mark all active dots on one side or other of bisector + // also set all fields in median data struct + // save indices of closest dots on either side + + for (j = 0; j < nlist; j++) { + i = dotlist[j]; + if (dots[i].x[dim] <= valuehalf) { // in lower part + medme.totallo += dots[i].wt; + dotmark[i] = 0; + if (dots[i].x[dim] > medme.valuelo) { // my closest dot + medme.valuelo = dots[i].x[dim]; + medme.wtlo = dots[i].wt; + medme.countlo = 1; + indexlo = i; + } else if (dots[i].x[dim] == medme.valuelo) { // tied for closest + medme.wtlo += dots[i].wt; + medme.countlo++; + } + } + else { // in upper part + medme.totalhi += dots[i].wt; + dotmark[i] = 1; + if (dots[i].x[dim] < medme.valuehi) { // my closest dot + medme.valuehi = dots[i].x[dim]; + medme.wthi = dots[i].wt; + medme.counthi = 1; + indexhi = i; + } else if (dots[i].x[dim] == medme.valuehi) { // tied for closest + medme.wthi += dots[i].wt; + medme.counthi++; + } + } + } + + // combine median data struct across current subset of procs + + counters[0]++; + MPI_Allreduce(&medme,&med,1,med_type,med_op,comm); + + // test median guess for convergence + // move additional dots that are next to cut across it + + if (wtlo + med.totallo < targetlo) { // lower half TOO SMALL + + wtlo += med.totallo; + valuehalf = med.valuehi; + + if (med.counthi == 1) { // only one dot to move + if (wtlo + med.wthi < targetlo) { // move it, keep iterating + if (me == med.prochi) dotmark[indexhi] = 0; + } + else { // only move if beneficial + if (wtlo + med.wthi - targetlo < targetlo - wtlo) + if (me == med.prochi) dotmark[indexhi] = 0; + break; // all done + } + } + else { // multiple dots to move + breakflag = 0; + wtok = 0.0; + if (medme.valuehi == med.valuehi) wtok = medme.wthi; + if (wtlo + med.wthi >= targetlo) { // all done + MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm); + wtmax = targetlo - wtlo; + if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax); + breakflag = 1; + } // wtok = most I can move + for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) { + i = dotlist[j]; + if (dots[i].x[dim] == med.valuehi) { // only move if better + if (wtsum + dots[i].wt - wtok < wtok - wtsum) + dotmark[i] = 0; + wtsum += dots[i].wt; + } + } + if (breakflag) break; // done if moved enough + } + + wtlo += med.wthi; + if (targetlo-wtlo <= tolerance) break; // close enough + + valuemin = med.valuehi; // iterate again + markactive = 1; + } + + else if (wthi + med.totalhi < targethi) { // upper half TOO SMALL + + wthi += med.totalhi; + valuehalf = med.valuelo; + + if (med.countlo == 1) { // only one dot to move + if (wthi + med.wtlo < targethi) { // move it, keep iterating + if (me == med.proclo) dotmark[indexlo] = 1; + } + else { // only move if beneficial + if (wthi + med.wtlo - targethi < targethi - wthi) + if (me == med.proclo) dotmark[indexlo] = 1; + break; // all done + } + } + else { // multiple dots to move + breakflag = 0; + wtok = 0.0; + if (medme.valuelo == med.valuelo) wtok = medme.wtlo; + if (wthi + med.wtlo >= targethi) { // all done + MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm); + wtmax = targethi - wthi; + if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax); + breakflag = 1; + } // wtok = most I can move + for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) { + i = dotlist[j]; + if (dots[i].x[dim] == med.valuelo) { // only move if better + if (wtsum + dots[i].wt - wtok < wtok - wtsum) + dotmark[i] = 1; + wtsum += dots[i].wt; + } + } + if (breakflag) break; // done if moved enough + } + + wthi += med.wtlo; + if (targethi-wthi <= tolerance) break; // close enough + + valuemax = med.valuelo; // iterate again + markactive = 0; + } + + else // Goldilocks result: both partitions just right + break; + + // shrink the active list + + k = 0; + for (j = 0; j < nlist; j++) { + i = dotlist[j]; + if (dotmark[i] == markactive) dotlist[k++] = i; + } + nlist = k; + } + + // cut produces 2 sub-boxes with reduced size in dim + // compare smaller of the 2 sizes to previous dims + // keep dim that has the largest smaller + + smaller = MIN(valuehalf-lo[dim],hi[dim]-valuehalf); + if (smaller > largest) { + largest = smaller; + dim_select = dim; + valuehalf_select = valuehalf; + memcpy(dotmark_select,dotmark,ndot*sizeof(int)); + } + } + + // copy results for best dim cut into dim,valuehalf,dotmark + + dim = dim_select; + valuehalf = valuehalf_select; + memcpy(dotmark,dotmark_select,ndot*sizeof(int)); + + // found median + // store cut info only if I am procmid + + if (me == procmid) { + cut = valuehalf; + cutdim = dim; + } + + // use cut to shrink my RCB bounding box + + if (me < procmid) hi[dim] = valuehalf; + else lo[dim] = valuehalf; + + // outgoing = number of dots to ship to partner + // nkeep = number of dots that have never migrated + + markactive = (me < procpartner); + for (i = 0, keep = 0, outgoing = 0; i < ndot; i++) + if (dotmark[i] == markactive) outgoing++; + else if (i < nkeep) keep++; + nkeep = keep; + + // alert partner how many dots I'll send, read how many I'll recv + + MPI_Send(&outgoing,1,MPI_INT,procpartner,0,world); + incoming = 0; + if (readnumber) { + MPI_Recv(&incoming,1,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE); + if (readnumber == 2) { + MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE); + incoming += incoming2; + } + } + + // check if need to alloc more space + + int ndotnew = ndot - outgoing + incoming; + if (ndotnew > maxdot) { + while (maxdot < ndotnew) maxdot += DELTA; + dots = (Dot *) memory->srealloc(dots,maxdot*sizeof(Dot),"RCB::dots"); + counters[6]++; + } + + counters[1] += outgoing; + counters[2] += incoming; + if (ndotnew > counters[3]) counters[3] = ndotnew; + if (maxdot > counters[4]) counters[4] = maxdot; + + // malloc comm send buffer + + if (outgoing > maxbuf) { + memory->sfree(buf); + maxbuf = outgoing; + buf = (Dot *) memory->smalloc(maxbuf*sizeof(Dot),"RCB:buf"); + } + + // fill buffer with dots that are marked for sending + // pack down the unmarked ones + + keep = outgoing = 0; + for (i = 0; i < ndot; i++) { + if (dotmark[i] == markactive) + memcpy(&buf[outgoing++],&dots[i],sizeof(Dot)); + else + memcpy(&dots[keep++],&dots[i],sizeof(Dot)); + } + + // post receives for dots + + if (readnumber > 0) { + MPI_Irecv(&dots[keep],incoming*sizeof(Dot),MPI_CHAR, + procpartner,1,world,&request); + if (readnumber == 2) { + keep += incoming - incoming2; + MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR, + procpartner2,1,world,&request2); + } + } + + // handshake before sending dots to insure recvs have been posted + + if (readnumber > 0) { + MPI_Send(NULL,0,MPI_INT,procpartner,0,world); + if (readnumber == 2) MPI_Send(NULL,0,MPI_INT,procpartner2,0,world); + } + MPI_Recv(NULL,0,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE); + + // send dots to partner + + MPI_Rsend(buf,outgoing*sizeof(Dot),MPI_CHAR,procpartner,1,world); + + // wait until all dots are received + + if (readnumber > 0) { + MPI_Wait(&request,MPI_STATUS_IGNORE); + if (readnumber == 2) MPI_Wait(&request2,MPI_STATUS_IGNORE); + } + + ndot = ndotnew; + + // cut partition in half, create new communicators of 1/2 size + + int split; + if (me < procmid) { + procupper = procmid - 1; + split = 0; + } else { + proclower = procmid; + split = 1; + } + + MPI_Comm_split(comm,split,me,&comm_half); + MPI_Comm_free(&comm); + comm = comm_half; + } + + // clean up + + MPI_Comm_free(&comm); + + // set public variables with results of rebalance + + nfinal = ndot; + + if (nfinal > maxrecv) { + memory->destroy(recvproc); + memory->destroy(recvindex); + maxrecv = nfinal; + memory->create(recvproc,maxrecv,"RCB:recvproc"); + memory->create(recvindex,maxrecv,"RCB:recvindex"); + } + + for (i = 0; i < nfinal; i++) { + recvproc[i] = dots[i].proc; + recvindex[i] = dots[i].index; + } +} + +/* ---------------------------------------------------------------------- + perform RCB balancing of N particles at coords X in bounding box LO/HI + OLD version: each RCB cut is made in longest dimension of sub-box + if wt = NULL, ignore per-particle weights + if wt defined, per-particle weights > 0.0 + dimension = 2 or 3 + as documented in rcb.h: + sets noriginal,nfinal,nkeep,recvproc,recvindex,lo,hi + all proc particles will be inside or on surface of 3-d box + defined by final lo/hi + // NOTE: worry about re-use of data structs for fix balance? +------------------------------------------------------------------------- */ + +void RCB::compute_old(int dimension, int n, double **x, double *wt, + double *bboxlo, double *bboxhi) { int i,j,k; int keep,outgoing,incoming,incoming2; diff --git a/src/rcb.h b/src/rcb.h index 7a82d42f93..90b82f5952 100644 --- a/src/rcb.h +++ b/src/rcb.h @@ -42,6 +42,7 @@ class RCB : protected Pointers { RCB(class LAMMPS *); ~RCB(); void compute(int, int, double **, double *, double *, double *); + void compute_old(int, int, double **, double *, double *, double *); void invert(int sortflag = 0); bigint memory_usage(); @@ -99,6 +100,7 @@ class RCB : protected Pointers { int maxlist; int *dotlist; int *dotmark; + int *dotmark_select; int maxbuf; Dot *buf; diff --git a/src/region_block.cpp b/src/region_block.cpp index f1787d2ca2..769edb1489 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -401,7 +401,7 @@ double RegBlock::find_closest_point(int i, double *x, zc = p[2]; } - point_on_line_segment(corners[i][3],corners[i][4],x,p); + point_on_line_segment(corners[i][3],corners[i][0],x,p); d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) + (p[2]-x[2])*(p[2]-x[2]); if (d2 < d2min) { diff --git a/src/region_cylinder.h b/src/region_cylinder.h index bc5255b343..e065c7d3f1 100644 --- a/src/region_cylinder.h +++ b/src/region_cylinder.h @@ -78,6 +78,6 @@ Self-explanatory. E: Variable for region cylinder is invalid style -Only equal-style varaibles are allowed. +Only equal-style variables are allowed. */ diff --git a/src/region_sphere.h b/src/region_sphere.h index 9e1fb4e739..c003a91651 100644 --- a/src/region_sphere.h +++ b/src/region_sphere.h @@ -69,6 +69,6 @@ Self-explanatory. E: Variable for region sphere is invalid style -Only equal-style varaibles are allowed. +Only equal-style variables are allowed. */ diff --git a/src/rerun.cpp b/src/rerun.cpp index 493e5dca10..6081a6fc47 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -124,7 +124,7 @@ void Rerun::command(int narg, char **arg) if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]); else rd->setup_reader(0,NULL); - // perform the psuedo run + // perform the pseudo run // invoke lmp->init() only once // read all relevant snapshots // use setup_minimal() since atoms are already owned by correct procs diff --git a/src/run.h b/src/run.h index 5f6accbfac..727b23f1c4 100644 --- a/src/run.h +++ b/src/run.h @@ -71,6 +71,6 @@ Self-explanatory. E: Too many timesteps -The cummulative timesteps must fit in a 64-bit integer. +The cumulative timesteps must fit in a 64-bit integer. */ diff --git a/src/thermo.cpp b/src/thermo.cpp index 3d3a28cde8..dbbeff4998 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -55,7 +55,8 @@ using namespace MathConst; // customize a new keyword by adding to this list: -// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, part, timeremain +// step, elapsed, elaplong, dt, time, cpu, tpcpu, spcpu, cpuremain, +// part, timeremain // atoms, temp, press, pe, ke, etotal, enthalpy // evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail // vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz, @@ -394,6 +395,11 @@ void Thermo::compute(int flag) if (flushflag) fflush(logfile); } } + + // set to 1, so that subsequent invocations of CPU time will be non-zero + // e.g. via variables in print command + + firststep = 1; } /* ---------------------------------------------------------------------- @@ -1054,7 +1060,7 @@ int Thermo::add_variable(const char *id) compute a single thermodynamic value, word is any keyword in custom list called when a variable is evaluated by Variable class return value as double in answer - return 0 if str is recoginzed keyword, 1 if unrecognized + return 0 if str is recognized keyword, 1 if unrecognized customize a new keyword by adding to if statement ------------------------------------------------------------------------- */ diff --git a/src/thermo.h b/src/thermo.h index ddbe3cc95b..d87e8fce3d 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -95,7 +95,7 @@ class Thermo : protected Pointers { char **id_fix; // their IDs class Fix **fixes; // list of ptrs to the Fix objects - int nvariable; // # of variables evaulated by thermo + int nvariable; // # of variables evaluated by thermo char **id_variable; // list of variable names int *variables; // list of Variable indices @@ -236,7 +236,7 @@ E: Lost atoms: original %ld current %ld Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. W: Lost atoms: original %ld current %ld @@ -244,7 +244,7 @@ W: Lost atoms: original %ld current %ld Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. E: Thermo style does not use temp diff --git a/src/variable.cpp b/src/variable.cpp index 67c8951974..3eea50a463 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1004,7 +1004,7 @@ void Variable::compute_atom(int ivar, int igroup, return length of vector and result pointer to vector values if length == 0 or -1 (mismatch), generate an error if variable already computed on this timestep, just return - else evaulate the formula and its length, store results in VecVar entry + else evaluate the formula and its length, store results in VecVar entry ------------------------------------------------------------------------- */ int Variable::compute_vector(int ivar, double **result) @@ -2747,7 +2747,7 @@ double Variable::collapse_tree(Tree *tree) /* ---------------------------------------------------------------------- evaluate an atom-style or vector-style variable parse tree index I = atom I or vector index I - tree was created by one-time parsing of formula string via evaulate() + tree was created by one-time parsing of formula string via evaluate() customize by adding a function: sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(), atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(), diff --git a/src/variable.h b/src/variable.h index 042ce5b3fe..76607e96b4 100644 --- a/src/variable.h +++ b/src/variable.h @@ -210,7 +210,7 @@ This is to insure they stay in sync. E: Variable has circular dependency A circular dependency is when variable "a" in used by variable "b" and -variable "b" is also used by varaible "a". Circular dependencies with +variable "b" is also used by variable "a". Circular dependencies with longer chains of dependence are also not allowed. E: Python variable does not match Python function @@ -355,7 +355,7 @@ Self-explanatory. E: Non digit character between brackets in variable -Self-explantory. +Self-explanatory. E: Mismatched brackets in variable diff --git a/src/version.h b/src/version.h index 9f6021787c..e0aa18371c 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "21 Feb 2017" +#define LAMMPS_VERSION "10 Mar 2017" diff --git a/tools/eff/cfg2lammps.py b/tools/eff/cfg2lammps.py index 1bf364aa93..49830dbb09 100644 --- a/tools/eff/cfg2lammps.py +++ b/tools/eff/cfg2lammps.py @@ -217,7 +217,7 @@ def generate_lammps_input(infile): if line.find("e_field_packet_duration")>=0: continue if line.find("set_limit")>=0: - continue # need to add this contraint + continue # need to add this constraint if line.find("set_limit_stiffness")>=0: continue if line.find("output_position")>=0: diff --git a/tools/i-pi/drivers/driver.f90 b/tools/i-pi/drivers/driver.f90 index 9ff992dab3..646f1e9add 100644 --- a/tools/i-pi/drivers/driver.f90 +++ b/tools/i-pi/drivers/driver.f90 @@ -67,7 +67,7 @@ INTEGER i ! parse the command line parameters - ! intialize defaults + ! initialize defaults ccmd = 0 inet = 1 host = "localhost"//achar(0) diff --git a/tools/i-pi/ipi/engine/atoms.py b/tools/i-pi/ipi/engine/atoms.py index 02ffcd7551..fd52ccf96b 100644 --- a/tools/i-pi/ipi/engine/atoms.py +++ b/tools/i-pi/ipi/engine/atoms.py @@ -120,7 +120,7 @@ class Atoms(dobject): Each replica and the centroid coordinate are all held as Atoms objects, and so slices of the global position and momentum arrays must be used in - the initialisation so that they always agree with each other. + the initialization so that they always agree with each other. Args: natoms: An integer giving the number of atoms. diff --git a/tools/i-pi/ipi/engine/initializer.py b/tools/i-pi/ipi/engine/initializer.py index 466677938a..de629c7f96 100644 --- a/tools/i-pi/ipi/engine/initializer.py +++ b/tools/i-pi/ipi/engine/initializer.py @@ -70,7 +70,7 @@ class InitBase(dobject): Args: value: A string which specifies what value to initialize the simulation property to. - mode: A string specifiying what style of initialization should be + mode: A string specifying what style of initialization should be used to read the data. units: A string giving which unit the value is in. """ @@ -97,7 +97,7 @@ class InitIndexed(InitBase): Args: value: A string which specifies what value to initialize the simulation property to. - mode: A string specifiying what style of initialization should be + mode: A string specifying what style of initialization should be used to read the data. units: A string giving which unit the value is in. index: Which atom to initialize the value of. diff --git a/tools/i-pi/ipi/engine/properties.py b/tools/i-pi/ipi/engine/properties.py index 1ea07bda87..a76aca1faf 100644 --- a/tools/i-pi/ipi/engine/properties.py +++ b/tools/i-pi/ipi/engine/properties.py @@ -460,7 +460,7 @@ class Properties(dobject): key: A string contained in property_dict. Returns: - The property labelled by the keyword key, along with its unit + The property labeled by the keyword key, along with its unit keyword, and the argument lists for the function used to calculate the property specified by the keyword key. """ @@ -1216,7 +1216,7 @@ class Trajectories(dobject): key: A string contained in trajectory_dict. Returns: - The trajectory labelled by the keyword key, along with its unit + The trajectory labeled by the keyword key, along with its unit keyword, and the argument lists for the function used to calculate the trajectory specified by the keyword key. """ diff --git a/tools/i-pi/ipi/engine/simulation.py b/tools/i-pi/ipi/engine/simulation.py index 42645939ee..3c16a99621 100644 --- a/tools/i-pi/ipi/engine/simulation.py +++ b/tools/i-pi/ipi/engine/simulation.py @@ -49,7 +49,7 @@ class Simulation(dobject): """Main simulation object. Contains all the references and the main dynamics loop. Also handles the - initialisation and output. + initialization and output. Attributes: beads: A beads object giving the atom positions. diff --git a/tools/i-pi/ipi/engine/thermostats.py b/tools/i-pi/ipi/engine/thermostats.py index 5375bb917e..1fb048ec27 100644 --- a/tools/i-pi/ipi/engine/thermostats.py +++ b/tools/i-pi/ipi/engine/thermostats.py @@ -691,7 +691,7 @@ class ThermoNMGLE(Thermostat): """ def get_C(self): - """Calculates C from temp (if C is not set explicitely).""" + """Calculates C from temp (if C is not set explicitly).""" rv = np.ndarray((self.nb, self.ns+1, self.ns+1), float) for b in range(0,self.nb): diff --git a/tools/i-pi/ipi/interfaces/sockets.py b/tools/i-pi/ipi/interfaces/sockets.py index 998a87d113..2783d31e06 100644 --- a/tools/i-pi/ipi/interfaces/sockets.py +++ b/tools/i-pi/ipi/interfaces/sockets.py @@ -243,7 +243,7 @@ class DriverSocket(socket.socket): return np.fromstring(self._buf[0:blen], dest.dtype).reshape(dest.shape) def initialize(self, rid, pars): - """Sends the initialisation string to the driver. + """Sends the initialization string to the driver. Args: rid: The index of the request, i.e. the replica that @@ -456,13 +456,13 @@ class InterfaceSocket(object): """Adds a request. Note that the pars dictionary need to be sent as a string of a - standard format so that the initialisation of the driver can be done. + standard format so that the initialization of the driver can be done. Args: atoms: An Atoms object giving the atom positions. cell: A Cell object giving the system box. pars: An optional dictionary giving the parameters to be sent to the - driver for initialisation. Defaults to {}. + driver for initialization. Defaults to {}. reqid: An optional integer that identifies requests of the same type, e.g. the bead index diff --git a/tools/i-pi/ipi/utils/depend.py b/tools/i-pi/ipi/utils/depend.py index 1ca361f781..4b87323533 100644 --- a/tools/i-pi/ipi/utils/depend.py +++ b/tools/i-pi/ipi/utils/depend.py @@ -115,7 +115,7 @@ class depend_base(object): def __init__(self, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None): """Initialises depend_base. - An unusual initialisation routine, as it has to be able to deal with the + An unusual initialization routine, as it has to be able to deal with the depend array mechanism for returning slices as new depend arrays. This is the reason for the penultimate if statement; it automatically diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT index b57d0e76c8..6ec463efab 100644 --- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT +++ b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT @@ -2,7 +2,7 @@ The simulation consists of a mixture of isobutane and water. Over time (less than 1 ns), the two molecules phase-separate. The GAFF parameters are applied only to the isobutane molecule. -(The water molecule paramters are defined explicitly in +(The water molecule parameters are defined explicitly in src/moltemplate_force_fields/tip3p_2004.lt) WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD. diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py index 786a6a8a86..919cfa51af 100644 --- a/tools/moltemplate/src/bonds_by_type.py +++ b/tools/moltemplate/src/bonds_by_type.py @@ -315,7 +315,7 @@ if __name__ == "__main__": elif argv[i][0] == '-': raise ttree_lex.InputError('Error('+g_program_name+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') + 'Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 diff --git a/tools/moltemplate/src/chargepairs_by_type.py b/tools/moltemplate/src/chargepairs_by_type.py index 0d006abd5a..3de8131141 100644 --- a/tools/moltemplate/src/chargepairs_by_type.py +++ b/tools/moltemplate/src/chargepairs_by_type.py @@ -328,7 +328,7 @@ if __name__ == "__main__": elif argv[i][0] == '-': raise ttree_lex.InputError('Error('+g_program_name+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') + 'Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py index adcb5a0369..25c73219dd 100644 --- a/tools/moltemplate/src/dump2data.py +++ b/tools/moltemplate/src/dump2data.py @@ -458,7 +458,7 @@ def ParseArgs(argv, del(argv[i:i+2]) elif ((argv[i][0] == '-') and (__name__ == "__main__")): - raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n') + raise InputError('Error(dump2data): Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py index c77d820434..743419eb2b 100644 --- a/tools/moltemplate/src/lttree.py +++ b/tools/moltemplate/src/lttree.py @@ -165,7 +165,7 @@ def LttreeParseArgs(argv, settings): elif ((argv[i][0] == '-') and (__name__ == "__main__")): #elif (__name__ == "__main__"): raise InputError('Error('+g_program_name+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') + 'Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh index 3a8d17bcd6..d6f76a2483 100755 --- a/tools/moltemplate/src/moltemplate.sh +++ b/tools/moltemplate/src/moltemplate.sh @@ -57,7 +57,7 @@ ERR_INTERNAL() echo " !!!!!! Possible internal error !!!!!!" >&2 echo "This could be a bug in moltemplate." >&2 echo "Please report this error." >&2 - echo "(And please include the last few lines of moltemplate output preceeding this.)" >&2 + echo "(And please include the last few lines of moltemplate output preceding this.)" >&2 echo " Thank you." >&2 exit 100 } diff --git a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh index 7ef489d5f0..92e7e2c42a 100755 --- a/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh +++ b/tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh @@ -159,7 +159,7 @@ echo " # ---------------------------------------------------------------------- #echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\"" echo " # The basic atom nomenclature and conventions are explained here:" echo " # http://ambermd.org/antechamber/gaff.pdf" -echo " # For reference, the original gaff.dat file and format documenation are here:" +echo " # For reference, the original gaff.dat file and format documentation are here:" echo " # http://ambermd.org/AmberTools-get.html" echo " # http://ambermd.org/formats.html#parm.dat" echo " # ----------------------------------------------------------------------" diff --git a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt b/tools/moltemplate/src/moltemplate_force_fields/gaff.lt index 82063a721b..683dbf4ee4 100644 --- a/tools/moltemplate/src/moltemplate_force_fields/gaff.lt +++ b/tools/moltemplate/src/moltemplate_force_fields/gaff.lt @@ -44,7 +44,7 @@ GAFF { # ---------------------------------------------------------------------- # The basic atom nomenclature and conventions are explained here: # http://ambermd.org/antechamber/gaff.pdf - # For reference, the original gaff.dat file and format documenation are here: + # For reference, the original gaff.dat file and format documentation are here: # http://ambermd.org/AmberTools-get.html # http://ambermd.org/formats.html#parm.dat # ---------------------------------------------------------------------- diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT index 3bb903968a..ab7c32530a 100644 --- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT +++ b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT @@ -5,7 +5,7 @@ NOTE: THE "oplsaa_moltemplate.py" SCRIPT HAS MOVED TO THE "../src/" DIRECTORY. Description: Unfortunately, moltemplate does not come with a file containing OPLSAA -paramters which is ready to use. You must build it yourself. +parameters which is ready to use. You must build it yourself. This directory has tools and instructions to explain how to do this. ----------------------------- diff --git a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py index 059aacaafb..5a2ce05c4a 100755 --- a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py +++ b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py @@ -109,7 +109,7 @@ atom_lookup={} #this dictionary contains all the atom ffid's as a key and the nu #atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms atom=[[-10000,-10000] for i in range(0,max_atomType+1)] #charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type +#vdw_by_type={} # lookup epsilon & sigma parameters by atom type charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py index ee9884302b..13fc012015 100644 --- a/tools/moltemplate/src/nbody_by_type.py +++ b/tools/moltemplate/src/nbody_by_type.py @@ -524,7 +524,7 @@ if __name__ == "__main__": elif argv[i][0] == '-': raise InputError('Error('+g_program_name+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') + 'Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 diff --git a/tools/moltemplate/src/ttree.py b/tools/moltemplate/src/ttree.py index 87c385f27b..dda1880c1d 100644 --- a/tools/moltemplate/src/ttree.py +++ b/tools/moltemplate/src/ttree.py @@ -2489,7 +2489,7 @@ class StaticObj(object): raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n' ' Error near '+lex.error_leader()+'\n' ' new '+class_name_str+'\n' - 'Bracketed number should be preceeded by a class name.') + 'Bracketed number should be preceded by a class name.') class_names = [] weights = [] num_by_type = [] @@ -2979,7 +2979,7 @@ class StaticObj(object): # Dots in class names can appear for 2 reasons: # 1) as part of a path like "../" describing the location # where this class was defined relative to the caller. - # In that case it will be preceeded or followed by + # In that case it will be preceded or followed by # either another dot '.', or a slash '/' # 2) as part of a "suffix" which appears after the name # containing instructions which modify how to @@ -4434,7 +4434,7 @@ def ExtractFormattingCommands(suffix): if suffix[-1] != ')': # Format functions are always followed by parens return None, None else: - idot = suffix.find('.') # Format functions usually preceeded by '.' + idot = suffix.find('.') # Format functions usually preceded by '.' ioparen = suffix.find('(') icparen = suffix.find(')') format_fname = suffix[idot+1:ioparen] @@ -5113,7 +5113,7 @@ def BasicUIParseArgs(argv, settings): elif ((argv[i][0] == '-') and (__name__ == "__main__")): #elif (__name__ == "__main__"): raise InputError('Error('+g_filename+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') + 'Unrecognized command line argument \"'+argv[i]+'\"\n') else: i += 1 @@ -5177,7 +5177,7 @@ def BasicUI(settings, # Parsing, and compiling is a multi-pass process. - # Step 1: Read in the StaticObj (class) defintions, without checking + # Step 1: Read in the StaticObj (class) definitions, without checking # whether or not the instance_children refer to valid StaticObj types. sys.stderr.write('parsing the class definitions...') static_tree_root.Parse(settings.lex) diff --git a/tools/moltemplate/src/ttree_lex.py b/tools/moltemplate/src/ttree_lex.py index a8bb10a73c..d0938047c7 100644 --- a/tools/moltemplate/src/ttree_lex.py +++ b/tools/moltemplate/src/ttree_lex.py @@ -1107,7 +1107,7 @@ def _DeleteLineFromTemplate(tmpl_list, tmpl_list is an alternating list of VarRefs and TextBlocks. To identify the line, the index corresponding to one of the entries in the tmpl_list is used. (Usually it is a VarRef) - The text after the preceeding newline, and the text up to the next newline + The text after the preceding newline, and the text up to the next newline (starting from the beginning of the current entry, if a TextBlock) is deleted, including any VarRef (variables) located in between. @@ -1505,7 +1505,7 @@ class TemplateLexer(TtreeShlex): new member function (ReadTemplate()), which can read in a block of raw text, (halting at an (non-escaped) terminal character), and split the text into alternating blocks of text and variables. (As far as this lexer is - concerned, "variables" are simply tokens preceeded by $ or @ characters, + concerned, "variables" are simply tokens preceded by $ or @ characters, and surrounded by optional curly-brackets {}.) """ @@ -1652,7 +1652,7 @@ class TemplateLexer(TtreeShlex): (for example, '}' in "\}" does not cause terminate parsing). In that case, the text is considered normal text. (However the '\' character is also stripped out. It is also stripped out if it - preceeds any characters in "other_esc_chars", which is + precedes any characters in "other_esc_chars", which is the second argument. Otherwise it is left in the text block.) """ diff --git a/tools/msi2lmp/frc_files/cvff_aug.frc b/tools/msi2lmp/frc_files/cvff_aug.frc index 9fcdd30068..75af9ace24 100644 --- a/tools/msi2lmp/frc_files/cvff_aug.frc +++ b/tools/msi2lmp/frc_files/cvff_aug.frc @@ -209,7 +209,7 @@ #define cvff_aug -> This specifes the use of the ionic parameter types +> This specifies the use of the ionic parameter types !Ver Ref Function Label !---- --- --------------------------------- ------ diff --git a/tools/msi2lmp/frc_files/pcff.frc b/tools/msi2lmp/frc_files/pcff.frc index ce24f000cb..a06b04202a 100644 --- a/tools/msi2lmp/frc_files/pcff.frc +++ b/tools/msi2lmp/frc_files/pcff.frc @@ -158,7 +158,7 @@ 1.0 1 op 15.99940 O 2 sp2 aromatic in 5 membered ring 3.0 10 osh 15.99491 O 2 oxygen atom in terminal hydroxyl group on silicon 1.0 1 osi 16.00000 O 2 siloxane oxygen - 3.0 10 oss 15.99491 O 2 oxygen atom betweem two silicons + 3.0 10 oss 15.99491 O 2 oxygen atom between two silicons 2.0 5 oz 15.99940 O 2 ester oxygen in carbonate 1.0 1 p 30.97380 P 4 general phosphorous atom 1.0 1 p= 30.97380 P 5 phosphazene phosphorous atom diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index e07a4486db..377ab1a6c3 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -172,7 +172,7 @@ extern int periodic; /* 0= nonperiodic 1= 3-D periodic */ extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */ extern int forcefield; /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below, * FF_TYPE_CLASS1 = ClassI, FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/ -extern int ljtypeflag; /* how LJ paramters are stored: 0 = A-B, 1 = r-eps */ +extern int ljtypeflag; /* how LJ parameters are stored: 0 = A-B, 1 = r-eps */ extern int centerflag; /* 1= center box 0= keep box */ extern int hintflag; /* 1= print style hint comments 0= no hints */ extern int pflag; /* print level: 0, 1, 2, 3 */ diff --git a/tools/phonon/dynmat.cpp b/tools/phonon/dynmat.cpp index eb91647ed2..e82f473130 100644 --- a/tools/phonon/dynmat.cpp +++ b/tools/phonon/dynmat.cpp @@ -3,7 +3,7 @@ #include "version.h" #include "global.h" -// to intialize the class +// to initialize the class DynMat::DynMat(int narg, char **arg) { attyp = NULL; diff --git a/tools/pymol_asphere/src/cartesian.cpp b/tools/pymol_asphere/src/cartesian.cpp index 38550db0e7..a244d07dac 100644 --- a/tools/pymol_asphere/src/cartesian.cpp +++ b/tools/pymol_asphere/src/cartesian.cpp @@ -4,7 +4,7 @@ * Also contains quaternion structures and operations * * Cartesian point of doubles: cPt - * Cartesian point of intergers: iPt + * Cartesian point of integers: iPt * Vector of doubles: vectorPt * Color of doubles: colorPt * Quaternion: Quaternion diff --git a/tools/pymol_asphere/src/cartesian.h b/tools/pymol_asphere/src/cartesian.h index a486b5163e..a5acd70b33 100644 --- a/tools/pymol_asphere/src/cartesian.h +++ b/tools/pymol_asphere/src/cartesian.h @@ -4,7 +4,7 @@ * Also contains quaternion structures and operations * * Cartesian point of doubles: cPt - * Cartesian point of intergers: iPt + * Cartesian point of integers: iPt * Vector of doubles: vectorPt * Color of doubles: colorPt * Quaternion: Quaternion diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py index 3b7e7c46c7..36a24dcd39 100644 --- a/tools/python/pizza/dump.py +++ b/tools/python/pizza/dump.py @@ -448,7 +448,7 @@ class dump: # -------------------------------------------------------------------- # scale coords to 0-1 for all snapshots or just one - # use 6 params as h-matrix to treat orthongonal or triclinic boxes + # use 6 params as h-matrix to treat orthogonal or triclinic boxes def scale(self,*list): if len(list) == 0: @@ -512,7 +512,7 @@ class dump: # -------------------------------------------------------------------- # unscale coords from 0-1 to box size for all snapshots or just one - # use 6 params as h-matrix to treat orthongonal or triclinic boxes + # use 6 params as h-matrix to treat orthogonal or triclinic boxes def unscale(self,*list): if len(list) == 0: