diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 2281f57fbd..3e5e1a74a9 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -135,7 +135,7 @@

LAMMPS Documentation

-

7 Sep 2016 version

+

13 Sep 2016 version

Version info:

diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 69c6609b6c..88bc54ce5a 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -247,15 +247,15 @@ inside the parenthesis is treated as an “immediate” variable and evaluated as an equal-style variable. This is a way to use numeric formulas in an input script without having to assign them to variable names. For example, these 3 input script lines:

-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
+
variable X equal (xlo+xhi)/2+sqrt(v_area)
 region 1 block $X 2 INF INF EDGE EDGE
 variable X delete
-

+
+

can be replaced by

-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
-
+
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+
+

so that you do not have to define (or discard) a temporary variable X.

Note that neither the curly-bracket or immediate form of variables can contain nested $ characters for other variables to substitute for. diff --git a/doc/html/Section_example.html b/doc/html/Section_example.html index 9c2e1a0c72..95a590b02f 100644 --- a/doc/html/Section_example.html +++ b/doc/html/Section_example.html @@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.

Here is how you can run and visualize one of the sample problems:

-
-cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem
-
+
cd indent
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+lmp_linux -in in.indent            # run the problem
+
+

Running the simulation produces the files dump.indent and log.lammps. You can visualize the dump file of snapshots with a variety of 3rd-party tools highlighted on the @@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools. See the dump image doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser.

-
-% convert -loop 1 *.jpg foo.gif
-
+
% convert -loop 1 *.jpg foo.gif
+
+

7.2. Uppercase directories

--++ diff --git a/doc/html/Section_tools.html b/doc/html/Section_tools.html index 1daccc93c4..0e3948b6a0 100644 --- a/doc/html/Section_tools.html +++ b/doc/html/Section_tools.html @@ -204,7 +204,7 @@ own sub-directories with their own Makefiles.

  • eff
  • emacs
  • fep
    • -
  • i-pi
    • +
  • i-pi
  • ipp
  • kate
  • lmp2arc
    • diff --git a/doc/html/atom_modify.html b/doc/html/atom_modify.html index 0922591416..b2e3f8585d 100644 --- a/doc/html/atom_modify.html +++ b/doc/html/atom_modify.html @@ -128,9 +128,9 @@

    atom_modify command

    Syntax

    -
    -atom_modify keyword values ...
-
    +
    atom_modify keyword values ...
+
    +

    Examples

    -
    -atom_modify map hash
-atom_modify map array sort 10000 2.0
-atom_modify first colloid
-
    +
    atom_modify map hash
+atom_modify map array sort 10000 2.0
+atom_modify first colloid
+
    +

    Description

    diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html index a2cbd22a72..2ed9ccbab0 100644 --- a/doc/html/atom_style.html +++ b/doc/html/atom_style.html @@ -128,9 +128,9 @@

    atom_style command

    Syntax

    -
    -atom_style style args
-
    +
    atom_style style args
+
    +
    • style = angle or atomic or body or bond or charge or dipole or dpd or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid
    @@ -150,15 +150,15 @@ args = none for any style except the following

    Examples

    -
    -atom_style atomic
-atom_style bond
-atom_style full
-atom_style body nparticle 2 10
-atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 2 5
-atom_style template myMols
-
    +
    atom_style atomic
+atom_style bond
+atom_style full
+atom_style body nparticle 2 10
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle 2 5
+atom_style template myMols
+
    +

    Description

    diff --git a/doc/html/body.html b/doc/html/body.html index 5aaa8ec563..6a2be8aff8 100644 --- a/doc/html/body.html +++ b/doc/html/body.html @@ -247,11 +247,11 @@ mentioned above, the

    The atom_style body command for this body style takes two additional arguments:

    -
    -atom_style body nparticle Nmin Nmax
-Nmin = minimum # of sub-particles in any body in the system
-Nmax = maximum # of sub-particles in any body in the system
-
    +
    atom_style body nparticle Nmin Nmax
+Nmin = minimum # of sub-particles in any body in the system
+Nmax = maximum # of sub-particles in any body in the system
+
    +

    The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle.

    When the read_data command reads a data file for this @@ -313,11 +313,11 @@ used for 2d models. One example use of this body style is for 2d discrete element models, as described in Fraige. Similar to body style nparticle, the atom_style body command for this body style takes two additional arguments:

    -
    -atom_style body rounded/polygon Nmin Nmax
-Nmin = minimum # of vertices in any body in the system
-Nmax = maximum # of vertices in any body in the system
-
    +
    atom_style body rounded/polygon Nmin Nmax
+Nmin = minimum # of vertices in any body in the system
+Nmax = maximum # of vertices in any body in the system
+
    +

    The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle.

    When the read_data command reads a data file for this diff --git a/doc/html/change_box.html b/doc/html/change_box.html index 5fd817925f..fc034cbe2f 100644 --- a/doc/html/change_box.html +++ b/doc/html/change_box.html @@ -128,9 +128,9 @@

    change_box command

    Syntax

    -
    -change_box group-ID parameter args ... keyword args ...
-
    +
    change_box group-ID parameter args ... keyword args ...
+
    +
    • group-ID = ID of group of atoms to (optionally) displace
    • one or more parameter/arg pairs may be appended
      • @@ -175,10 +175,10 @@ parameter = x or y or z or xy or xz

    Examples

    -
    -change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
-change_box all x scale 1.1 y volume z volume remap
-
    +
    change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap
+
    +

    Description

    @@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes. 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
-
    -
    -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
-
    +
    change_box all x final -10 20
+create_atoms 1 single -5 5 5   # this will fail to insert an atom
+
    +
    +
    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
+
    +

    Note

    Unlike the earlier “displace_box” version of this command, atom @@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the x, y, z keywords. If the preceding keyword “key” had a volume style, then both it and the current keyword apply to the keyword preceding “key”. I.e. this sequence of keywords is allowed:

    -
    -change_box all x scale 1.1 y volume z volume
-
    +
    change_box all x scale 1.1 y volume z volume
+
    +

    The volume style changes the associated dimension so that the overall box volume is unchanged relative to its value before the preceding keyword was invoked.

    If the following command is used, then the z box length will shrink by the same 1.1 factor the x box length was increased by:

    -
    -change_box all x scale 1.1 z volume
-
    +
    change_box all x scale 1.1 z volume
+
    +

    If the following command is used, then the y,z box lengths will each shrink by sqrt(1.1) to keep the volume constant. In this case, the y,z box lengths shrink so as to keep their relative aspect ratio constant:

    -
    -change_box all"x scale 1.1 y volume z volume
-
    +
    change_box all"x scale 1.1 y volume z volume
+
    +

    If the following command is used, then the final box will be a factor of 10% larger in x and y, and a factor of 21% smaller in z, so as to keep the volume constant:

    -
    -change_box all x scale 1.1 z volume y scale 1.1 z volume
-
    +
    change_box all x scale 1.1 z volume y scale 1.1 z volume
+
    +

    Note

    For solids or liquids, when one dimension of the box is diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html index efedfa0512..55452e3a0f 100644 --- a/doc/html/compute_dipole_chunk.html +++ b/doc/html/compute_dipole_chunk.html @@ -181,11 +181,11 @@ and how they are set for each atom. You can reset the image flags

    The simplest way to output the results of the compute com/chunk calculation to a file is to use the fix ave/time command, for example:

    -
    -compute cc1 all chunk/atom molecule
-compute myChunk all dipole/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
    +
    compute cc1 all chunk/atom molecule
+compute myChunk all dipole/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
    +

    Output info:

    This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html index d718f90f47..b93575cfc5 100644 --- a/doc/html/compute_inertia_chunk.html +++ b/doc/html/compute_inertia_chunk.html @@ -177,11 +177,11 @@ how they are set for each atom. You can reset the image flags

    The simplest way to output the results of the compute inertia/chunk calculation to a file is to use the fix ave/time command, for example:

    -
    -compute cc1 all chunk/atom molecule
-compute myChunk all inertia/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
    +
    compute cc1 all chunk/atom molecule
+compute myChunk all inertia/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
    +

    Output info:

    This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html index 6a017dc79b..00b22b9256 100644 --- a/doc/html/compute_ke_atom_eff.html +++ b/doc/html/compute_ke_atom_eff.html @@ -168,11 +168,11 @@ eFF.

    thermodynamic output by using the thermo_modify command, as shown in the following example:

    -
    -compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
    +
    compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
    +

    The value of the kinetic energy will be 0.0 for atoms (nuclei or electrons) not in the specified compute group.

    Output info:

    diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html index ff0e0b4e68..b614a9d25b 100644 --- a/doc/html/compute_ke_eff.html +++ b/doc/html/compute_ke_eff.html @@ -169,11 +169,11 @@ the thermo_modify command, as shown in the following example:

    -
    -compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
    +
    compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
    +

    See compute temp/eff.

    Output info:

    This compute calculates a global scalar (the KE). This value can be diff --git a/doc/html/compute_modify.html b/doc/html/compute_modify.html index 6556686bb9..8c31af05b2 100644 --- a/doc/html/compute_modify.html +++ b/doc/html/compute_modify.html @@ -128,9 +128,9 @@

    compute_modify command

    Syntax

    -
    -compute_modify compute-ID keyword value ...
-
    +
    compute_modify compute-ID keyword value ...
+
    +
    • compute-ID = ID of the compute to modify
    • one or more keyword/value pairs may be listed
      • @@ -145,10 +145,10 @@ compute_modify compute-ID keyword value ...

    Examples

    -
    -compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600
-
    +
    compute_modify myTemp extra 0
+compute_modify newtemp dynamic yes extra 600
+
    +

    Description

    diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html index b5de90dfdb..fafebf006b 100644 --- a/doc/html/compute_pe_atom.html +++ b/doc/html/compute_pe_atom.html @@ -185,11 +185,11 @@ command.

    As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output:

    -
    -compute              peratom all pe/atom
-compute              pe all reduce sum c_peratom
-thermo_style        custom step temp etotal press pe c_pe
-
    +
    compute              peratom all pe/atom
+compute              pe all reduce sum c_peratom
+thermo_style custom step temp etotal press pe c_pe
+
    +

    Note

    The per-atom energy does not any Lennard-Jones tail corrections diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html index f91b814e33..9fdc98e352 100644 --- a/doc/html/compute_property_atom.html +++ b/doc/html/compute_property_atom.html @@ -136,25 +136,25 @@

  • property/atom = style name of this compute command
  • input = one or more atom attributes
    • -
    -possible attributes = id, mol, proc, type, mass,
-                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-                   vx, vy, vz, fx, fy, fz,
-                      q, mux, muy, muz, mu,
-                      radius, diameter, omegax, omegay, omegaz,
-                   angmomx, angmomy, angmomz,
-                   shapex,shapey, shapez,
-                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
-                   end1x, end1y, end1z, end2x, end2y, end2z,
-                   corner1x, corner1y, corner1z,
-                   corner2x, corner2y, corner2z,
-                   corner3x, corner3y, corner3z,
-                   nbonds,
-                      vfrac, s0,
-                   spin, eradius, ervel, erforce,
-                      rho, drho, e, de, cv,
-                      i_name, d_name
-
    +
    possible attributes = id, mol, proc, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                   angmomx, angmomy, angmomz,
+                   shapex,shapey, shapez,
+                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                   end1x, end1y, end1z, end2x, end2y, end2z,
+                   corner1x, corner1y, corner1z,
+                   corner2x, corner2y, corner2z,
+                   corner3x, corner3y, corner3z,
+                   nbonds,
+                      vfrac, s0,
+                   spin, eradius, ervel, erforce,
+                      rho, drho, e, de, cv,
+                      i_name, d_name
+
    +
    id = atom ID
 mol = molecule ID
 proc = ID of processor that owns atom
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html
index 7cf73b649d..2012335a47 100644
--- a/doc/html/compute_property_chunk.html
+++ b/doc/html/compute_property_chunk.html
@@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).
    
 
    The simplest way to output the results of the compute property/chunk
 calculation to a file is to use the fix ave/time
 command, for example:
    
-
    -compute cc1 all chunk/atom molecule
-compute myChunk1 all property/chunk cc1 count
-compute myChunk2 all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
-
    
+
    compute cc1 all chunk/atom molecule
+compute myChunk1 all property/chunk cc1 count
+compute myChunk2 all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
+
    
+
    
 
    Output info:
    
 
    This compute calculates a global vector or global array depending on
 the number of input values.  The length of the vector or number of
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 56a155c53a..519bc9ff3c 100644
--- a/doc/html/compute_reduce.html
+++ b/doc/html/compute_reduce.html
@@ -148,14 +148,14 @@
 
  • one or more inputs can be listed
    • 
 
  • input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • 
 
-
    -x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom or local vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom or local vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
    
+
    x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom or local vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom or local vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
    
+
    
 
      
 
    • zero or more keyword/args pairs may be appended
      • 
 
    • keyword = replace
      • 
@@ -168,13 +168,13 @@ v_name = per-atom vector calculated by an atom-style variable with name

    Examples

    -
    -compute 1 all reduce sum c_force
-compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press[2] f_ave v_myKE
-compute 2 all reduce min c_press[*] f_ave v_myKE
-compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
-
    +
    compute 1 all reduce sum c_force
+compute 1 all reduce/region subbox sum c_force
+compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 2 all reduce min c_press[*] f_ave v_myKE
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+
    +

    Description

    @@ -211,7 +211,7 @@ component) or can be the result of a variable.

    Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form “*” or “*n” or “n*” or +specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading @@ -222,18 +222,18 @@ means all indices from m to n (inclusive).

    had been listed one by one. E.g. these 2 compute reduce commands are equivalent, since the compute stress/atom command creates a per-atom array with 6 columns:

    -
    -compute myPress all stress/atom NULL
-compute 2 all reduce min myPress[*]
-compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
-                         myPress[4] myPress[5] myPress[6]
-
    +
    compute myPress all stress/atom NULL
+compute 2 all reduce min myPress[*]
+compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
+                         myPress[4] myPress[5] myPress[6]
+
    +

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

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual compute doc page for details. If no bracketed integer @@ -243,7 +243,7 @@ by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual fix doc page for details. Note that some fixes only produce their values on certain @@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “v_”, a variable name must follow which has +

    If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. It must be an atom-style variable. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or @@ -271,12 +271,12 @@ Then, instead of performing a min/max on the vec1 input vector, the stored index is used to select the Nth element of the vec1 vector.

    Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows:

    -
    -compute 1 all property/local batom1 batom2
-compute      2 all bond/local dist
-compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
-thermo_style custom step temp c_3[1] c_3[2] c_3[3]
-
    +
    compute 1 all property/local batom1 batom2
+compute      2 all bond/local dist
+compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3[1] c_3[2] c_3[3]
+
    +

    The first two input values in the compute reduce command are vectors with the IDs of the 2 atoms in each bond, using the compute property/local command. The last input value is bond distance, using the compute bond/local command. Instead of taking the diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html index 7f7d5630fa..154d01a909 100644 --- a/doc/html/compute_rigid_local.html +++ b/doc/html/compute_rigid_local.html @@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local vector or array from one timestep to the next.

    Here is an example of how to use this compute to dump rigid body info to a file:

    -
    -compute 1 all rigid/local myRigid mol x y z fx fy fz
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
-
    +
    compute 1 all rigid/local myRigid mol x y z fx fy fz
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
+
    +

    This section explains the rigid body attributes that can be specified.

    The id attribute is the atomID of the atom which owns the rigid body, which is diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html index 81927952be..4751726a56 100644 --- a/doc/html/compute_temp_cs.html +++ b/doc/html/compute_temp_cs.html @@ -140,10 +140,10 @@

    Examples

    -
    -compute oxygen_c-s all temp/cs O_core O_shell
-compute core_shells all temp/cs cores shells
-
    +
    compute oxygen_c-s all temp/cs O_core O_shell
+compute core_shells all temp/cs cores shells
+
    +

    Description

    diff --git a/doc/html/compute_temp_eff.html b/doc/html/compute_temp_eff.html index d11ad256a8..4dadf7de39 100644 --- a/doc/html/compute_temp_eff.html +++ b/doc/html/compute_temp_eff.html @@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the thermo_modify command, as shown in the following example:

    -
    -compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
    +
    compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
    +

    A 6-component kinetic energy tensor is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as the above formula, except that diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html index 8d6198637d..5701aeee75 100644 --- a/doc/html/compute_ti.html +++ b/doc/html/compute_ti.html @@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2

    Examples

    -
    -compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
-compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
-
    +
    compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
+compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
+
    +

    Description

    @@ -192,7 +192,7 @@ with respect to lambda.

    numeric values can be used, as in the 1st example above. Or a wildcard asterisk can be used in place of or in conjunction with the atype argument to select multiple atom types. This takes the form -“*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then +“*” or “n” or “n” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html index ed4cd612a1..630ee3bac6 100644 --- a/doc/html/compute_voronoi_atom.html +++ b/doc/html/compute_voronoi_atom.html @@ -158,14 +158,14 @@ or face_threshold or neighbors or peratom

    Examples

    -
    -compute 1 all voronoi/atom
-compute 2 precipitate voronoi/atom surface matrix
-compute 3b precipitate voronoi/atom radius v_r
-compute 4 solute voronoi/atom only_group
-compute 5 defects voronoi/atom occupation
-compute 6 all voronoi/atom neighbors yes
-
    +
    compute 1 all voronoi/atom
+compute 2 precipitate voronoi/atom surface matrix
+compute 3b precipitate voronoi/atom radius v_r
+compute 4 solute voronoi/atom only_group
+compute 5 defects voronoi/atom occupation
+compute 6 all voronoi/atom neighbors yes
+
    +

    Description

    @@ -199,11 +199,11 @@ can be obtained by running a “reduce sum” compute on c_2[3]

    If the radius keyword is specified with an atom style variable as the argument, a poly-disperse Voronoi tessellation is performed. Examples for radius variables are

    -
    -variable r1 atom (type==1)*0.1+(type==2)*0.4
-compute radius all property/atom radius
-variable r2 atom c_radius
-
    +
    variable r1 atom (type==1)*0.1+(type==2)*0.4
+compute radius all property/atom radius
+variable r2 atom c_radius
+
    +

    Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms and 0.4 units for type 2 atoms, and v_r2 accesses the radius property present in atom_style sphere for granular models.

    @@ -247,10 +247,10 @@ uses local values from a compute as input. See dump local command to write a file containing all the Voronoi neighbors in a system:

    -
    -compute 6 all voronoi/atom neighbors yes
-dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
-
    +
    compute 6 all voronoi/atom neighbors yes
+dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
+
    +

    If the face_threshold keyword is used, then only faces with areas greater than the threshold are stored.

    diff --git a/doc/html/delete_bonds.html b/doc/html/delete_bonds.html index b10ff2515d..18e52920f4 100644 --- a/doc/html/delete_bonds.html +++ b/doc/html/delete_bonds.html @@ -128,9 +128,9 @@

    delete_bonds command

    Syntax

    -
    -delete_bonds group-ID style arg keyword ...
-
    +
    delete_bonds group-ID style arg keyword ...
+
    +

    • group-ID = group ID

      • @@ -157,12 +157,12 @@ delete_bonds group-ID style arg keyword ...

    Examples

    -
    -delete_bonds frozen multi remove
-delete_bonds all atom 4 special
-delete_bonds all bond 0*3 special
-delete_bonds all stats
-
    +
    delete_bonds frozen multi remove
+delete_bonds all atom 4 special
+delete_bonds all bond 0*3 special
+delete_bonds all stats
+
    +

    Description

    @@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types (atom types, bond types, etc). A value of 0 is only relevant for style bond; see details below. In all cases, a wildcard asterisk can be used in place of or in conjunction with the type argument to -specify a range of types. This takes the form “*” or “*n” or “n*” or +specify a range of types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of types, then an asterisk with no numeric values means all types from 0 to N. A leading asterisk means all types from 0 to n (inclusive). A trailing asterisk means all types diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html index fe30f6ab11..d967731158 100644 --- a/doc/html/dihedral_table.html +++ b/doc/html/dihedral_table.html @@ -131,9 +131,9 @@

    dihedral_style table/omp command

    Syntax

    -
    -dihedral_style table style Ntable
-
    +
    dihedral_style table style Ntable
+
    +
    • style = linear or spline = method of interpolation
    • Ntable = size of the internal lookup table
      • @@ -141,12 +141,12 @@ dihedral_style table style Ntable

    Examples

    -
    -dihedral_style table spline 400
-dihedral_style table linear 1000
-dihedral_coeff 1 file.table DIH_TABLE1
-dihedral_coeff 2 file.table DIH_TABLE2
-
    +
    dihedral_style table spline 400
+dihedral_style table linear 1000
+dihedral_coeff 1 file.table DIH_TABLE1
+dihedral_coeff 2 file.table DIH_TABLE2
+
    +

    Description

    @@ -185,23 +185,23 @@ or blank lines.

    # Table of the potential and its negative derivative
    -
    -DIH_TABLE1                   (keyword is the first text on line)
-N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
-                             (blank line)
-1 -168.0 -1.40351172223 0.0423346818422
-2 -156.0 -1.70447981034 0.00811786522531
-3 -144.0 -1.62956100432 -0.0184129719987
-...
-30 180.0 -0.707106781187 0.0719306095245
-
    +
    DIH_TABLE1                   (keyword is the first text on line)
+N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                             (blank line)
+1 -168.0 -1.40351172223 0.0423346818422
+2 -156.0 -1.70447981034 0.00811786522531
+3 -144.0 -1.62956100432 -0.0184129719987
+...
+30 180.0 -0.707106781187 0.0719306095245
+
    +
    # Example 2: table of the potential. Forces omitted
    -
    -DIH_TABLE2
-N 30 NOF CHECKU testU.dat CHECKF testF.dat
-
    +
    DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat
+
    +
    1 -168.0 -1.40351172223
 2 -156.0 -1.70447981034
 3 -144.0 -1.62956100432
diff --git a/doc/html/dump.html b/doc/html/dump.html
index d76697dbba..b47465bc33 100644
--- a/doc/html/dump.html
+++ b/doc/html/dump.html
@@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom

    Examples

    -
    -dump myDump all atom 100 dump.atom
-dump myDump all atom/mpiio 100 dump.atom.mpiio
-dump myDump all atom/gz 100 dump.atom.gz
-dump 2 subgroup atom 50 dump.run.bin
-dump 2 subgroup atom 50 dump.run.mpiio.bin
-dump 4a all custom 100 dump.myforce.* id type x y vx fx
-dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
-dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
-dump 1 all xtc 1000 file.xtc
-
    +
    dump myDump all atom 100 dump.atom
+dump myDump all atom/mpiio 100 dump.atom.mpiio
+dump myDump all atom/gz 100 dump.atom.gz
+dump 2 subgroup atom 50 dump.run.bin
+dump 2 subgroup atom 50 dump.run.mpiio.bin
+dump 4a all custom 100 dump.myforce.* id type x y vx fx
+dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
+dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
+dump 1 all xtc 1000 file.xtc
+
    +

    Description

    @@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value. See the bounding box which encloses the triclinic simulation box is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic box, formatted as follows:

    -
    -ITEM: BOX BOUNDS xy xz yz xx yy zz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz
-
    +
    ITEM: BOX BOUNDS xy xz yz xx yy zz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+
    +

    The presence of the text “xy xz yz” in the ITEM line indicates that the 3 tilt factors will be included on each of the 3 following lines. This bounding box is convenient for many visualization programs. The @@ -541,7 +541,7 @@ styles.

    reference values from a compute or fix, like the custom, cfg, or local styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple -values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the +values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all @@ -552,12 +552,12 @@ from m to n (inclusive).

    had been listed one by one. E.g. these 2 dump commands are equivalent, since the compute stress/atom command creates a per-atom array with 6 columns:

    -
    -compute myPress all stress/atom NULL
-dump 2 all custom 100 tmp.dump id myPress[*]
-dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
-                                  myPress[4] myPress[5] myPress[6]
-
    +
    compute myPress all stress/atom NULL
+dump 2 all custom 100 tmp.dump id myPress[*]
+dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
+                                  myPress[4] myPress[5] myPress[6]
+
    +

    This section explains the local attributes that can be specified as part of the local style.

    @@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple values.

    Here is an example of how to dump bond info for a system, including the distance and energy of each bond:

    -
    -compute 1 all property/local batom1 batom2 btype
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
-
    +
    compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+
    +

    This section explains the atom attributes that can be specified as part of the custom and cfg styles.

    diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html index b77890476a..8bd838f671 100644 --- a/doc/html/dump_custom_vtk.html +++ b/doc/html/dump_custom_vtk.html @@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name

    Examples

    -
    -dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
-
    +
    dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
+
    +

    The style custom/vtk is similar to the custom style but uses the VTK library to write data to VTK simple legacy or XML format depending on the filename extension specified. This can be either -*.vtk for the legacy format or *.vtp and *.vtu, respectively, +**.vtk* for the legacy format or **.vtp* and **.vtu*, respectively, for the XML format; see the VTK homepage for a detailed description of these formats. Since this naming convention conflicts with the way binary output is usually specified (see below), diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html index 08afa5c7c6..492ef0a5f5 100644 --- a/doc/html/dump_modify.html +++ b/doc/html/dump_modify.html @@ -128,9 +128,9 @@

    dump_modify command

    Syntax

    -
    -dump_modify dump-ID keyword values ...
-
    +
    dump_modify dump-ID keyword values ...
+
    +
    • dump-ID = ID of dump to modify
    • one or more keyword/value pairs may be appended
      • @@ -228,16 +228,16 @@ dump_modify dump-ID keyword values ...

    Examples

    -
    -dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
-dump_modify 1 format float %20.15g scale yes
-dump_modify myDump image yes scale no flush yes
-dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000 sfactor 0.1
-dump_modify 1 every 1000 nfile 20
-dump_modify 1 every v_myVar
-dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
-
    +
    dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
+dump_modify 1 format float %20.15g scale yes
+dump_modify myDump image yes scale no flush yes
+dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+dump_modify xtcdump precision 10000 sfactor 0.1
+dump_modify 1 every 1000 nfile 20
+dump_modify 1 every v_myVar
+dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
+
    +

    Description

    @@ -318,19 +318,19 @@ to the dump file. The every keyword cannot be used with the dump dcd style.

    For example, the following commands will write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:

    -
    -variable     s equal logfreq(10,3,10)
-dump         1 all atom 100 tmp.dump
-dump_modify 1 every v_s first yes
-
    +
    variable     s equal logfreq(10,3,10)
+dump         1 all atom 100 tmp.dump
+dump_modify  1 every v_s first yes
+
    +

    The following commands would write snapshots at the timesteps listed in file tmp.times:

    -
    -variable        f file tmp.times
-variable     s equal next(f)
-dump         1 all atom 100 tmp.dump
-dump_modify 1 every v_s
-
    +
    variable        f file tmp.times
+variable     s equal next(f)
+dump         1 all atom 100 tmp.dump
+dump_modify  1 every v_s
+
    +

    Note

    When using a file-style variable with the every keyword, the @@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a (large) integer, then you need to use an appropriate format. For example, these commands:

    -
    -compute     1 all property/local batom1 batom2
-dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-dump_modify 1 format "%d %0.0f %0.0f"
-
    +
    compute     1 all property/local batom1 batom2
+dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
+dump_modify 1 format "%d %0.0f %0.0f"
+
    +

    will output the two atom IDs for atoms in each bond as integers. If the dump_modify command were omitted, they would appear as floating-point values, assuming they were large integers (more than 6 @@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.

    The specified type should be an integer from 1 to Ntypes = the number of atom types. A wildcard asterisk can be used in place of or in conjunction with the type argument to specify a range of atom -types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the +types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N @@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.

    atoms in individual molecules with a different color. See the examples/pour/in.pour.2d.molecule input script for an example of how this is used.

    -
    -variable        colors string &
+
    variable        colors string &
                 "red green blue yellow white &
                 purple pink orange lime gray"
 variable     mol atom mol%10
 dump         1 all image 250 image.*.jpg v_mol type &
              zoom 1.6 adiam 1.5
-dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
-
    
+dump_modify  1 pad 5 amap 0 10 sa 1 10 ${colors}
+
    +

    In this case, 10 colors are defined, and molecule IDs are mapped to one of the colors, even if there are 1000s of molecules.

    @@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.

    The specified type should be an integer from 1 to Nbondtypes = the number of bond types. A wildcard asterisk can be used in place of or in conjunction with the type argument to specify a range of bond -types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the +types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of bond types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N diff --git a/doc/html/fix_atom_swap.html b/doc/html/fix_atom_swap.html index a56f3b4f8b..862d6932af 100644 --- a/doc/html/fix_atom_swap.html +++ b/doc/html/fix_atom_swap.html @@ -156,11 +156,11 @@

    Examples

    -
    -fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
-fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
-fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
-
    +
    fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
+fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
+fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
+
    +

    Description

    @@ -250,7 +250,9 @@ system (the quantity used when performing GCMC moves), you MUST enable the fix_modify energy option for that fix. The doc pages for individual fix commands specify if this should be done.

    -

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

    +
    +
    +

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

    This fix writes the state of the fix to binary restart files. This includes information about the random number generator seed, the next timestep for MC exchanges, etc. See the read_restart command for info on how to diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html index 72641a5006..b8459a1d96 100644 --- a/doc/html/fix_ave_atom.html +++ b/doc/html/fix_ave_atom.html @@ -140,22 +140,22 @@ one or more input values can be listed

  • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
    • -
    -x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
    +
    x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
    +

    Examples

    -
    -fix 1 all ave/atom 1 100 100 vx vy vz
-fix 1 all ave/atom 10 20 1000 c_my_stress[1]
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-
    +
    fix 1 all ave/atom 1 100 100 vx vy vz
+fix 1 all ave/atom 10 20 1000 c_my_stress[1]
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+
    +

    Description

    @@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce per-atom vectors.

    Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form “*” or “*n” or “n*” or +specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading @@ -192,13 +192,13 @@ means all indices from m to n (inclusive).

    had been listed one by one. E.g. these 2 fix ave/atom commands are equivalent, since the compute stress/atom command creates a per-atom array with 6 columns:

    -
    -compute my_stress all stress/atom NULL
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
-                              c_my_stress[3] c_my_stress[4] &
-                              c_my_stress[5] c_my_stress[6]
-
    +
    compute my_stress all stress/atom NULL
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
+                              c_my_stress[3] c_my_stress[4] &
+                              c_my_stress[5] c_my_stress[6]
+
    +

    The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used in order to contribute to the @@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates, which can be provided by the compute property/atom command via its xu,yu,zu attributes.

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of @@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the fix is used. If a bracketed term containing an index I is appended, the Ith column of @@ -246,13 +246,15 @@ compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “v_”, a variable name must follow which has +

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

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various output commands.

    diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index a6293fb62e..564b91e3ef 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -141,16 +141,16 @@
  • one or more input values can be listed
  • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
    • -
    -vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-density/number, density/mass = number or mass density
-temp = temperature
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
    +
    vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+density/number, density/mass = number or mass density
+temp = temperature
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
    +
    • zero or more keyword/arg pairs may be appended
    • keyword = norm or ave or bias or adof or cdof or file or overwrite or title1 or title2 or title3
      • @@ -185,12 +185,12 @@ v_name = per-atom vector calculated by an atom-style variable with name

    Examples

    -
    -fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
-fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-
    +
    fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
+fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+
    +

    NOTE:

    If you are trying to replace a deprectated fix ave/spatial command with the newer, more flexible fix ave/chunk and compute chunk/atom commands, you simply need to split @@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable produce global quantities.

    Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form “*” or “*n” or “n*” or +specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading @@ -253,11 +253,11 @@ means all indices from m to n (inclusive).

    had been listed one by one. E.g. these 2 fix ave/chunk commands are equivalent, since the compute property/atom command creates, in this case, a per-atom array with 3 columns:

    -
    -compute myAng all property/atom angmomx angmomy angmomz
-fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
-fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
-
    +
    compute myAng all property/atom angmomx angmomy angmomz
+fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
+fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
+
    +

    Note

    This fix works by creating an array of size Nchunk by Nvalues @@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set of atoms to calculate their temperature. The compute allows the center-of-mass velocity of each chunk to be subtracted before calculating the temperature; this fix does not.

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array @@ -357,7 +357,7 @@ calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array @@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with own fix styles and add them to LAMMPS. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

    -

    If a value begins with “v_”, a variable name must follow which has +

    If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. Variables of style atom can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they @@ -502,8 +502,10 @@ value of the units keyword is reduced, the coordinate values w be in unitless reduced units (0-1). This is not true for the Coord1 value of style bin/sphere or bin/cylinder which both represent radial dimensions. Those values are always in distance units.

    +
    -

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

    +
    +

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

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

    This fix computes a global array of values which can be accessed by diff --git a/doc/html/fix_ave_correlate_long.html b/doc/html/fix_ave_correlate_long.html index a673143beb..ccd754dbaf 100644 --- a/doc/html/fix_ave_correlate_long.html +++ b/doc/html/fix_ave_correlate_long.html @@ -139,13 +139,13 @@

  • one or more input values can be listed
  • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • -
    -c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID
-v_name = global value calculated by an equal-style variable with name
-
    +
    c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
+
    +
    • zero or more keyword/arg pairs may be appended
    • keyword = type or start or file or overwrite or title1 or title2 or ncorr or p or m
      • @@ -177,12 +177,12 @@ v_name = global value calculated by an equal-style variable with name

    Examples

    -
    -fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate/long 1 10000 &
-          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
-       type upper title1 "My correlation data" nlen 15 ncount 3
-
    +
    fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+       type upper title1 "My correlation data" nlen 15 ncount 3
+
    +

    Description

    @@ -221,7 +221,9 @@ steps can be calculated.

    4*ncorr*nlen*8 bytes. With the default values of the parameters, this corresponds to about 10 KB.

    For the meaning of the additional optional keywords, see the fix ave/correlate doc page.

    -

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

    +
    +
    +

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

    Since this fix in intended for the calculation of time correlation functions over very long MD simulations, the information about this fix is written automatically to binary restart files, so that the time diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html index bb07687b4a..e8291ddeb4 100644 --- a/doc/html/fix_ave_histo.html +++ b/doc/html/fix_ave_histo.html @@ -145,15 +145,15 @@

  • one or more input values can be listed
  • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • -
    -x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-
    +
    x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+
    +
    • zero or more keyword/arg pairs may be appended
    • keyword = mode or file or ave or start or beyond or overwrite or title1 or title2 or title3
      • @@ -185,13 +185,13 @@ v_name[I] = value calculated by a vector-style variable with name

    Examples

    -
    -fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
-fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
-fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
-
    +
    fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
+fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
+fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
+
    +

    Description

    @@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array is used.

    Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form “*” or “*n” or “n*” or +specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading @@ -243,11 +243,11 @@ means all indices from m to n (inclusive).

    vector or columns of the array had been listed one by one. E.g. these 2 fix ave/histo commands are equivalent, since the compute com/chunk command creates a global array with 3 columns:

    -
    -compute myCOM all com/chunk
-fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
-fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
-
    +
    compute myCOM all com/chunk
+fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+
    +

    If the fix ave/histo/weight command is used, exactly two values must be specified. If the values are vectors, they must be the same length. The first value (a scalar or vector) is what is histogrammed @@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.

    self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the compute property/atom command and then specifying an input value from that compute.

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If mode = scalar, then if no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of @@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo. Or it can be a compute defined not in your input script, but by thermodynamic output or other fixes such as fix nvt or fix temp/rescale. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and add them to LAMMPS.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If mode = scalar, then if no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the @@ -309,7 +309,7 @@ values.

    Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.

    -

    If a value begins with “v_”, a variable name must follow which has +

    If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. If mode = scalar, then only equal-style or vector-style variables can be used, which both produce global values. In this mode, a vector-style variable requires @@ -399,8 +399,10 @@ values for each of these, so they do not need to be specified.

    describes the six values that are printed at the first of each section of output. The third describes the 4 values printed for each bin in the histogram.

    +
    -

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

    +
    +

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

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

    This fix produces a global vector and global array which can be diff --git a/doc/html/fix_ave_time.html b/doc/html/fix_ave_time.html index 2d41fdc0dc..6c6744c5e6 100644 --- a/doc/html/fix_ave_time.html +++ b/doc/html/fix_ave_time.html @@ -140,14 +140,14 @@

  • one or more input values can be listed
  • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • -
    -c_ID = global scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = global scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-
    +
    c_ID = global scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = global scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+
    +
    • zero or more keyword/arg pairs may be appended
    • keyword = mode or file or ave or start or off or overwrite or title1 or title2 or title3
      • @@ -179,13 +179,13 @@ v_name[I] = value calculated by a vector-style variable with name

    Examples

    -
    -fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
-                              title1 "My output values"
-fix 1 all ave/time 100 5 1000 c_thermo_press[*]
-fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
-
    +
    fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
+fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
+                              title1 "My output values"
+fix 1 all ave/time 100 5 1000 c_thermo_press[*]
+fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
+
    +

    Description

    @@ -228,7 +228,7 @@ is used. All vectors must be the same length, which is the length of the vector or number of rows in the array.

    Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form “*” or “*n” or “n*” or +specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading @@ -239,11 +239,11 @@ means all indices from m to n (inclusive).

    vector or columns of the array had been listed one by one. E.g. these 2 fix ave/time commands are equivalent, since the compute rdf command creates, in this case, a global array with 3 columns, each of length 50:

    -
    -compute myRDF all rdf 50 1 2
-fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
-fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
-
    +
    compute myRDF all rdf 50 1 2
+fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
+fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
+
    +

    The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used in order to contribute to the @@ -261,7 +261,7 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc.

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If mode = scalar, then if no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of @@ -277,7 +277,7 @@ can thus be accessed by fix ave/time. Or it can be a compute defined not in your input script, but by thermodynamic output or other fixes such as fix nvt or fix temp/rescale. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and add them to LAMMPS.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If mode = scalar, then if no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the @@ -290,7 +290,7 @@ specify multiple values.

    Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.

    -

    If a value begins with “v_”, a variable name must follow which has +

    If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. If mode = scalar, then only equal-style or vector-style variables can be used, which both produce global values. In this mode, a vector-style variable requires @@ -383,8 +383,10 @@ so the title3 setting is ignored when mode = scalar.

    describes the two values that are printed at the first of each section of output. In the third line the values are replaced with the appropriate fields from the fix ave/time command.

    +
    -

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

    +
    +

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

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

    This fix produces a global scalar or global vector or global array diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html index ef0c90e2a9..9be191ab77 100644 --- a/doc/html/fix_bond_break.html +++ b/doc/html/fix_bond_break.html @@ -224,8 +224,10 @@ dramatically released when the bond is broken. More generally, you may need to thermostat your system to compensate for energy changes resulting from broken bonds (and angles, dihedrals, impropers).

    +
    -

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

    +
    +

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

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

    This fix computes two statistics which it stores in a global vector of diff --git a/doc/html/fix_bond_create.html b/doc/html/fix_bond_create.html index 8854f57578..8ab79a00a5 100644 --- a/doc/html/fix_bond_create.html +++ b/doc/html/fix_bond_create.html @@ -265,7 +265,7 @@ percolation simulation.

    1st, 2nd, and 3rd neighbors of each atom (within the bond topology of the system) for use in weighting pairwise interactions for bonded atoms. Note that adding a single bond always adds a new 1st neighbor -but may also induce *many* new 2nd and 3rd neighbors, depending on the +but may also induce many new 2nd and 3rd neighbors, depending on the molecular topology of your system. The “extra special per atom” parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3 @@ -320,8 +320,10 @@ dramatically when the bond is formed. More generally, you may need to thermostat your system to compensate for energy changes resulting from created bonds (and angles, dihedrals, impropers).

    +
    -

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

    +
    +

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

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

    This fix computes two statistics which it stores in a global vector of diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html index 367d9b091c..8ac1624b80 100644 --- a/doc/html/fix_colvars.html +++ b/doc/html/fix_colvars.html @@ -200,7 +200,9 @@ wrapped back into the simulation cell at each re-neighboring instead.

    fix that thermostats all atoms in the fix colvars group. This will be used to provide the colvars module with the current thermostat target temperature.

    -

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

    +
    +
    +

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

    This fix writes the current status of the colvars module into binary restart files. This is in addition to the text mode status file that is written by the colvars module itself and the diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html index d23425a85b..e8ad31ffb0 100644 --- a/doc/html/fix_deform.html +++ b/doc/html/fix_deform.html @@ -272,9 +272,9 @@ e.g. picoseconds for “metal” units). Tensile strain is unitless and is defined as delta/L0, where L0 is the original box length and delta is the change relative to the original length. The box length L as a function of time will change as

    -
    -L(t) = L0 (1 + erate*dt)
-
    +
    L(t) = L0 (1 + erate*dt)
+
    +

    where dt is the elapsed time (in time units). Thus if erate R is specified as 0.1 and time units are picoseconds, this means the box length will increase by 10% of its original length every picosecond. @@ -295,9 +295,9 @@ e.g. picoseconds for “metal” units). Tensile strain is unitless and is defined as delta/L0, where L0 is the original box length and delta is the change relative to the original length.

    The box length L as a function of time will change as

    -
    -L(t) = L0 exp(trate*dt)
-
    +
    L(t) = L0 exp(trate*dt)
+
    +

    where dt is the elapsed time (in time units). Thus if trate R is specified as ln(1.1) and time units are picoseconds, this means the box length will increase by 10% of its current (not original) length @@ -341,9 +341,9 @@ dimensions, so that they respond to the tensile strain dynamically.

    The wiggle style oscillates the specified box length dimension sinusoidally with the specified amplitude and period. I.e. the box length L as a function of time is given by

    -
    -L(t) = L0 + A sin(2*pi t/Tp)
-
    +
    L(t) = L0 + A sin(2*pi t/Tp)
+
    +

    where L0 is its initial length. If the amplitude A is a positive number the box initially expands, then contracts, etc. If A is negative then the box initially contracts, then expands, etc. The @@ -370,13 +370,13 @@ arbitrary variable.

    Here is an example of using the variable style to perform the same box deformation as the wiggle style formula listed above, where we assume that the current timestep = 0.

    -
    -variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 x variable v_displace v_rate remap v
-
    +
    variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 x variable v_displace v_rate remap v
+
    +

    For the scale, vel, erate, trate, volume, wiggle, and variable styles, the box length is expanded or compressed around its mid point.

    @@ -413,9 +413,9 @@ to the shear direction (e.g. y box length for xy deformation) and offset is the displacement distance in the shear direction (e.g. x direction for xy deformation) from the unstrained orientation.

    The tilt factor T as a function of time will change as

    -
    -T(t) = T0 + L0*erate*dt
-
    +
    T(t) = T0 + L0*erate*dt
+
    +

    where T0 is the initial tilt factor, L0 is the original length of the box perpendicular to the shear direction (e.g. y box length for xy deformation), and dt is the elapsed time (in time units). Thus if @@ -441,9 +441,9 @@ where length is the box length perpendicular to the shear direction distance in the shear direction (e.g. x direction for xy deformation) from the unstrained orientation.

    The tilt factor T as a function of time will change as

    -
    -T(t) = T0 exp(trate*dt)
-
    +
    T(t) = T0 exp(trate*dt)
+
    +

    where T0 is the initial tilt factor and dt is the elapsed time (in time units). Thus if trate R is specified as ln(1.1) and time units are picoseconds, this means the shear strain or tilt factor will @@ -464,9 +464,9 @@ parameter), then this effect on the shear strain is ignored.

    The wiggle style oscillates the specified tilt factor sinusoidally with the specified amplitude and period. I.e. the tilt factor T as a function of time is given by

    -
    -T(t) = T0 + A sin(2*pi t/Tp)
-
    +
    T(t) = T0 + A sin(2*pi t/Tp)
+
    +

    where T0 is its initial value. If the amplitude A is a positive number the tilt factor initially becomes more positive, then more negative, etc. If A is negative then the tilt factor initially @@ -492,13 +492,13 @@ arbitrary variable.

    Here is an example of using the variable style to perform the same box deformation as the wiggle style formula listed above, where we assume that the current timestep = 0.

    -
    -variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 xy variable v_displace v_rate remap v
-
    +
    variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 xy variable v_displace v_rate remap v
+
    +

    All of the tilt styles change the xy, xz, yz tilt factors during a simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes @@ -633,7 +633,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands.

    diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html index 566b353255..6e7e0be54f 100644 --- a/doc/html/fix_deposit.html +++ b/doc/html/fix_deposit.html @@ -355,7 +355,9 @@ count is changing due to adding particles, you typically should use the compute_modify dynamic yes command for the temperature compute you are using.

    -

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

    +
    +
    +

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

    This fix writes the state of the deposition to binary restart files. This includes information about how many particles have been depositied, the random number generator seed, the next timestep for deposition, etc. See the diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html index 5864fe2ce5..c464c735a2 100644 --- a/doc/html/fix_drag.html +++ b/doc/html/fix_drag.html @@ -156,7 +156,9 @@ include that dimension in the distance calculation or force application.

    This command can be used to steer one or more atoms to a new location in the simulation.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html index 6a078677dc..7134e2dbf5 100644 --- a/doc/html/fix_drude_transform.html +++ b/doc/html/fix_drude_transform.html @@ -219,14 +219,14 @@ Nose-Hoover thermostating fixes. The fix drude/transform/inverse command must appear after any Nose-Hoover thermostating fixes.

    Example:

    -
    -fix fDIRECT all drude/transform/direct
-fix fNVT gCORES nvt temp 300.0 300.0 100
-fix fNVT gDRUDES nvt temp 1.0 1.0 100
-fix fINVERSE all drude/transform/inverse
-compute TDRUDE all temp/drude
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
-
    +
    fix fDIRECT all drude/transform/direct
+fix fNVT gCORES nvt temp 300.0 300.0 100
+fix fNVT gDRUDES nvt temp 1.0 1.0 100
+fix fINVERSE all drude/transform/inverse
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+
    +

    In this example, gCORES is the group of the atom cores and gDRUDES is the group of the Drude particles (electrons). The centers of mass of the Drude oscillators will be thermostated at 300.0 and the @@ -240,14 +240,14 @@ the other one should be nvt. You must add a compute temp/com a that of its group (the Drude cores) but the pressure be the overall pressure thermo_press.

    Example:

    -
    -compute cTEMP_CORE gCORES temp/com
-fix fDIRECT all drude/transform/direct
-fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
-fix_modify fNPT temp cTEMP_CORE press thermo_press
-fix fNVT gDRUDES nvt temp 5.0 5.0 100
-fix fINVERSE all drude/transform/inverse
-
    +
    compute cTEMP_CORE gCORES temp/com
+fix fDIRECT all drude/transform/direct
+fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
+fix_modify fNPT temp cTEMP_CORE press thermo_press
+fix fNVT gDRUDES nvt temp 5.0 5.0 100
+fix fINVERSE all drude/transform/inverse
+
    +

    In this example, gCORES is the group of the atom cores and gDRUDES is the group of the Drude particles. The centers of mass of the Drude oscillators will be thermostated at 298.0 and the internal degrees of @@ -259,8 +259,10 @@ to add a fix momentum command:

    fix fMOMENTUM all momentum 100 linear 1 1 1
    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html index 6ddd5f9067..c724217123 100644 --- a/doc/html/fix_efield.html +++ b/doc/html/fix_efield.html @@ -148,10 +148,10 @@

    Examples

    -
    -fix kick external-field efield 1.0 0.0 0.0
-fix kick external-field efield 0.0 0.0 v_oscillate
-
    +
    fix kick external-field efield 1.0 0.0 0.0
+fix kick external-field efield 0.0 0.0 v_oscillate
+
    +

    Description

    @@ -218,8 +218,10 @@ variable formulas, i.e. that -Grad(E) = F. For example, if the force due to the electric field were a spring-like F = kx, then the energy formula should be E = -0.5kx^2. If you don’t do this correctly, the minimization will not converge properly.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify energy option is supported by this fix to add the potential “energy” inferred by the added force due to diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html index 264a4cf9ba..d2a176da50 100644 --- a/doc/html/fix_external.html +++ b/doc/html/fix_external.html @@ -167,9 +167,9 @@ in the group, once every Napply steps, similar to the way the Napply, the force values produced by one callback will persist, and be used multiple times to update atom forces.

    The callback function “foo” is invoked by the fix as:

    -
    -foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
-
    +
    foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
+
    +

    The arguments are as follows:

    • ptr = pointer provided by and simply passed back to external driver
      • @@ -194,9 +194,9 @@ array. The fix adds these forces to each atom in the group, once every Napply steps, similar to the way the       fix addforce command works.

      The name of the public force array provided by the FixExternal class is

      -
      -double **fexternal;
-
      +
      double **fexternal;
+
      +

      It is allocated by the FixExternal class as an (N,3) array where N is the number of atoms owned by a processor. The 3 corresponds to the fx, fy, fz components of force.

      @@ -212,16 +212,18 @@ to the added forces must also be set so as to be consistent with the added forces. Otherwise the minimization will not converge correctly.

      This can be done from the external driver by calling this public method of the FixExternal class:

      -
      -void set_energy(double eng);
-
      +
      void set_energy(double eng);
+
      +

      where eng is the potential energy. Eng is an extensive quantity, meaning it should be the sum over per-atom energies of all affected atoms. It should also be provided in energy units consistent with the simulation. See the details below for how to insure this energy setting is used appropriately in a minimization.

      +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify energy option is supported by this fix to add the potential “energy” set by the external driver to the diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html index 2210a5c5c4..02f1da98e6 100644 --- a/doc/html/fix_gcmc.html +++ b/doc/html/fix_gcmc.html @@ -168,11 +168,11 @@ keyword = mol, region, maxangle, pressure, <

    Examples

    -
    -fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
-fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
-
    +
    fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
+fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+
    +

    Description

    @@ -239,12 +239,12 @@ used in fix nvt. Otherwise, the imaginary reservoir will not be in thermal equilibrium with the simulation cell. Also, it is important that the temperature used by fix nvt be dynamic, which can be achieved as follows:

    -
    -compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
-fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp
-
    +
    compute mdtemp mdatoms temp
+compute_modify mdtemp dynamic yes
+fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
+fix_modify mdnvt temp mdtemp
+
    +

    Note that neighbor lists are re-built every timestep that this fix is invoked, so you should not set N to be too small. However, periodic rebuilds are necessary in order to avoid dangerous rebuilds and missed @@ -363,9 +363,9 @@ therefore, you will want to use the compute_modify command to insure that the current number of atoms is used as a normalizing factor each time temperature is computed. Here is the necessary command:

    -
    -compute_modify thermo_temp dynamic yes
-
    +
    compute_modify thermo_temp dynamic yes
+
    +

    If LJ units are used, note that a value of 0.18292026 is used by this fix as the reduced value for Planck’s constant. This value was derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 * @@ -375,7 +375,9 @@ mass = 39.948 amu.

    of the group-ID value. The grouptype keyword assigns all inserted atoms of the specified type to the group of the group-ID value.

    -

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

    +
    +
    +

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

    This fix writes the state of the fix to binary restart files. This includes information about the random number generator seed, the next timestep for MC exchanges, etc. See the read_restart command for info on how to diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html index e51ed41bf3..9f9296aea3 100644 --- a/doc/html/fix_gle.html +++ b/doc/html/fix_gle.html @@ -145,7 +145,7 @@

    noneq Cmatrix = file to read the non-equilibrium covariance matrix from every stride = apply the GLE once every time steps. Reduces the accuracy

    -
    of the integration of the GLE, but has *no effect* on the accuracy of equilibrium +
    of the integration of the GLE, but has no effect on the accuracy of equilibrium sampling. It might change sampling properties when used together with noneq.
    @@ -207,7 +207,9 @@ Prony series form of the memory kernel used by GLD into an appropriate input matrix for fix gle. While the GLE scheme is more general, the form used by fix gld can be more directly related to the representation of an implicit solvent environment.

    -

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

    +
    +
    +

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

    The instantaneous values of the extended variables are written to binary restart files. Because the state of the random number generator is not saved in restart files, this means you cannot diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html index f10e0f3416..e770f8e7fe 100644 --- a/doc/html/fix_gravity.html +++ b/doc/html/fix_gravity.html @@ -156,13 +156,13 @@

    Examples

    -
    -fix 1 all gravity 1.0 chute 24.0
-fix 1 all gravity v_increase chute 24.0
-fix 1 all gravity 1.0 spherical 0.0 -180.0
-fix 1 all gravity 10.0 spherical v_phi v_theta
-fix 1 all gravity 100.0 vector 1 1 0
-
    +
    fix 1 all gravity 1.0 chute 24.0
+fix 1 all gravity v_increase chute 24.0
+fix 1 all gravity 1.0 spherical 0.0 -180.0
+fix 1 all gravity 10.0 spherical v_phi v_theta
+fix 1 all gravity 100.0 vector 1 1 0
+
    +

    Description

    @@ -220,8 +220,10 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify energy option is supported by this fix to add the gravitational potential energy of the system to the diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html index 2e88845d31..fb5b0f55e7 100644 --- a/doc/html/fix_heat.html +++ b/doc/html/fix_heat.html @@ -147,11 +147,11 @@

    Examples

    -
    -fix 3 qin heat 1 1.0
-fix 3 qin heat 10 v_flux
-fix 4 qout heat 1 -1.0 region top
-
    +
    fix 3 qin heat 1 1.0
+fix 3 qin heat 10 v_flux
+fix 4 qout heat 1 -1.0 region top
+
    +

    Description

    @@ -219,7 +219,9 @@ their velocities. Thus you must still use an integration fix (e.g. fix nve) on the affected atoms. This fix should not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin fix.

    -

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

    +
    +
    +

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

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

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_imd.html b/doc/html/fix_imd.html index 3245c8523d..5c92083e88 100644 --- a/doc/html/fix_imd.html +++ b/doc/html/fix_imd.html @@ -237,7 +237,9 @@ they were real objects. See the +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html index 40917601b7..615515d668 100644 --- a/doc/html/fix_ipi.html +++ b/doc/html/fix_ipi.html @@ -173,7 +173,9 @@ configurations make sense. It is assumed that the species in the i-PI input are listed in the same order as in the data file of LAMMPS. The initial configuration is ignored, as it will be substituted with the coordinates received from i-PI before forces are ever evaluated.

    -

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

    +
    +
    +

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

    There is no restart information associated with this fix, since all the dynamical parameters are dealt with by i-PI.

    diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html index bf67a0e983..40cfbcd9cc 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -375,8 +375,10 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. Because the state of the random number generator is not saved in restart files, this means you cannot do “exact” restarts with this fix, where the simulation continues on the same as diff --git a/doc/html/fix_langevin_eff.html b/doc/html/fix_langevin_eff.html index dea014ff7b..506e61e35c 100644 --- a/doc/html/fix_langevin_eff.html +++ b/doc/html/fix_langevin_eff.html @@ -178,7 +178,9 @@ interactions ( command, except that the thermostatting is also applied to the radial electron velocity for electron particles.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. Because the state of the random number generator is not saved in restart files, this means you cannot do “exact” restarts with this fix, where the simulation continues on the same as diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html index 5ca4e990b6..aefe19517d 100644 --- a/doc/html/fix_lb_momentum.html +++ b/doc/html/fix_lb_momentum.html @@ -167,7 +167,9 @@ and the fluid velocities at each lattice site.

    be changed by specifying the keyword linear, along with a set of three flags set to 0/1 in order to exclude/ include the corresponding dimension.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html index 8d27f6cd24..8a5281c6c3 100644 --- a/doc/html/fix_lb_pc.html +++ b/doc/html/fix_lb_pc.html @@ -149,7 +149,9 @@ described by group-ID, experiencing velocity-dependent hydrodynamic forces, using the integration algorithm described in Mackay et al.. This integration algorithm should only be used if a user-specified value for the force-coupling constant used in fix lb/fluid has been set; do not use this integration algorithm if the force coupling constant has been set by default.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html index 8bda0b4a82..ca3adc0748 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -202,7 +202,9 @@ central atoms interact with one another.

    the rigid fix (although it includes fewer optional arguments, and assumes the constituent atoms are point particles); see fix rigid for a complete documentation.

    -

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

    +
    +
    +

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

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

    Similar to the fix rigid command: The rigid diff --git a/doc/html/fix_lb_viscous.html b/doc/html/fix_lb_viscous.html index 876c9eb1f0..efc00565c9 100644 --- a/doc/html/fix_lb_viscous.html +++ b/doc/html/fix_lb_viscous.html @@ -164,8 +164,10 @@ hydrodynamic forces to the particles.

    test runs, see Mackay et al.. Please include a citation to this paper if this fix is used in work contributing to published research.

    +
    -

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

    +
    +

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

    As described in the fix viscous documentation:

    “No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/html/fix_lineforce.html b/doc/html/fix_lineforce.html index 2734d0ff4e..5ca8460a42 100644 --- a/doc/html/fix_lineforce.html +++ b/doc/html/fix_lineforce.html @@ -151,7 +151,9 @@ remains. This is done by subtracting out components of force in the plane perpendicular to the line.

    If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html index ad7177b2bd..66cf61d80e 100644 --- a/doc/html/fix_move.html +++ b/doc/html/fix_move.html @@ -160,11 +160,11 @@

    Examples

    -
    -fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
-fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
-fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
-
    +
    fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+
    +

    Description

    @@ -202,9 +202,9 @@ command.

    The linear style moves atoms at a constant velocity, so that their position X = (x,y,z) as a function of time is given in vector notation as

    -
    -X(t) = X0 + V * delta
-
    +
    X(t) = X0 + V * delta
+
    +

    where X0 = (x0,y0,z0) is their position at the time the fix is specified, V is the specified velocity vector with components (Vx,Vy,Vz), and delta is the time elapsed since the fix was @@ -216,17 +216,17 @@ the corresponding force component on the atom.

    Note that the linear style is identical to using the variable style with an equal-style variable that uses the vdisplace() function. E.g.

    -
    -variable V equal 10.0
+
    variable V equal 10.0
 variable x equal vdisplace(0.0,$V)
 fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
-
    
+
    +

    The wiggle style moves atoms in an oscillatory fashion, so that their position X = (x,y,z) as a function of time is given in vector notation as

    -
    -X(t) = X0 + A sin(omega*delta)
-
    +
    X(t) = X0 + A sin(omega*delta)
+
    +

    where X0 = (x0,y0,z0) is their position at the time the fix is specified, A is the specified amplitude vector with components (Ax,Ay,Az), omega is 2 PI / period, and delta is the time @@ -239,14 +239,14 @@ corresponding force component on the atom.

    Note that the wiggle style is identical to using the variable style with equal-style variables that use the swiggle() and cwiggle() functions. E.g.

    -
    -variable A equal 10.0
+
    variable A equal 10.0
 variable T equal 5.0
 variable omega equal 2.0*PI/$T
 variable x equal swiggle(0.0,$A,$T)
 variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
-
    
+
    +

    The rotate style rotates atoms around a rotation axis R = (Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The period of the rotation is also specified. The direction of rotation for the @@ -302,8 +302,10 @@ are in lattice spacings. The been previously used to define the lattice spacing. Each of these 3 quantities may be dependent on the x,y,z dimension, since the lattice spacings can be different in x,y,z.

    +
    -

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

    +
    +

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

    This fix writes the original coordinates of moving atoms to binary restart files, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_msst.html b/doc/html/fix_msst.html index c54106e01e..f5a8d09ba8 100644 --- a/doc/html/fix_msst.html +++ b/doc/html/fix_msst.html @@ -197,14 +197,16 @@ LAMMPS, but are not implemented for MSST.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
    +
    compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+
    +

    See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”. The group for the new computes is “all”.

    -

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

    +
    +
    +

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

    This fix writes the state of all internal variables to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an @@ -228,15 +230,15 @@ equations. See also

    To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested:

    -
    -fix           msst all msst z
-fix_modify       msst energy yes
-variable dhug    equal f_msst[1]
-variable dray    equal f_msst[2]
-variable lgr_vel equal f_msst[3]
-variable lgr_pos equal f_msst[4]
-thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
-
    +
    fix           msst all msst z
+fix_modify       msst energy yes
+variable dhug    equal f_msst[1]
+variable dray    equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+
    +

    These fixes compute a global scalar and a global vector of 4 quantities, which can be accessed by various output commands. The scalar values calculated by this fix are “extensive”; the vector values are “intensive”.

    diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html index 1e50f393e0..4b5777e1e2 100644 --- a/doc/html/fix_neb.html +++ b/doc/html/fix_neb.html @@ -190,7 +190,9 @@ forces on atoms in this replica are described in the

    The inter-replica forces for the other replicas are unchanged from the first equation.

    -

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

    + +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html index d11bbb105e..5e8d66853c 100644 --- a/doc/html/fix_nh_eff.html +++ b/doc/html/fix_nh_eff.html @@ -134,9 +134,9 @@

    fix nph/eff command

    Syntax

    -
    -fix ID group-ID style_name keyword value ...
-
    +
    fix ID group-ID style_name keyword value ...
+
    +
    -

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

    +
    +
    +

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

    See the doc page for the fix nvt, npt, and nph commands for details.

    diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html index 2c2d1a4d0a..d7c91846db 100644 --- a/doc/html/fix_nph_asphere.html +++ b/doc/html/fix_nph_asphere.html @@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/asphere” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-
    +
    compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+
    +

    See the compute temp/asphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -207,7 +207,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    + +
    +

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

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html index ec7a15a0cd..0529dba9db 100644 --- a/doc/html/fix_nph_sphere.html +++ b/doc/html/fix_nph_sphere.html @@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/sphere” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-
    +
    compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+
    +

    See the compute temp/sphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -207,7 +207,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html index 2216a34678..203bb248e0 100644 --- a/doc/html/fix_npt_asphere.html +++ b/doc/html/fix_npt_asphere.html @@ -182,10 +182,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/asphere” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-
    +
    compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+
    +

    See the compute temp/asphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -227,7 +227,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html index b037898463..7a21169513 100644 --- a/doc/html/fix_npt_body.html +++ b/doc/html/fix_npt_body.html @@ -179,10 +179,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/body” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp all temp/body
-compute fix-ID_press all pressure fix-ID_temp
-
    +
    compute fix-ID_temp all temp/body
+compute fix-ID_press all pressure fix-ID_temp
+
    +

    See the compute temp/body and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -224,7 +224,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html index f05e786221..1d5d6ed867 100644 --- a/doc/html/fix_npt_sphere.html +++ b/doc/html/fix_npt_sphere.html @@ -181,10 +181,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/sphere” and “pressure”, as if these commands had been issued:

    -
    -compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-
    +
    compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+
    +

    See the compute temp/sphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -226,7 +226,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html index 88dbabd521..435fea89b4 100644 --- a/doc/html/fix_nve_asphere.html +++ b/doc/html/fix_nve_asphere.html @@ -153,7 +153,9 @@ group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_asphere_noforce.html b/doc/html/fix_nve_asphere_noforce.html index dd98e2ce40..75760b0c6a 100644 --- a/doc/html/fix_nve_asphere_noforce.html +++ b/doc/html/fix_nve_asphere_noforce.html @@ -150,8 +150,10 @@ angularm 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 pair_style lubricuteU command.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html index 45816df757..cd459a4379 100644 --- a/doc/html/fix_nve_body.html +++ b/doc/html/fix_nve_body.html @@ -151,7 +151,9 @@ consistent with the microcanonical ensemble. See

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html index 5b6a9bb8ab..5168b08db0 100644 --- a/doc/html/fix_nve_line.html +++ b/doc/html/fix_nve_line.html @@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See using line segment particles.

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html index 149e6de046..06d68cd6ae 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -159,7 +159,7 @@ keyword = every atoms constrained to a curved surface (manifold) in the group each timestep. The constraint is handled by RATTLE (Andersen) written out for the special case of single-particle constraints as -explained in (Paquay). V is volume; E is energy. This way, +explained in (Paquay). V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with fix langevin, this generates Brownian motion of particles constrained to a curved @@ -172,18 +172,20 @@ manifolds this can be achieved with region and create_atoms commands, but for more complex surfaces it might be more useful to write a script.

    The manifold args may be equal-style variables, like so:

    -
    -variable R equal "ramp(5.0,3.0)"
-fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
-
    +
    variable R equal "ramp(5.0,3.0)"
+fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
+
    +

    In this case, the manifold parameter will change in time according to the variable. This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles. Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html index 2a70998598..e0e8bf5189 100644 --- a/doc/html/fix_nve_sphere.html +++ b/doc/html/fix_nve_sphere.html @@ -189,8 +189,10 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html index 1462555ef2..e707401c30 100644 --- a/doc/html/fix_nve_tri.html +++ b/doc/html/fix_nve_tri.html @@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See using triangular particles.

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html index 473db13d7f..08a1bea12b 100644 --- a/doc/html/fix_nvt_asphere.html +++ b/doc/html/fix_nvt_asphere.html @@ -169,9 +169,9 @@ keywords.

    This fix computes a temperature each timestep. To do this, the fix creates its own compute of style “temp/asphere”, as if this command had been issued:

    -
    -compute fix-ID_temp group-ID temp/asphere
-
    +
    compute fix-ID_temp group-ID temp/asphere
+
    +

    See the compute temp/asphere command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as @@ -213,7 +213,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html index 57ba66659d..9fecb55fc4 100644 --- a/doc/html/fix_nvt_body.html +++ b/doc/html/fix_nvt_body.html @@ -166,9 +166,9 @@ keywords.

    This fix computes a temperature each timestep. To do this, the fix creates its own compute of style “temp/body”, as if this command had been issued:

    -
    -compute fix-ID_temp group-ID temp/body
-
    +
    compute fix-ID_temp group-ID temp/body
+
    +

    See the compute temp/body command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as @@ -210,7 +210,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html index 09875bceb8..a2592ab7e7 100644 --- a/doc/html/fix_nvt_sllod.html +++ b/doc/html/fix_nvt_sllod.html @@ -194,9 +194,9 @@ keywords.

    This fix computes a temperature each timestep. To do this, the fix creates its own compute of style “temp/deform”, as if this command had been issued:

    -
    -compute fix-ID_temp group-ID temp/deform
-
    +
    compute fix-ID_temp group-ID temp/deform
+
    +

    See the compute temp/deform command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as @@ -238,7 +238,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nvt_sllod_eff.html b/doc/html/fix_nvt_sllod_eff.html index c175a68bdc..8492983e42 100644 --- a/doc/html/fix_nvt_sllod_eff.html +++ b/doc/html/fix_nvt_sllod_eff.html @@ -157,7 +157,9 @@ creates (as discussed in the compute temp/deform/eff commmand that includes the eFF contribution to the temperature from the electron radial velocity.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html index 6a27b967ed..fc5b3ddab1 100644 --- a/doc/html/fix_nvt_sphere.html +++ b/doc/html/fix_nvt_sphere.html @@ -169,9 +169,9 @@ keywords.

    This fix computes a temperature each timestep. To do this, the fix creates its own compute of style “temp/sphere”, as if this command had been issued:

    -
    -compute fix-ID_temp group-ID temp/sphere
-
    +
    compute fix-ID_temp group-ID temp/sphere
+
    +

    See the compute temp/sphere command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as @@ -213,7 +213,9 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    -

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

    +
    +
    +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html index 3094e830ae..40d369afee 100644 --- a/doc/html/fix_phonon.html +++ b/doc/html/fix_phonon.html @@ -128,9 +128,9 @@

    fix phonon command

    Syntax

    -
    -fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
-
    +
    fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
+
    +
    • ID, group-ID are documented in fix command
    • phonon = style name of this fix command
      • @@ -239,7 +239,9 @@ even degrade the performance of lammps in case the unit cell is too large.

      energy/distance^2/mass units. The coordinates for q points in the log file is in the units of the basis vectors of the corresponding reciprocal lattice.

      -

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

      +
    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify temp option is supported by this fix. You can use it to change the temperature compute from thermo_temp diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html index ee3f050be4..ca471ec2c3 100644 --- a/doc/html/fix_pour.html +++ b/doc/html/fix_pour.html @@ -316,8 +316,10 @@ can prevent particles from being inserted. The ignore keyword causes the overlap check to skip any line or triangle particles. Obviously you should only use it if there is in fact no overlap of the line or triangle particles with the insertion region.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. This means you must be careful when restarting a pouring simulation, when the restart file was written in the middle of the pouring operation. Specifically, you should use a new fix pour diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html index 05e428f671..addd4b9ecf 100644 --- a/doc/html/fix_qeq.html +++ b/doc/html/fix_qeq.html @@ -162,13 +162,13 @@

    Examples

    -
    -fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
-fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
-fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
-fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
-fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
-
    +
    fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
+fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
+fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
+
    +

    Description

    @@ -292,7 +292,9 @@ 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.

    -

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

    +
    +
    +

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

    No information about these fixes is written to binary restart files. No global scalar or vector or per-atom quantities are stored by these fixes for access by various output commands. No parameter of these fixes can be used with the start/stop keywords of the run diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html index 3bf7a12a5c..c7382d021d 100644 --- a/doc/html/fix_qeq_comb.html +++ b/doc/html/fix_qeq_comb.html @@ -195,8 +195,10 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html index 665de2e845..cc02c2516a 100644 --- a/doc/html/fix_qeq_reax.html +++ b/doc/html/fix_qeq_reax.html @@ -180,7 +180,9 @@ exponent. Note that these 3 quantities are also in the ReaxFF potential file, except that eta is defined here as twice the eta value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units of this fix are hard-coded to be A, eV, and electronic charge.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command.

    diff --git a/doc/html/fix_qmmm.html b/doc/html/fix_qmmm.html index fa8cf47576..1adbcf6567 100644 --- a/doc/html/fix_qmmm.html +++ b/doc/html/fix_qmmm.html @@ -156,7 +156,9 @@ other QM codes. This will allow the LAMMPS side of the implementation to be adapted if necessary before being finalized.

    Details about how to use this fix are currently documented in the description of the QM/MM interface code itself in lib/qmmm/README.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html index cffd9b2764..2f8934ddd0 100644 --- a/doc/html/fix_qtb.html +++ b/doc/html/fix_qtb.html @@ -147,12 +147,12 @@

    Examples

    -
    -fix 1 all nve
-fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
-fix 2 all nph iso 1.01325 1.01325 1
-fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
-
    +
    fix 1 all nve
+fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+fix 2 all nph iso 1.01325 1.01325 1
+fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+
    +

    Description

    @@ -219,7 +219,7 @@ runs on different numbers of processors.

    vibrational modes with frequencies higher than f_max will not be modulated. If we denote &Delta;<i>t</i> as the time interval for the MD integration, f_max is always reset by the code to make -<i>&alpha;</i> = (int)(2*f_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a +<i>&alpha;</i> = (int)(2f_max&Delta;<i>t</i>)<sup><i>-1</i></sup> a positive integer and print out relative information. An appropriate value for the cutoff frequency f_max would be around 2~3 <i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html index e8c6d12136..0275b0ad0e 100644 --- a/doc/html/fix_reax_bonds.html +++ b/doc/html/fix_reax_bonds.html @@ -157,8 +157,10 @@ 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 command.

    The format of the output file should be self-explantory.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_reaxc_species.html b/doc/html/fix_reaxc_species.html index fb72dd69c4..d4f4f182bd 100644 --- a/doc/html/fix_reaxc_species.html +++ b/doc/html/fix_reaxc_species.html @@ -215,8 +215,10 @@ i.e. Nrepeat*Nevery can not exceed Nfreq.

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on timesteps 90,92,94,96,98,100 will be used to compute the average bond-order for the species analysis output on timestep 100.

    +
    -

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

    +
    +

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

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

    This fix computes both a global vector of length 2 and a per-atom diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html index 08de66a8eb..29f7570dc9 100644 --- a/doc/html/fix_saed_vtk.html +++ b/doc/html/fix_saed_vtk.html @@ -128,9 +128,9 @@

    fix saed/vtk command

    Syntax

    -
    -fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
-
    +
    fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
+
    +
    • ID, group-ID are documented in fix command
    • saed/vtk = style name of this fix command
      • @@ -154,14 +154,14 @@ keyword = file or ave or start or file or

      Examples

      -
      -compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
-
      -
      -fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed
-
      +
      compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+
      +
      +
      fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+
      +

      Description

      @@ -182,10 +182,10 @@ specified values may represent calculations performed by saed computes which store their own “group” definitions.

      Fix saed/vtk is designed to work only with compute saed values, e.g.

      -
      -compute 3 top saed 0.0251 Al O
-fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
-
      +
      compute 3 top saed 0.0251 Al O
+fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
+
      +

      The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used in order to contribute to the @@ -209,19 +209,19 @@ vtk image data formatting. The filename assigned by the file keyword i appended with _N.vtk where N is an index (0,1,2...) to account for multiple diffraction intensity outputs.

      By default the header contains the following information (with example data):

      -
      -# vtk DataFile Version 3.0 c_SAED
-Image data set
-ASCII
-DATASET STRUCTURED_POINTS
-DIMENSIONS 337 219 209
-ASPECT_RATIO 0.00507953 0.00785161 0.00821458
-ORIGIN -0.853361 -0.855826 -0.854316
-POINT_DATA 15424827
-SCALARS intensity float
-LOOKUP_TABLE default
-...data
-
      +
      # vtk DataFile Version 3.0 c_SAED
+Image data set
+ASCII
+DATASET STRUCTURED_POINTS
+DIMENSIONS 337 219 209
+ASPECT_RATIO 0.00507953 0.00785161 0.00821458
+ORIGIN -0.853361 -0.855826 -0.854316
+POINT_DATA 15424827
+SCALARS intensity float
+LOOKUP_TABLE default
+...data
+
      +

      In this example, kspace is sampled across a 337 x 219 x 209 point mesh where the mesh spacing is approximately 0.005, 0.007, and 0.008 inv(length) units in the k1, k2, and k3 directions, respectively. @@ -264,7 +264,9 @@ intensity outputs.

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

      -

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

      +
      +
      +

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

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

      No parameter of this fix can be used with the start/stop keywords of diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html index 0c2d9bc519..5be23f5d7b 100644 --- a/doc/html/fix_smd.html +++ b/doc/html/fix_smd.html @@ -212,7 +212,9 @@ over the pulling force in direction of the spring is recorded and can then later be used to compute the potential of mean force (PMF) by averaging over multiple independent trajectories along the same pulling path.

      -

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

      +
      +
      +

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

      The fix stores the direction of the spring, current pulling target distance and the running PMF to binary restart files. See the read_restart command for info on how to diff --git a/doc/html/fix_smd_adjust_dt.html b/doc/html/fix_smd_adjust_dt.html index 734c433f36..ebf49b94ca 100644 --- a/doc/html/fix_smd_adjust_dt.html +++ b/doc/html/fix_smd_adjust_dt.html @@ -128,9 +128,9 @@

      fix smd/adjust_dt command

      Syntax

      -
      -fix ID group-ID smd/adjust_dt arg
-
      +
      fix ID group-ID smd/adjust_dt arg
+
      +
      • ID, group-ID are documented in fix command
      • smd/adjust_dt = style name of this fix command
        • @@ -142,9 +142,9 @@ fix ID group-ID smd/adjust_dt arg

      Examples

      -
      -fix 1 all smd/adjust_dt 0.1
-
      +
      fix 1 all smd/adjust_dt 0.1
+
      +

      Description

      @@ -157,7 +157,9 @@ stable maximum time step.

      This fix inquires the minimum stable time increment across all particles contained in the group for which this fix is defined. An additional safety factor s_fact is applied to the time increment.

      See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

      -

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

      +
      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization.

      diff --git a/doc/html/fix_smd_integrate_tlsph.html b/doc/html/fix_smd_integrate_tlsph.html index 04c9db062a..194f99be37 100644 --- a/doc/html/fix_smd_integrate_tlsph.html +++ b/doc/html/fix_smd_integrate_tlsph.html @@ -128,9 +128,9 @@

      fix smd/integrate_tlsph command

      Syntax

      -
      -fix ID group-ID smd/integrate_tlsph keyword values
-
      +
      fix ID group-ID smd/integrate_tlsph keyword values
+
      +
      • ID, group-ID are documented in fix command
      • smd/integrate_tlsph = style name of this fix command
        • @@ -144,10 +144,10 @@ fix ID group-ID smd/integrate_tlsph keyword values

      Examples

      -
      -fix 1 all smd/integrate_tlsph
-fix 1 all smd/integrate_tlsph limit_velocity 1000
-
      +
      fix 1 all smd/integrate_tlsph
+fix 1 all smd/integrate_tlsph limit_velocity 1000
+
      +

      Description

      @@ -155,7 +155,9 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000

      See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

      The limit_velocity keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit.

      -

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

      +
      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

      diff --git a/doc/html/fix_smd_integrate_ulsph.html b/doc/html/fix_smd_integrate_ulsph.html index 58bd9fda2c..e45d7d3f31 100644 --- a/doc/html/fix_smd_integrate_ulsph.html +++ b/doc/html/fix_smd_integrate_ulsph.html @@ -128,9 +128,9 @@

      fix smd/integrate_ulsph command

      Syntax

      -
      -fix ID group-ID smd/integrate_ulsph keyword
-
      +
      fix ID group-ID smd/integrate_ulsph keyword
+
      +
      • ID, group-ID are documented in fix command
      • smd/integrate_ulsph = style name of this fix command
        • @@ -148,12 +148,12 @@ max_nn = maximum number of neighbors

      Examples

      -
      -fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
-
      -
      -fix 1 all smd/integrate_ulsph limit_velocity 1000
-
      +
      fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+
      +
      +
      fix 1 all smd/integrate_ulsph limit_velocity 1000
+
      +

      Description

      @@ -161,10 +161,12 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

      The adjust_radius keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains within the interval min_nn to max_nn. The parameter adjust_radius_factor determines the amount of adjustment per timestep. Typical values are -*adjust_radius_factor*=1.02, *min_nn*=15, and *max_nn*=20.

      +adjust_radius_factor=1.02, min_nn=15, and max_nn=20.

      The limit_velocity keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit.

      -

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

      +
      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

      diff --git a/doc/html/fix_smd_move_triangulated_surface.html b/doc/html/fix_smd_move_triangulated_surface.html index e3c04397e7..689017806f 100644 --- a/doc/html/fix_smd_move_triangulated_surface.html +++ b/doc/html/fix_smd_move_triangulated_surface.html @@ -128,53 +128,55 @@

      fix smd/move_tri_surf command

      Syntax

      -
      -fix ID group-ID smd/move_tri_surf keyword
-
      +
      fix ID group-ID smd/move_tri_surf keyword
+
      +
      • ID, group-ID are documented in fix command
      • smd/move_tri_surf keyword = style name of this fix command
        • -
      • keyword = *LINEAR or *WIGGLE or *ROTATE
        • +
      • keyword = **LINEAR* or **WIGGLE* or **ROTATE*
      -
      -*LINEAR args = Vx Vy Vz
-   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-*WIGGLE args = Vx Vy Vz max_travel
-   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
-   max_travel = wiggle amplitude
-*ROTATE args = Px Py Pz Rx Ry Rz period
-   Px,Py,Pz = origin point of axis of rotation (distance units)
-   Rx,Ry,Rz = axis of rotation vector
-   period = period of rotation (time units)
-
      +
      **LINEAR* args = Vx Vy Vz
+   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+**WIGGLE* args = Vx Vy Vz max_travel
+   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+   max_travel = wiggle amplitude
+**ROTATE* args = Px Py Pz Rx Ry Rz period
+   Px,Py,Pz = origin point of axis of rotation (distance units)
+   Rx,Ry,Rz = axis of rotation vector
+   period = period of rotation (time units)
+
      +

      Examples

      -
      -fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
-fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
-fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
-
      +
      fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
+fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
+fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
+
      +

      Description

      This fix applies only to rigid surfaces read from .STL files via fix smd/wall_surface . It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. The rigid surfaces can thus be moved along simple trajectories during the simulation.

      -

      The *LINEAR style moves particles with the specified constant velocity +

      The **LINEAR* style moves particles with the specified constant velocity vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle to V = (Vx,Vy,Vz).

      -

      The *WIGGLE style moves particles in an oscillatory fashion. +

      The **WIGGLE* style moves particles in an oscillatory fashion. Particles are moved along (vx, vy, vz) with constant velocity until a displacement of max_travel is reached. Then, the velocity vector is reversed. This process is repeated.

      -

      The *ROTATE style rotates particles around a rotation axis R = (Rx,Ry,Rz) that +

      The **ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the rotation is also specified. This style also sets the velocity of each particle 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 particle.

      See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

      -

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

      +
      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

      diff --git a/doc/html/fix_smd_setvel.html b/doc/html/fix_smd_setvel.html index 16fc5abc50..cb8449f1c0 100644 --- a/doc/html/fix_smd_setvel.html +++ b/doc/html/fix_smd_setvel.html @@ -146,9 +146,9 @@

      Examples

      -
      -fix top_velocity top_group setvel 1.0 0.0 0.0
-
      +
      fix top_velocity top_group setvel 1.0 0.0 0.0
+
      +

      Description

      @@ -174,8 +174,10 @@ coordinates. Thus it is easy to specify a spatially-dependent velocity field with optional time-dependence as well.

      If the region keyword is used, the particle must also be in the specified geometric region in order to have its velocity set by this command.

      +
      -

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

      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization None of the fix_modify options are relevant to this fix.

      diff --git a/doc/html/fix_smd_wall_surface.html b/doc/html/fix_smd_wall_surface.html index f51d51f6a6..92d197d542 100644 --- a/doc/html/fix_smd_wall_surface.html +++ b/doc/html/fix_smd_wall_surface.html @@ -128,9 +128,9 @@

      fix smd/wall_surface command

      Syntax

      -
      -fix ID group-ID smd/wall_surface arg type mol-ID
-
      +
      fix ID group-ID smd/wall_surface arg type mol-ID
+
      +
      • ID, group-ID are documented in fix command
      • smd/wall_surface = style name of this fix command
        • @@ -146,9 +146,9 @@ fix ID group-ID smd/wall_surface arg type mol-ID

      Examples

      -
      -fix stl_surf all smd/wall_surface tool.stl 2 65535
-
      +
      fix stl_surf all smd/wall_surface tool.stl 2 65535
+
      +

      Description

      @@ -160,7 +160,9 @@ It is possible to move the triangulated surface via the this PDF guide to use Smooth Mach Dynamics in LAMMPS.

      -

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

      +
      +
      +

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

      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

      diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html index 413066a788..a1d40fbf68 100644 --- a/doc/html/fix_spring.html +++ b/doc/html/fix_spring.html @@ -215,7 +215,9 @@ spring command, if the rigid body will cross a periodic boundary. This is because image flags for rigid bodies are used in a different way, as explained on the fix rigid doc page.

      -

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

      +
      +
      +

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

      No information about this fix is written to binary restart files.

      The fix_modify energy option is supported by this fix to add the energy stored in the spring to the system’s potential diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html index 5ea20d8a43..7373fd8e56 100644 --- a/doc/html/fix_spring_chunk.html +++ b/doc/html/fix_spring_chunk.html @@ -166,7 +166,9 @@ the mass of the atom, and Mm is the total mass of all atoms in the chunk. Note that K thus represents the spring constant for the total force on each chunk of atoms, not for a spring applied to each atom.

      -

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

      +
      +
      +

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

      No information about this fix is written to binary restart files.

      The fix_modify energy option is supported by this fix to add the energy stored in all the springs to the system’s potential diff --git a/doc/html/fix_spring_self.html b/doc/html/fix_spring_self.html index 28e33fc5ed..dbc542e600 100644 --- a/doc/html/fix_spring_self.html +++ b/doc/html/fix_spring_self.html @@ -160,7 +160,9 @@ spring force is applied. By default, the restraint is applied in all directions, but it can be limited to the xy-, xz-, yz-plane and the x-, y-, or z-direction, thus restraining the atoms to a line or a plane, respectively.

      -

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

      +
      +
      +

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

      This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the same in a restarted simulation. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html index 0a885ed683..9d236aa13f 100644 --- a/doc/html/fix_store_state.html +++ b/doc/html/fix_store_state.html @@ -137,43 +137,43 @@

    • N = store atom attributes every N steps, N = 0 for initial store only
    • input = one or more atom attributes
    -
    -possible attributes = id, mol, type, mass,
-                   x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
-                   vx, vy, vz, fx, fy, fz,
-                      q, mux, muy, muz, mu,
-                      radius, diameter, omegax, omegay, omegaz,
-                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
-                      d_name, i_name
-
    -
    -id = atom ID
-mol = molecule ID
-type = atom type
-mass = atom mass
-x,y,z = unscaled atom coordinates
-xs,ys,zs = scaled atom coordinates
-xu,yu,zu = unwrapped atom coordinates
-xsu,ysu,zsu = scaled unwrapped atom coordinates
-ix,iy,iz = box image that the atom is in
-vx,vy,vz = atom velocities
-fx,fy,fz = forces on atoms
-q = atom charge
-mux,muy,muz = orientation of dipolar atom
-mu = magnitued of dipole moment of atom
-radius,diameter = radius.diameter of spherical particle
-omegax,omegay,omegaz = angular velocity of spherical particle
-angmomx,angmomy,angmomz = angular momentum of aspherical particle
-tqx,tqy,tqz = torque on finite-size particles
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-v_name = per-atom vector calculated by an atom-style variable with name
-d_name = per-atom floating point vector name, managed by fix property/atom
-i_name = per-atom integer vector name, managed by fix property/atom
-
    +
    possible attributes = id, mol, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+                      d_name, i_name
+
    +
    +
    id = atom ID
+mol = molecule ID
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+xsu,ysu,zsu = scaled unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipolar atom
+mu = magnitued of dipole moment of atom
+radius,diameter = radius.diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector name, managed by fix property/atom
+i_name = per-atom integer vector name, managed by fix property/atom
+
    +
    • zero or more keyword/value pairs may be appended
    • keyword = com
      • @@ -217,7 +217,9 @@ of the group of atoms, instead of storing the absolute position.

      The requested values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group.

      -

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

      +
    +
    +

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

    This fix writes the per-atom values it stores to binary restart files, so that the values can be restored when a simulation is restarted. See the read_restart command for info on how to re-specify a fix in an input script that diff --git a/doc/html/fix_temp_rescale_eff.html b/doc/html/fix_temp_rescale_eff.html index 4a5b09b42a..826fcfb6f4 100644 --- a/doc/html/fix_temp_rescale_eff.html +++ b/doc/html/fix_temp_rescale_eff.html @@ -154,7 +154,9 @@ their velocities.

    The operation of this fix is exactly like that described by the fix temp/rescale command, except that the rescaling is also applied to the radial electron velocity for electron particles.

    -

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

    +
    +
    +

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

    No information about this fix is written to binary restart files.

    The fix_modify temp option is supported by this fix. You can use it to assign a temperature compute diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html index 32b9de3cbb..1fa84393e7 100644 --- a/doc/html/fix_tfmc.html +++ b/doc/html/fix_tfmc.html @@ -228,8 +228,10 @@ translations or rotations of the fix group could be induced by these external forces, and removing them will lead to a violation of detailed balance.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files.

    None of the fix_modify options are relevant to this fix.

    diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html index 05f63ab2de..97325bd91e 100644 --- a/doc/html/fix_thermal_conductivity.html +++ b/doc/html/fix_thermal_conductivity.html @@ -180,12 +180,12 @@ of the 2 atoms is performed, to conserve kinetic energy. Over time, this induces a temperature gradient in the system which can be measured using commands such as the following, which writes the temperature profile (assuming z = edim) to the file tmp.profile:

    -
    -compute   ke all ke/atom
-variable  temp atom c_ke/1.5
-compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
-fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
-
    +
    compute   ke all ke/atom
+variable  temp atom c_ke/1.5
+compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
+
    +

    Note that by default, Nswap = 1, though this can be changed by the optional swap keyword. Setting this parameter appropriately, in conjunction with the swap rate N, allows the heat flux to be adjusted @@ -221,7 +221,9 @@ not in a regime of linear response. In this case you cannot accurately infer a thermal conductivity and should try increasing the Nevery parameter.

    -

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

    + +
    +

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

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

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html index 16fa977a8f..03773104e4 100644 --- a/doc/html/fix_viscosity.html +++ b/doc/html/fix_viscosity.html @@ -226,7 +226,9 @@ deform the simmulation box via the PPPM solver since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; thus it does not suffer from this limitation.

    -

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

    +
    +
    +

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

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

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html index e63286eaeb..5bf3e54e0a 100644 --- a/doc/html/fix_viscous.html +++ b/doc/html/fix_viscous.html @@ -194,8 +194,10 @@ performing the same operation as fix viscous. Also note that the gamma of fix viscous is related to the damping parameter of fix langevin, however the former is specified in units of force/velocity and the latter in units of time, so that it can more easily be used as a thermostat.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html index b6360f4ffb..08178f888a 100644 --- a/doc/html/fix_wall_gran.html +++ b/doc/html/fix_wall_gran.html @@ -128,9 +128,9 @@

    fix wall/gran command

    Syntax

    -
    -fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
-
    +
    fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
+
    +
    • ID, group-ID are documented in fix command
    • wall/gran = style name of this fix command
      • @@ -241,9 +241,9 @@ is perpendicular to the wall, it is more of a shaking motion. A zcylinder wall can only be wiggled in the z dimension.

      Each timestep, the position of a wiggled wall in the appropriate dim is set according to this equation:

      -
      -position = coord + A - A cos (omega * delta)
-
      +
      position = coord + A - A cos (omega * delta)
+
      +

      where coord is the specified initial position of the wall, A is the amplitude, omega is 2 PI / period, and delta is the time elapsed since the fix was specified. The velocity of the wall is set @@ -257,7 +257,9 @@ cylinder is moving in the z-direction along it’s axis. A dimension of the clockwise direction for vshear > 0 or counter-clockwise for vshear < 0. In this case, vshear is the tangential velocity of the wall at whatever radius has been defined.

      -

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

      +
    +
    +

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

    This fix writes the shear friction state of atoms interacting with the wall to binary restart files, so that a simulation can continue correctly if granular potentials with shear “history” effects diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html index baed71d961..ade80b4497 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -199,8 +199,10 @@ to define a wall position, but only when a numeric constant is used.

    A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index 9df5dfe8ef..4c6467cd42 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -162,11 +162,11 @@

    Examples

    -
    -fix xwalls all wall/reflect xlo EDGE xhi EDGE
-fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
-fix top all wall/reflect zhi v_pressdown
-
    +
    fix xwalls all wall/reflect xlo EDGE xhi EDGE
+fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
+fix top all wall/reflect zhi v_pressdown
+
    +

    Description

    @@ -215,22 +215,22 @@ define the lattice spacings.

    Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style variables.

    -
    -variable ramp equal ramp(0,10)
-fix 1 all wall/reflect xlo v_ramp
-
    -
    -variable linear equal vdisplace(0,20)
-fix 1 all wall/reflect xlo v_linear
-
    -
    -variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-
    -
    -variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-
    +
    variable ramp equal ramp(0,10)
+fix 1 all wall/reflect xlo v_ramp
+
    +
    +
    variable linear equal vdisplace(0,20)
+fix 1 all wall/reflect xlo v_linear
+
    +
    +
    variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+
    +
    +
    variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+
    +

    The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The vdisplace(c0,velocity) function does something similar using the equation position = c0 + velocity*delta, @@ -238,16 +238,16 @@ where delta is the elapsed time.

    The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period:

    -
    -position = c0 + A sin(omega*delta)
-
    +
    position = c0 + A sin(omega*delta)
+
    +

    The cwiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles:

    -
    -position = c0 + A (1 - cos(omega*delta))
-
    +
    position = c0 + A (1 - cos(omega*delta))
+
    +

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. @@ -264,8 +264,10 @@ by including their suffix, or you can use the suffix command in your input script.

    See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.

    +
    -

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

    +
    +

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

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/group.html b/doc/html/group.html index 009ce0deea..d21faf214a 100644 --- a/doc/html/group.html +++ b/doc/html/group.html @@ -257,22 +257,22 @@ 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.

    -
    -compute         1 all pe/atom
-compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0
-
    -
    -variable        eatom atom "c_1 > -3.0"
-group           hienergy variable eatom
-
    +
    compute         1 all pe/atom
+compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+
    +
    +
    variable        eatom atom "c_1 > -3.0"
+group           hienergy variable eatom
+
    +

    Note that these lines

    -
    -compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0
-
    +
    compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+
    +

    are necessary to insure that the “eatom” variable is current when the 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 @@ -353,8 +353,7 @@ being integrated by using a spherical region with a variable radius used to model a quench of the system, freezing atoms outside the shrinking sphere, then converting the remaining atoms to a static group and running further.

    -
    -variable        nsteps equal 5000
+
    variable        nsteps equal 5000
 variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
@@ -362,7 +361,8 @@ fix             1 mobile nve
 run             ${nsteps}
 group           mobile static
 run          ${nsteps}
-
    
+
    +

    Note

    All fixes and computes take a group ID as an argument, but they diff --git a/doc/html/if.html b/doc/html/if.html index fe0350f9d5..f2ba9d34e7 100644 --- a/doc/html/if.html +++ b/doc/html/if.html @@ -143,8 +143,7 @@

    Examples

    -
    -if "${steps} > 1000" then quit
+
    if "${steps} > 1000" then quit
 if "${myString} == a10" then quit
 if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
 if "(${eng} > 0.0) || ($n < 1000)" then &
@@ -153,9 +152,10 @@ elif $n<10000 &
   "timestep 0.01" &
 else &
   "timestep 0.02" &
-  "print 'Max step reached'"
+  "print 'Max step reached'"
 if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
-
    
+
    +

    Description

    @@ -249,10 +249,10 @@ clarity, you must enclose the entire expression in quotes.

    An expression is built out of numbers (which start with a digit or period or minus sign) or strings (which start with a letter and can contain alphanumeric characters or underscores):

    -
    -0.2, 100, 1.0e20, -15.4, etc
-InP, myString, a123, ab_23_cd, etc
-
    +
    0.2, 100, 1.0e20, -15.4, etc
+InP, myString, a123, ab_23_cd, etc
+
    +

    and Boolean operators:

    A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A
    diff --git a/doc/html/jump.html b/doc/html/jump.html index 8b2f4578a4..a87db9100d 100644 --- a/doc/html/jump.html +++ b/doc/html/jump.html @@ -158,22 +158,22 @@ script is re-opened and read again.

    The SELF option is not guaranteed to work when the current input script is being read through stdin (standard input), e.g.

    -
    -lmp_g++ < in.script
-
    +
    lmp_g++ < in.script
+
    +

    since the SELF option invokes the C-library rewind() call, which may not be supported for stdin on some systems or by some MPI implementations. This can be worked around by using the -in command-line argument, e.g.

    -
    -lmp_g++ -in in.script
-
    +
    lmp_g++ -in in.script
+
    +

    or by using the -var command-line argument to pass the script name as a variable to the input script. In the latter case, a variable called “fname” could be used in place of SELF, e.g.

    -
    -lmp_g++ -var fname in.script < in.script
-
    +
    lmp_g++ -var fname in.script < in.script
+
    +

    The 2nd argument to the jump command is optional. If specified, it is treated as a label and the new file is scanned (without executing commands) until the label is found, and commands are executed from @@ -198,9 +198,9 @@ scripts. In this example, LAMMPS is run on 40 processors, with 4 partitions of 10 procs each. An in.file containing the example variable and jump command will cause each partition to run a different simulation.

    -
    -mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
-
    +
    mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
+
    +
    variable f world script.1 script.2 script.3 script.4
 jump $f
    diff --git a/doc/html/kspace_modify.html b/doc/html/kspace_modify.html index 2019d48cff..961ea342d6 100644 --- a/doc/html/kspace_modify.html +++ b/doc/html/kspace_modify.html @@ -128,9 +128,9 @@

    kspace_modify command

    Syntax

    -
    -kspace_modify keyword value ...
-
    +
    kspace_modify keyword value ...
+
    +
    • one or more keyword/value pairs may be listed
    @@ -174,10 +174,10 @@ keyword = mesh or order or order/disp or mix/disp

    Examples

    -
    -kspace_modify mesh 24 24 30 order 6
-kspace_modify slab 3.0
-
    +
    kspace_modify mesh 24 24 30 order 6
+kspace_modify slab 3.0
+
    +

    Description

    diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html index 5cecc5b41d..53a0c22ce2 100644 --- a/doc/html/kspace_style.html +++ b/doc/html/kspace_style.html @@ -128,9 +128,9 @@

    kspace_style command

    Syntax

    -
    -kspace_style style value
-
    +
    kspace_style style value
+
    +
    • style = none or ewald or ewald/disp or ewald/omp or pppm or pppm/cg or pppm/disp or pppm/tip4p or pppm/stagger or pppm/disp/tip4p or pppm/gpu or pppm/kk or pppm/omp or pppm/cg/omp or pppm/tip4p/omp or msm or msm/cg or msm/omp or msm/cg/omp
    @@ -179,12 +179,12 @@ kspace_style style value

    Examples

    -
    -kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace_style none
-
    +
    kspace_style pppm 1.0e-4
+kspace_style pppm/cg 1.0e-5 1.0e-6
+kspace style msm 1.0e-4
+kspace_style none
+
    +

    Description

    @@ -422,9 +422,9 @@ must be periodic and the z dimension must be non-periodic.

    Default

    -
    -kspace_style none
-
    +
    kspace_style none
+
    +

    (Darden) Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).

    (Deserno) Deserno and Holm, J Chem Phys, 109, 7694 (1998).

    diff --git a/doc/html/lattice.html b/doc/html/lattice.html index 07d659915c..636cba7437 100644 --- a/doc/html/lattice.html +++ b/doc/html/lattice.html @@ -135,10 +135,10 @@
  • style = none or sc or bcc or fcc or hcp or diamond or sq or sq2 or hex or custom
  • scale = scale factor between lattice and simulation box
    • -
    -scale = reduced density rho* (for LJ units)
-scale = lattice constant in distance units (for all other units)
-
    +
    scale = reduced density rho* (for LJ units)
+scale = lattice constant in distance units (for all other units)
+
    +
    • zero or more keyword/value pairs may be appended
    • keyword = origin or orient or spacing or a1 or a2 or a3 or basis
      • @@ -349,21 +349,20 @@ in commands that use the spacings should be decipherable.

      Example commands for generating a Wurtzite crystal (courtesy of Aidan Thompson), with its 8 atom unit cell.

      -
      -variable a equal  4.340330
+
      variable a equal  4.340330
 variable b equal  $a*sqrt(3.0)
 variable c equal  $a*sqrt(8.0/3.0)
-
      
-
      -variable 1_3 equal 1.0/3.0
-variable 2_3 equal 2.0/3.0
-variable 1_6 equal 1.0/6.0
-variable 5_6 equal 5.0/6.0
-variable 1_12 equal 1.0/12.0
-variable 5_12 equal 5.0/12.0
-
      
-
      -lattice custom    1.0     &
+
      
+
      
+
      variable 1_3 equal 1.0/3.0
+variable 2_3 equal 2.0/3.0
+variable 1_6 equal 1.0/6.0
+variable 5_6 equal 5.0/6.0
+variable 1_12 equal 1.0/12.0
+variable 5_12 equal 5.0/12.0
+
      
+
      
+
      lattice custom    1.0     &
         a1      $a      0.0     0.0     &
         a2      0.0     $b      0.0     &
         a3      0.0     0.0     $c      &
@@ -375,16 +374,17 @@ lattice custom    1.0     &
         basis   0.5     0.5     0.625   &
         basis   ${1_3}  0.0     0.125   &
         basis   ${5_6}  0.5     0.125
-
      
-
      -region myreg block 0 1 0 1 0 1
-create_box      2 myreg
-create_atoms    1 box      &
-        basis   5       2       &
-        basis   6       2       &
-        basis   7       2       &
-        basis   8       2
-
      
+
    +
    +
    region myreg block 0 1 0 1 0 1
+create_box      2 myreg
+create_atoms    1 box      &
+        basis   5       2       &
+        basis   6       2       &
+        basis   7       2       &
+        basis   8       2
+
    +
    diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html index bd9a1f285f..5434586014 100644 --- a/doc/html/min_modify.html +++ b/doc/html/min_modify.html @@ -128,9 +128,9 @@

    min_modify command

    Syntax

    -
    -min_modify keyword values ...
-
    +
    min_modify keyword values ...
+
    +
    • one or more keyword/value pairs may be listed
    @@ -144,9 +144,9 @@ keyword = dmax or line

    Examples

    -
    -min_modify dmax 0.2
-
    +
    min_modify dmax 0.2
+
    +

    If the variable “d” were of style universe, and the same in.polymer input script were run on 3 partitions of processors, then the first 3 simulations would begin, one on each set of processors. Whichever @@ -214,8 +214,7 @@ and run another simulation, and so forth until all 8 simulations were finished.

    Jump and next commands can also be nested to enable multi-level loops. For example, this script will run 15 simulations in a double loop.

    -
    -variable i loop 3
+
    variable i loop 3
   variable j loop 5
   clear
   ...
@@ -226,7 +225,8 @@ variable i loop 3
   jump in.script
 next i
 jump in.script
-
    
+
    +

    Here is an example of a double loop which uses the if and jump commands to break out of the inner loop when a condition is met, then continues iterating thru the outer loop.

    diff --git a/doc/html/package.html b/doc/html/package.html index 7146faef4d..90477fc5ec 100644 --- a/doc/html/package.html +++ b/doc/html/package.html @@ -572,11 +572,11 @@ compilers is to use one thread for each available CPU core when performance.

    Here are examples of how to set the environment variable when launching LAMMPS:

    -
    -env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
-
    +
    env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
+env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
+mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
+
    +

    or you can set it permanently in your shell’s start-up script. All three of these examples use a total of 4 CPU cores.

    Note that different MPI implementations have different ways of passing diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html index 777cb46f10..eaf0a723c3 100644 --- a/doc/html/pair_brownian.html +++ b/doc/html/pair_brownian.html @@ -137,9 +137,9 @@

    pair_style brownian/poly/omp command

    Syntax

    -
    -pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
-
    +
    pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
+
    +
    • style = brownian or brownian/poly
    • mu = dynamic viscosity (dynamic viscosity units)
      • @@ -155,11 +155,11 @@ pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF

    Examples

    -
    -pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
-pair_coeff 1 1 2.05 2.8
-pair_coeff * *
-
    +
    pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+
    +

    Description

    diff --git a/doc/html/pair_dsmc.html b/doc/html/pair_dsmc.html index 4c971f1dd1..5f8ddd5600 100644 --- a/doc/html/pair_dsmc.html +++ b/doc/html/pair_dsmc.html @@ -128,9 +128,9 @@

    pair_style dsmc command

    Syntax

    -
    -pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
-
    +
    pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
+
    +
    • max_cell_size = global maximum cell size for DSMC interactions (distance units)
    • seed = random # seed (positive integer)
      • @@ -142,11 +142,11 @@ pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample

    Examples

    -
    -pair_style dsmc 2.5 34387 10 1.0 100 20
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0
-
    +
    pair_style dsmc 2.5 34387 10 1.0 100 20
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0
+
    +

    Description

    @@ -191,12 +191,12 @@ neighboring processors every timestep as they move. This makes it possible to perform all collisions between pairs of particles that are on the same processor. To ensure this occurs, you should use these commands:

    -
    -neighbor 0.0 bin
-neigh_modify every 1 delay 0 check no
-atom_modify sort 0 0.0
-communicate single cutoff 0.0
-
    +
    neighbor 0.0 bin
+neigh_modify every 1 delay 0 check no
+atom_modify sort 0 0.0
+communicate single cutoff 0.0
+
    +

    These commands ensure that LAMMPS communicates particles to neighboring processors every timestep and that no ghost atoms are created. The output statistics for a simulation run should indicate diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html index 60044d0faf..afe0cebcd6 100644 --- a/doc/html/pair_hybrid.html +++ b/doc/html/pair_hybrid.html @@ -137,27 +137,27 @@

    pair_style hybrid/overlay/omp command

    Syntax

    -
    -pair_style hybrid style1 args style2 args ...
-pair_style hybrid/overlay style1 args style2 args ...
-
    +
    pair_style hybrid style1 args style2 args ...
+pair_style hybrid/overlay style1 args style2 args ...
+
    +
    • style1,style2 = list of one or more pair styles and their arguments

    Examples

    -
    -pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
-pair_coeff 1*2 1*2 eam niu3
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.5 1.2
-
    -
    -pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * coul/long
-
    +
    pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
+pair_coeff 1*2 1*2 eam niu3
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.5 1.2
+
    +
    +
    pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * coul/long
+
    +

    Description

    @@ -218,22 +218,22 @@ these coefficients apply to.

    For example, consider a simulation with 3 atom types: types 1 and 2 are Ni atoms, type 3 are LJ atoms with charges. The following commands would set up a hybrid simulation:

    -
    -pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
-pair_coeff * * eam/alloy nialhjea Ni Ni NULL
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.8 1.3
-
    +
    pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
+pair_coeff * * eam/alloy nialhjea Ni Ni NULL
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.8 1.3
+
    +

    As an example of using the same pair style multiple times, consider a simulation with 2 atom types. Type 1 is Si, type 2 is C. The following commands would model the Si atoms with Tersoff, the C atoms with Tersoff, and the cross-interactions with Lennard-Jones:

    -
    -pair_style hybrid lj/cut 2.5 tersoff tersoff
-pair_coeff * * tersoff 1 Si.tersoff Si NULL
-pair_coeff * * tersoff 2 C.tersoff NULL C
-pair_coeff 1 2 lj/cut 1.0 1.5
-
    +
    pair_style hybrid lj/cut 2.5 tersoff tersoff
+pair_coeff * * tersoff 1 Si.tersoff Si NULL
+pair_coeff * * tersoff 2 C.tersoff NULL C
+pair_coeff 1 2 lj/cut 1.0 1.5
+
    +

    If pair coefficients are specified in the data file read via the read_data command, then the same rule applies. E.g. “eam/alloy” or “lj/cut” must be added after the atom type, for @@ -266,16 +266,16 @@ sub-style that has already been defined for that pair of atoms, then the new pair coefficients simply override the previous ones, as in the normal usage of the pair_coeff command. E.g. these two sets of commands are the same:

    -
    -pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 2 2 1.5 0.8
-
    -
    -pair_style hybrid/overlay lj/cut 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 2 2 lj/cut 1.5 0.8
-
    +
    pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 2 2 1.5 0.8
+
    +
    +
    pair_style hybrid/overlay lj/cut 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 2 2 lj/cut 1.5 0.8
+
    +

    Coefficients must be defined for each pair of atoms types via the pair_coeff command as described above, or in the data file or restart files read by the read_data or @@ -293,9 +293,9 @@ command. You can assign it to some sub-style and set the coefficients so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ potential). Or, for hybrid and hybrid/overlay simulations, you can use this form of the pair_coeff command in your input script:

    -
    -pair_coeff  2 3 none
-
    +
    pair_coeff   2 3 none
+
    +

    or this form in the “Pair Coeffs” section of the data file:

    3 none
    @@ -321,29 +321,29 @@ described by the different force fields do not mix.

    Here is an example for mixing CHARMM and AMBER: The global amber setting sets the 1-4 interactions to non-zero scaling factors and then overrides them with 0.0 only for CHARMM:

    -
    -special_bonds amber
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-
    +
    special_bonds amber
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
    +

    The this input achieves the same effect:

    -
    -special_bonds 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-
    +
    special_bonds 0.0 0.0 0.1
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
    +

    Here is an example for mixing Tersoff with OPLS/AA based on a data file that defines bonds for all atoms where for the Tersoff part of the system the force constants for the bonded interactions have been set to 0. Note the global settings are effectively lj/coul 0.0 0.0 0.5 as required for OPLS/AA:

    -
    -special_bonds lj/coul 1e-20 1e-20 0.5
-pair_hybrid tersoff lj/cut/coul/long 12.0
-pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
-
    +
    special_bonds lj/coul 1e-20 1e-20 0.5
+pair_hybrid tersoff lj/cut/coul/long 12.0
+pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
+
    +

    See the pair_modify doc page for details on the specific syntax, requirements and restrictions.

    @@ -358,7 +358,7 @@ ReaxFF, etc. The way to think about using these potentials in a hybrid setting is as follows.

    A subset of atom types is assigned to the many-body potential with a -single pair_coeff command, using “* *” to include +single pair_coeff command, using “* *” to include all types and the NULL keywords described above to exclude specific types not assigned to that potential. If types 1,3,4 were assigned in that way (but not type 2), this means that all many-body interactions @@ -388,16 +388,16 @@ atoms in one surface, and type 2 for atoms in the other, and you wish to use a Tersoff potential to compute interactions within each surface, but not between surfaces. Then either of these two command sequences would implement that model:

    -
    -pair_style hybrid tersoff
-pair_coeff * * tersoff SiC.tersoff C C
-pair_coeff 1 2 none
-
    -
    -pair_style tersoff
-pair_coeff * * SiC.tersoff C C
-neigh_modify exclude type 1 2
-
    +
    pair_style hybrid tersoff
+pair_coeff * * tersoff SiC.tersoff C C
+pair_coeff 1 2 none
+
    +
    +
    pair_style tersoff
+pair_coeff * * SiC.tersoff C C
+neigh_modify exclude type 1 2
+
    +

    Either way, only neighbor lists with 1-1 or 2-2 interactions would be passed to the Tersoff potential, which means it would compute no 3-body interactions containing both type 1 and 2 atoms.

    @@ -406,11 +406,11 @@ potentials together, in an overlapping manner. Imagine you have CNT (C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work:

    -
    -pair_style hybrid/overlay tersoff airebo 3.0
-pair_coeff * * tersoff SiC.tersoff.custom Si C
-pair_coeff * * airebo CH.airebo NULL C
-
    +
    pair_style hybrid/overlay tersoff airebo 3.0
+pair_coeff * * tersoff SiC.tersoff.custom Si C
+pair_coeff * * airebo CH.airebo NULL C
+
    +

    Note that to prevent the Tersoff potential from computing C/C interactions, you would need to modify the SiC.tersoff file to turn off C/C interaction, i.e. by setting the appropriate coefficients to diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html index c79f73301e..f36f573822 100644 --- a/doc/html/pair_line_lj.html +++ b/doc/html/pair_line_lj.html @@ -128,19 +128,19 @@

    pair_style line/lj command

    Syntax

    -
    -pair_style line/lj cutoff
-
    +
    pair_style line/lj cutoff
+
    +

    cutoff = global cutoff for interactions (distance units)

    Examples

    -
    -pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0 1.0 0.8 1.12
-pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
-pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
-
    +
    pair_style line/lj 3.0
+pair_coeff * * 1.0 1.0 1.0 0.8 1.12
+pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
+
    +

    Description

    diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html index c2fa31cce8..a57e98bbb1 100644 --- a/doc/html/pair_peri.html +++ b/doc/html/pair_peri.html @@ -143,31 +143,31 @@

    pair_style peri/eps command

    Syntax

    -
    -pair_style style
-
    +
    pair_style style
+
    +
    • style = peri/pmb or peri/lps or peri/ves or peri/eps

    Examples

    -
    -pair_style peri/pmb
-pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
-
    -
    -pair_style peri/lps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
-
    -
    -pair_style peri/ves
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
-
    -
    -pair_style peri/eps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
-
    +
    pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+
    +
    +
    pair_style peri/lps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
+
    +
    +
    pair_style peri/ves
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
+
    +
    +
    pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+
    +

    Description

    diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html index 91f1131efb..e2bae6d90b 100644 --- a/doc/html/pair_quip.html +++ b/doc/html/pair_quip.html @@ -128,17 +128,17 @@

    pair_style quip command

    Syntax

    -
    -pair_style quip
-
    +
    pair_style quip
+
    +

    Examples

    -
    -pair_style      quip
-pair_coeff      * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
-pair_coeff      * * sw_example.xml "IP SW" 14
-
    +
    pair_style      quip
+pair_coeff      * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
+pair_coeff      * * sw_example.xml "IP SW" 14
+
    +

    Description

    diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html index 3929a8cd0d..3093a0b62b 100644 --- a/doc/html/pair_reax.html +++ b/doc/html/pair_reax.html @@ -128,9 +128,9 @@

    pair_style reax command

    Syntax

    -
    -pair_style reax hbcut hbnewflag tripflag precision
-
    +
    pair_style reax hbcut hbnewflag tripflag precision
+
    +
    • hbcut = hydrogen-bond cutoff (optional) (distance units)
    • hbnewflag = use old or new hbond function style (0 or 1) (optional)
      • @@ -140,12 +140,12 @@ pair_style reax hbcut hbnewflag tripflag precision

    Examples

    -
    -pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3
-
    +
    pair_style reax
+pair_style reax 10.0 0 1 1.0e-5
+pair_coeff * * ffield.reax 3 1 2 2
+pair_coeff * * ffield.reax 3 NULL NULL 3
+
    +

    Description

    @@ -238,14 +238,14 @@ names in italics match those used in the ReaxFF FORTRAN library):

    To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script:

    -
    -compute reax all pair reax
-variable eb           equal c_reax[1]
-variable ea           equal c_reax[2]
-...
-variable eqeq         equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-
    +
    compute reax all pair reax
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+
    +

    Only a single pair_coeff command is used with the reax style which specifies a ReaxFF potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N @@ -286,9 +286,9 @@ enable this.

    elements are ordered as C, H, O, N in the ffield file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be H, you would use the following pair_coeff command:

    -
    -pair_coeff * * ffield.reax 1 1 4 2
-
    +
    pair_coeff * * ffield.reax 1 1 4 2
+
    +

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

    This pair style does not support the pair_modify diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html index 38e27022b9..bd96471c6b 100644 --- a/doc/html/pair_reax_c.html +++ b/doc/html/pair_reax_c.html @@ -131,9 +131,9 @@

    pair_style reax/c/kk command

    Syntax

    -
    -pair_style reax/c cfile keyword value
-
    +
    pair_style reax/c cfile keyword value
+
    +
    • cfile = NULL or name of a control file
    • zero or more keyword/value pairs may be appended
      • @@ -148,13 +148,13 @@ keyword = checkqeq or lgvdw or safezone or mincap

    Examples

    -
    -pair_style reax/c NULL
-pair_style reax/c controlfile checkqeq no
-pair_style reax/c NULL lgvdw yes
-pair_style reax/c NULL safezone 1.6 mincap 100
-pair_coeff * * ffield.reax C H O N
-
    +
    pair_style reax/c NULL
+pair_style reax/c controlfile checkqeq no
+pair_style reax/c NULL lgvdw yes
+pair_style reax/c NULL safezone 1.6 mincap 100
+pair_coeff * * ffield.reax C H O N
+
    +

    Description

    @@ -276,14 +276,14 @@ names in italics match those used in the original FORTRAN ReaxFF code):

    To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script:

    -
    -compute reax all pair reax/c
-variable eb           equal c_reax[1]
-variable ea           equal c_reax[2]
-...
-variable eqeq         equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-
    +
    compute reax all pair reax/c
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+
    +

    Only a single pair_coeff command is used with the reax/c style which specifies a ReaxFF potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N @@ -310,14 +310,14 @@ types that will be used with other potentials.

    elements are ordered as C, H, O, N in the ffield file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be H, you would use the following pair_coeff command:

    -
    -pair_coeff * * ffield.reax C C N H
-
    +
    pair_coeff * * ffield.reax C C N H
+
    +

    The format of a line in the control file is as follows:

    -
    -variable_name value
-
    +
    variable_name value
+
    +

    and it may be followed by an ”!” character and a trailing comment.

    If the value of a control variable is not specified, then default values are used. What follows is the list of variables along with a diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html index 25cbc618da..52dd7939f6 100644 --- a/doc/html/pair_smd_hertz.html +++ b/doc/html/pair_smd_hertz.html @@ -128,9 +128,9 @@

    pair_style smd/hertz command

    Syntax

    -
    -pair_style smd/hertz scale_factor
-
    +
    pair_style smd/hertz scale_factor
+
    +

    Examples

    @@ -146,7 +146,7 @@ The effect is that a particles cannot penetrate into each other. The parameter <contact_stiffness> has units of pressure and should equal roughly one half of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.

    The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close -particles can approach each other. Usually, *scale_factor*=1.0.

    +particles can approach each other. Usually, scale_factor=1.0.

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

    No mixing is performed automatically. diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html index 428893dfc3..9f4ba0991d 100644 --- a/doc/html/pair_smd_triangulated_surface.html +++ b/doc/html/pair_smd_triangulated_surface.html @@ -128,9 +128,9 @@

    pair_style smd/tri_surface command

    Syntax

    -
    -pair_style smd/tri_surface scale_factor
-
    +
    pair_style smd/tri_surface scale_factor
+
    +

    Examples

    @@ -147,7 +147,7 @@ The effect is that a particle cannot penetrate into the triangular surface. The parameter <contact_stiffness> has units of pressure and should equal roughly one half of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle

    The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close -particles can approach the triangulated surface. Usually, *scale_factor*=1.0.

    +particles can approach the triangulated surface. Usually, scale_factor=1.0.

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

    No mixing is performed automatically. diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html index 86a80963cc..4dc6adc479 100644 --- a/doc/html/pair_style.html +++ b/doc/html/pair_style.html @@ -128,9 +128,9 @@

    pair_style command

    Syntax

    -
    -pair_style style args
-
    +
    pair_style style args
+
    +
    • style = one of the styles from the list below
    • args = arguments used by a particular style
      • @@ -138,13 +138,13 @@ pair_style style args

    Examples

    -
    -pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none
-
    +
    pair_style lj/cut 2.5
+pair_style eam/alloy
+pair_style hybrid lj/charmm/coul/long 10.0 eam
+pair_style table linear 1000
+pair_style none
+
    +

    Description

    @@ -338,9 +338,9 @@ package.

    Default

    -
    -pair_style none
-
    +
    pair_style none
+
    +
    diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html index 8e8f15daf2..b2742247f9 100644 --- a/doc/html/pair_thole.html +++ b/doc/html/pair_thole.html @@ -134,9 +134,9 @@

    pair_style lj/cut/thole/long/omp command

    Syntax

    -
    -pair_style style args
-
    +
    pair_style style args
+
    +
    • style = thole or lj/cut/thole/long or lj/cut/thole/long/omp
    • args = list of arguments for a particular style
      • @@ -153,15 +153,15 @@ pair_style style args

    Examples

    -
    -pair_style hybrid/overlay ... thole 2.6 12.0
-pair_coeff 1 1 thole 1.0
-pair_coeff 1 2 thole 1.0 2.6 10.0
-pair_coeff * 2 thole 1.0 2.6
-
    -
    -pair_style lj/cut/thole/long 2.6 12.0
-
    +
    pair_style hybrid/overlay ... thole 2.6 12.0
+pair_coeff 1 1 thole 1.0
+pair_coeff 1 2 thole 1.0 2.6 10.0
+pair_coeff * 2 thole 1.0 2.6
+
    +
    +
    pair_style lj/cut/thole/long 2.6 12.0
+
    +

    Description

    diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html index bdda14e2e2..e6c6b24ddd 100644 --- a/doc/html/pair_tri_lj.html +++ b/doc/html/pair_tri_lj.html @@ -128,18 +128,18 @@

    pair_style tri/lj command

    Syntax

    -
    -pair_style tri/lj cutoff
-
    +
    pair_style tri/lj cutoff
+
    +

    cutoff = global cutoff for interactions (distance units)

    Examples

    -
    -pair_style tri/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-
    +
    pair_style tri/lj 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+
    +

    Description

    diff --git a/doc/html/prd.html b/doc/html/prd.html index a32fecfdce..ee0c7948c0 100644 --- a/doc/html/prd.html +++ b/doc/html/prd.html @@ -128,9 +128,9 @@

    prd command

    Syntax

    -
    -prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
-
    +
    prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
+
    +
    • N = # of timesteps to run (not including dephasing/quenching)
    • t_event = timestep interval between event checks
      • @@ -200,19 +200,19 @@ potentials, etc should be the same for every replica.

      A PRD run has several stages, which are repeated each time an “event” occurs in one of the replicas, as defined below. The logic for a PRD run is as follows:

      -
      -while (time remains):
-  dephase for n_dephase*t_dephase steps
-  until (event occurs on some replica):
-    run dynamics for t_event steps
-    quench
-    check for uncorrelated event on any replica
-  until (no correlated event occurs):
-    run dynamics for t_correlate steps
-    quench
-    check for correlated event on this replica
-  event replica shares state with all replicas
-
      +
      while (time remains):
+  dephase for n_dephase*t_dephase steps
+  until (event occurs on some replica):
+    run dynamics for t_event steps
+    quench
+    check for uncorrelated event on any replica
+  until (no correlated event occurs):
+    run dynamics for t_correlate steps
+    quench
+    check for correlated event on this replica
+  event replica shares state with all replicas
+
      +

      Before this loop begins, the state of the system on replica 0 is shared with all replicas, so that all replicas begin from the same initial state. The first potential energy basin is identified by diff --git a/doc/html/processors.html b/doc/html/processors.html index 15f24d6340..f0feeb91ba 100644 --- a/doc/html/processors.html +++ b/doc/html/processors.html @@ -162,15 +162,15 @@

    Examples

    -
    -processors * * 5
-processors 2 4 4
-processors * * 8 map xyz
-processors * * * grid numa
-processors * * * grid twolevel 4 * * 1
-processors 4 8 16 grid custom myfile
-processors * * * part 1 2 multiple
-
    +
    processors * * 5
+processors 2 4 4
+processors * * 8 map xyz
+processors * * * grid numa
+processors * * * grid twolevel 4 * * 1
+processors 4 8 16 grid custom myfile
+processors * * * part 1 2 multiple
+
    +

    Description

    @@ -428,7 +428,7 @@ option.

    Default

    -

    The option defaults are Px Py Pz = * * *, grid = onelevel, and map = +

    The option defaults are Px Py Pz = * * *, grid = onelevel, and map = cart.

    diff --git a/doc/html/python.html b/doc/html/python.html index 6700435a9f..f78a9df834 100644 --- a/doc/html/python.html +++ b/doc/html/python.html @@ -161,35 +161,35 @@ keyword = invoke or input or return or format

    Examples

    -
    -python pForce input 2 v_x 20.0 return v_f format fff file force.py
-python pForce invoke
-
    -
    -python factorial input 1 myN return v_fac format ii here """
-def factorial(n):
-  if n == 1: return n
-  return n * factorial(n-1)
- """
-
    -
    -python loop input 1 SELF return v_value format -f here """
-def loop(lmpptr,N,cut0):
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-
    +
    python pForce input 2 v_x 20.0 return v_f format fff file force.py
+python pForce invoke
+
    +
    +
    python factorial input 1 myN return v_fac format ii here """
+def factorial(n):
+  if n == 1: return n
+  return n * factorial(n-1)
+ """
+
    +
    +
    python loop input 1 SELF return v_value format -f here """
+def loop(lmpptr,N,cut0):
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+
    +
    # loop N times, increasing cutoff each time
    -
    - for i in range(N):
-   cut = cut0 + i*0.1
-   lmp.set_variable("cut",cut)               # set a variable in LAMMPS
-   lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
-   lmp.command("pair_coeff * * 1.0 1.0")
-   lmp.command("run 100")
-"""
-
    +
     for i in range(N):
+   cut = cut0 + i*0.1
+   lmp.set_variable("cut",cut)               # set a variable in LAMMPS
+   lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
+   lmp.command("pair_coeff * * 1.0 1.0")
+   lmp.command("run 100")
+"""
+
    +

    Description

    @@ -263,10 +263,10 @@ numeric or string value, as specified by the format keyword.

    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:

    -
    -variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-
    +
    variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+
    +

    The two commands can appear in either order in the input script so long as both are specified before the Python function is invoked for the first time.

    @@ -417,29 +417,29 @@ Python wraps the various functions included in the LAMMPS library interface.

    A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py:

    -
    -def loop(N,cut0,thresh,lmpptr):
-  print "LOOP ARGS",N,cut0,thresh,lmpptr
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-  natoms = lmp.get_natoms()
-
    -
    -for i in range(N):
-  cut = cut0 + i*0.1
-
    -
    -lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-#lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
-
    -
    -lmp.command("pair_coeff * * 1.0 1.0")       # ditto
-lmp.command("run 10")                       # ditto
-pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
-print "PE",pe/natoms,thresh
-if pe/natoms < thresh: return
-
    +
    def loop(N,cut0,thresh,lmpptr):
+  print "LOOP ARGS",N,cut0,thresh,lmpptr
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+  natoms = lmp.get_natoms()
+
    +
    +
    for i in range(N):
+  cut = cut0 + i*0.1
+
    +
    +
    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
+#lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+
    +
    +
    lmp.command("pair_coeff * * 1.0 1.0")       # ditto
+lmp.command("run 10")                       # ditto
+pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
+print "PE",pe/natoms,thresh
+if pe/natoms < thresh: return
+
    +

    with these input script commands:

    python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
 python          loop invoke
diff --git a/doc/html/read_dump.html b/doc/html/read_dump.html
index 5e2e9f96eb..603ab46785 100644
--- a/doc/html/read_dump.html
+++ b/doc/html/read_dump.html
@@ -128,9 +128,9 @@
 
    read_dump command
    
 
    
 
    Syntax
    
-
    -read_dump file Nstep field1 field2 ... keyword values ...
-
    
+
    read_dump file Nstep field1 field2 ... keyword values ...
+
    
+
    
 
      
 
    • file = name of dump file to read
      • 
 
    • Nstep = snapshot timestep to read from file
      • 
@@ -168,18 +168,18 @@ field = x or y or z or vx or vy or
 
    
 
    
 
    Examples
    
-
    -read_dump dump.file 5000 x y z
-read_dump dump.xyz 5 x y z box no format xyz
-read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
-read_dump dump.dcd 0 x y z box yes format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-read_dump dump.file 5000 x y vx vy trim yes
-read_dump ../run7/dump.file.gz 10000 x y z box yes
-read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
-read_dump dump.dcd 0 x y z format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-
    
+
    read_dump dump.file 5000 x y z
+read_dump dump.xyz 5 x y z box no format xyz
+read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
+read_dump dump.dcd 0 x y z box yes format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+read_dump dump.file 5000 x y vx vy trim yes
+read_dump ../run7/dump.file.gz 10000 x y z box yes
+read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
+read_dump dump.dcd 0 x y z format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+
    
+
    
 
    
 
    
 
    Description
    
diff --git a/doc/html/restart.html b/doc/html/restart.html
index 3f169da485..d6fc25f246 100644
--- a/doc/html/restart.html
+++ b/doc/html/restart.html
@@ -150,14 +150,14 @@
 
    
 
    
 
    Examples
    
-
    -restart 0
-restart 1000 poly.restart
-restart 1000 poly.restart.mpiio
-restart 1000 restart.*.equil
-restart 10000 poly.%.1 poly.%.2 nfile 10
-restart v_mystep poly.restart
-
    
+
    restart 0
+restart 1000 poly.restart
+restart 1000 poly.restart.mpiio
+restart 1000 restart.*.equil
+restart 10000 poly.%.1 poly.%.2 nfile 10
+restart v_mystep poly.restart
+
    
+
    
 
    
 
    
 
    Description
    
@@ -226,10 +226,10 @@ options for For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:
    
-
    -variable     s equal stride(1100,1200,1)
-restart              v_s tmp.restart
-
    
+
    variable     s equal stride(1100,1200,1)
+restart              v_s tmp.restart
+
    
+
    
 
    
 
    See the read_restart command for information about
 what is stored in a restart file.
    
diff --git a/doc/html/run_style.html b/doc/html/run_style.html
index b00835c7e1..9ef0e69f67 100644
--- a/doc/html/run_style.html
+++ b/doc/html/run_style.html
@@ -128,9 +128,9 @@
 
    run_style command
    
 
    
 
    Syntax
    
-
    -run_style style args
-
    
+
    run_style style args
+
    
+
    
 
      
 
    • style = verlet or verlet/split or respa or respa/omp
      • 
 
    
@@ -175,14 +175,14 @@ run_style style args
 
    
 
    
 
    Examples
    
-
    -run_style verlet
-run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
-
    
-
    -run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
-
    
+
    run_style verlet
+run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
+
    
+
    
+
    run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
+
    
+
    
 
    
 
    
 
    Description
    
@@ -219,9 +219,9 @@ its onn optimal layout, then require the 2nd partition’s layout to
 match the integer multiple constraint.  See the
 processors command with its part keyword for a way
 to control this, e.g.
    
-
    -procssors * * * part 1 2 multiple
-
    
+
    procssors * * * part 1 2 multiple
+
    
+
    
 
    You can also use the partition command to explicitly
 specity the processor layout on each partition.  E.g. for 2 partitions
 of 60 and 15 processors each:
    
@@ -314,10 +314,10 @@ angstrom “healing distance” (the distance between the outer and inne
 cutoffs) works reasonably well.  We thus recommend the following
 settings for use of the respa style without SHAKE in biomolecular
 simulations:
    
-
    -timestep  4.0
-run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
-
    
+
    timestep  4.0
+run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
+
    
+
    
 
    With these settings, users can expect good energy conservation and
 roughly a 2.5 fold speedup over the verlet style with a 0.5 fmsec
 timestep.
    
@@ -332,11 +332,11 @@ respa in order to freeze out these high frequency motions and increase
 the size of the time steps in the respa hierarchy.  The following
 settings can be used for biomolecular simulations with SHAKE and
 rRESPA:
    
-
    -fix             2 all shake 0.000001 500 0 m 1.0 a 1
-timestep        4.0
-run_style   respa 2 2 inner 1 4.0 5.0 outer 2
-
    
+
    fix             2 all shake 0.000001 500 0 m 1.0 a 1
+timestep        4.0
+run_style    respa 2 2 inner 1 4.0 5.0 outer 2
+
    
+
    
 
    With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the verlet style with SHAKE and a
 2.0 fmsec timestep.
    
@@ -348,10 +348,10 @@ keywords.  A 2-fold or more speedup can be obtained while maintaining
 good energy conservation.  In real units, for a pure LJ fluid at
 liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
 Kcal/mol, the following settings seem to work well:
    
-
    -timestep  36.0
-run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
-
    
+
    timestep  36.0
+run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
+
    
+
    
 
    
 
    The respa/omp styles is a variant of respa adapted for use with
 pair, bond, angle, dihedral, improper, or kspace styles with an omp
@@ -384,9 +384,9 @@ conserving energy to adequate precision.
    
 
    
 
    
 
    Default
    
-
    -run_style verlet
-
    
+
    run_style verlet
+
    
+
    
 
    
 
    (Tuckerman) Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
 (1992).
    
diff --git a/doc/html/set.html b/doc/html/set.html
index 075dbb3510..89ea2eb1ff 100644
--- a/doc/html/set.html
+++ b/doc/html/set.html
@@ -214,17 +214,17 @@
 
    
 
    
 
    Examples
    
-
    -set group solvent type 2
-set group solvent type/fraction 2 0.5 12393
-set group edge bond 4
-set region half charge 0.5
-set type 3 charge 0.5
-set type 1*3 charge 0.5
-set atom * charge v_atomfile
-set atom 100*200 x 0.5 y 1.0
-set atom 1492 type 3
-
    
+
    set group solvent type 2
+set group solvent type/fraction 2 0.5 12393
+set group edge bond 4
+set region half charge 0.5
+set type 3 charge 0.5
+set type 1*3 charge 0.5
+set atom * charge v_atomfile
+set atom 100*200 x 0.5 y 1.0
+set atom 1492 type 3
+
    
+
    
 
    
 
    
 
    Description
    
@@ -252,7 +252,7 @@ style type selects all the atoms in a range of types.  The style
 mol selects all the atoms in a range of molecule IDs.
    
 
    In each of the range cases, the range can be specified as a single
 numeric value, or a wildcard asterisk can be used to specify a range
-of values.  This takes the form “*” or “*n” or “n*” or “m*n”.  For
+of values.  This takes the form “*” or “n” or “n” or “m*n”.  For
 example, for the style type, if N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html
index d431cc49b3..08a1e3f74c 100644
--- a/doc/html/special_bonds.html
+++ b/doc/html/special_bonds.html
@@ -128,9 +128,9 @@
 
    special_bonds command
    
 
    
 
    Syntax
    
-
    -special_bonds keyword values ...
-
    
+
    special_bonds keyword values ...
+
    
+
    
 
      
 
    • one or more keyword/value pairs may be appended
      • 
 
    • keyword = amber or charmm or dreiding or fene or lj/coul or lj or coul or angle or dihedral or extra
      • 
@@ -152,14 +152,14 @@ special_bonds keyword values ...
   N = number of extra 1-2,1-3,1-4 interactions to save space for

    Examples:

    -
    -special_bonds amber
-special_bonds charmm
-special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2
-
    +
    special_bonds amber
+special_bonds charmm
+special_bonds fene dihedral no
+special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
+special_bonds lj/coul 0 1 1 extra 2
+
    +

    Description

    @@ -301,7 +301,7 @@ current system has.

    the system). If new bonds are created (or molecules added containing atoms with more special neighbors), the size of this list needs to grow. Note that adding a single bond always adds a new 1st neighbor -but may also induce *many* new 2nd and 3rd neighbors, depending on the +but may also induce many new 2nd and 3rd neighbors, depending on the molecular topology of your system. Using the extra keyword leaves empty space in the list for this N additional 1st, 2nd, or 3rd neighbors to be added. If you do not do this, you may get an error @@ -325,14 +325,14 @@ Coul: coul 0.0 0.0 1.0

    because the LJ settings are reset to their default values each time the command is issued.

    Likewise

    -
    -special_bonds amber
-special_bonds extra 2
-
    +
    special_bonds amber
+special_bonds extra 2
+
    +

    is not the same as this single command:

    -
    -special_bonds amber extra 2
-
    +
    special_bonds amber extra 2
+
    +

    since in the former case, the 2nd command will reset all the LJ and Coulombic weights to 0.0 (the default).

    One exception to this rule is the extra option itself. It is not diff --git a/doc/html/tad.html b/doc/html/tad.html index e4bab3f210..d4f05d75ae 100644 --- a/doc/html/tad.html +++ b/doc/html/tad.html @@ -128,9 +128,9 @@

    tad command

    Syntax

    -
    -tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
-
    +
    tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
+
    +
    • N = # of timesteps to run (not including dephasing/quenching)
    • t_event = timestep interval between event checks
      • @@ -162,15 +162,15 @@ tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...

    Examples

    -
    -tad 2000 50 1800 2300 0.01 0.01 event
-tad 2000 50 1800 2300 0.01 0.01 event &
-    min 1e-05 1e-05 100 100 &
-    neb 0.0 0.01 200 200 20 &
-    min_style cg &
-    neb_style fire &
-    neb_log log.neb
-
    +
    tad 2000 50 1800 2300 0.01 0.01 event
+tad 2000 50 1800 2300 0.01 0.01 event &
+    min 1e-05 1e-05 100 100 &
+    neb 0.0 0.01 200 200 20 &
+    min_style cg &
+    neb_style fire &
+    neb_log log.neb
+
    +

    Description

    @@ -215,19 +215,19 @@ partitions remain idle. See -while (time remains): - while (time < tstop): - until (event occurs): - run dynamics for t_event steps - quench - run neb calculation using all replicas - compute tlo from energy barrier - update earliest event - update tstop - reflect back into current basin - execute earliest event - +
    while (time remains):
+  while (time < tstop):
+    until (event occurs):
+      run dynamics for t_event steps
+      quench
+    run neb calculation using all replicas
+    compute tlo from energy barrier
+    update earliest event
+    update tstop
+    reflect back into current basin
+  execute earliest event
+
    +

    Before this outer loop begins, the initial potential energy basin is identified by quenching (an energy minimization, see below) the initial state and storing the resulting coordinates for reference.

    @@ -298,7 +298,7 @@ at the low temperature.

    current basin to the stopping time. This last number can be used to judge whether the stopping time is too short or too long (see above).

    t_lo is the low-temperature event time when the current basin was -entered, in units of timestep. del*t_lo* is the time of each detected +entered, in units of timestep. delt_lo is the time of each detected event, measured relative to t_lo. delt_lo is equal to the high-temperature time since entering the current basin, scaled by an exponential factor that depends on the hi/lo temperature ratio and the diff --git a/doc/html/thermo.html b/doc/html/thermo.html index 7a5cb15c32..8567a3fd63 100644 --- a/doc/html/thermo.html +++ b/doc/html/thermo.html @@ -162,10 +162,10 @@ this context. Other similar math functions could easily be added as options for equal-style variables.

    For example, the following commands will output thermodynamic info at timesteps 0,10,20,30,100,200,300,1000,2000,etc:

    -
    -variable     s equal logfreq(10,3,10)
-thermo               v_s
-
    +
    variable     s equal logfreq(10,3,10)
+thermo               v_s
+
    +

    Restrictions

    diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html index 4f0f68acae..5a6e41bfc9 100644 --- a/doc/html/thermo_style.html +++ b/doc/html/thermo_style.html @@ -128,9 +128,9 @@

    thermo_style command

    Syntax

    -
    -thermo_style style args
-
    +
    thermo_style style args
+
    +
    • style = one or multi or custom
    • args = list of arguments for a particular style
      • @@ -207,12 +207,12 @@ thermo_style style args

    Examples

    -
    -thermo_style multi
-thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp etotal c_myTemp v_abc
-thermo_style custom step temp etotal c_myTemp[*] v_abc
-
    +
    thermo_style multi
+thermo_style custom step temp pe etotal press vol
+thermo_style custom step temp etotal c_myTemp v_abc
+thermo_style custom step temp etotal c_myTemp[*] v_abc
+
    +

    Description

    @@ -260,9 +260,9 @@ the thermo_modify command after it.

    computed: “temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc. By default this is done by using a temperature compute which is created when LAMMPS starts up, as if this command had been issued:

    -
    -compute thermo_temp all temp
-
    +
    compute thermo_temp all temp
+
    +

    See the compute temp command for details. Note that the ID of this compute is thermo_temp and the group is all. You can change the attributes of this temperature (e.g. its @@ -275,9 +275,9 @@ This is done via the pressure compute which is created when LAMMPS starts up, as if this command had been issued:

    -
    -compute thermo_press all pressure thermo_temp
-
    +
    compute thermo_press all pressure thermo_temp
+
    +

    See the compute pressure command for details. Note that the ID of this compute is thermo_press and the group is all. You can change the attributes of this pressure via the @@ -290,9 +290,9 @@ that requires a pressure. This is done via the be computed: “pe”, “etotal”, “ebond”, etc. This is done by using a pe compute which is created when LAMMPS starts up, as if this command had been issued:

    -
    -compute thermo_pe all pe
-
    +
    compute thermo_pe all pe
+
    +

    See the compute pe command for details. Note that the ID of this compute is thermo_pe and the group is all. You can change the attributes of this potential energy via the @@ -394,7 +394,7 @@ of these quantities in terms of the internal LAMMPS cell dimensions

    For output values from a compute or fix, the bracketed index I used to index a vector, as in c_ID[I] or f_ID[I], can be specified using a wildcard asterisk with the index to effectively specify -multiple values. This takes the form “*” or “*n” or “n*” or “m*n”. +multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk @@ -405,13 +405,13 @@ indices from m to n (inclusive).

    vector had been listed one by one. E.g. these 2 thermo_style commands are equivalent, since the compute temp command creates a global vector with 6 values.

    -
    -compute myTemp all temp
-thermo_style custom step temp etotal c_myTemp[*]
-thermo_style custom step temp etotal &
-             c_myTemp[1] c_myTemp[2] c_myTemp[3] &
-             c_myTemp[4] c_myTemp[5] c_myTemp[6]
-
    +
    compute myTemp all temp
+thermo_style custom step temp etotal c_myTemp[*]
+thermo_style custom step temp etotal &
+             c_myTemp[1] c_myTemp[2] c_myTemp[3] &
+             c_myTemp[4] c_myTemp[5] c_myTemp[6]
+
    +

    The c_ID and c_ID[I] and c_ID[I][J] keywords allow global values calculated by a compute to be output. As discussed on the @@ -490,9 +490,9 @@ division by “natoms” in the variable formula if this is not the case

    Default

    -
    -thermo_style one
-
    +
    thermo_style one
+
    +
    diff --git a/doc/html/units.html b/doc/html/units.html index e80e207a23..9dc8285c6d 100644 --- a/doc/html/units.html +++ b/doc/html/units.html @@ -187,7 +187,7 @@ results from a unitless LJ simulation into physical quantities.

  • pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
  • dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
  • charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2
    • -
  • dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
    • +
  • dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
  • electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
  • density = mass/volume, where rho* = rho sigma^dim
    • diff --git a/doc/html/variable.html b/doc/html/variable.html index f7fd72fac0..f5eb258506 100644 --- a/doc/html/variable.html +++ b/doc/html/variable.html @@ -197,8 +197,7 @@

    Examples

    -
    -variable x index run1 run2 run3 run4 run5 run6 run7 run8
+
    variable x index run1 run2 run3 run4 run5 run6 run7 run8
 variable LoopVar loop $n
 variable beta equal temp/3.0
 variable b1 equal x[234]+0.5*vol
@@ -215,7 +214,8 @@ variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
 variable x uloop 15 pad
 variable str format x %.6g
 variable x delete
-
    
+
    +

    Description

    @@ -470,10 +470,10 @@ appear in the set, will remain 0.0.

    to match a function name specified in a python command which returns a value to this variable as defined by its return keyword. For example these two commands would be self-consistent:

    -
    -variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-
    +
    variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+
    +

    The two commands can appear in either order so long as both are specified before the Python function is invoked for the first time.

    Each time the variable is evaluated, the associated Python function is @@ -527,9 +527,9 @@ variety of quantities. The syntax for each kind of quantity is simple, but multiple quantities can be nested and combined in various ways to build up formulas of arbitrary complexity. For example, this is a valid (though strange) variable formula:

    -
    -variable x equal "pe + c_MyTemp / vol^(1/3)"
-
    +
    variable x equal "pe + c_MyTemp / vol^(1/3)"
+
    +

    Specifically, a formula can contain numbers, constants, thermo keywords, math operators, math functions, group functions, region functions, atom values, atom vectors, compute references, fix @@ -618,9 +618,9 @@ of LAMMPS will be smaller. This can be used to have input scripts adapt automatically to LAMMPS versions, when non-backwards compatible syntax changes are introduced. Here is an illustrative example (which will not work, since the version has been introduced more recently):

    -
    -if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
-
    +
    if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
+
    +

    The thermo keywords allowed in a formula are those defined by the thermo_style custom command. Thermo keywords that require a compute to calculate their values such as @@ -719,9 +719,9 @@ 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 of a run, according to this formula:

    -
    -value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
-
    +
    value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
+
    +

    The run begins on startstep and ends on stopstep. Startstep and stopstep can span multiple runs, using the start and stop keywords of the run command. See the run command for @@ -790,9 +790,9 @@ sequence of output timesteps:

    velocity, and uses the elapsed time to change the value by a linear displacement due to the applied velocity over the course of a run, according to this formula:

    -
    -value = value0 + velocity*(timestep-startstep)*dt
-
    +
    value = value0 + velocity*(timestep-startstep)*dt
+
    +

    where dt = the timestep size.

    The run begins on startstep. Startstep can span multiple runs, using the start keyword of the run command. See the @@ -803,10 +803,10 @@ timestep-startstep.

    x = value0, y = amplitude, z = period. They use the elapsed time to oscillate the value by a sin() or cos() function over the course of a run, according to one of these formulas, where omega = 2 PI / period:

    -
    -value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
-value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
-
    +
    value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
+value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
+
    +

    where dt = the timestep size.

    The run begins on startstep. Startstep can span multiple runs, using the start keyword of the run command. See the @@ -952,16 +952,16 @@ features or LAMMPS, respa allows to check whether the inner/middle/oute mode of r-RESPA is supported. In the various style categories, the checking is also done using suffix flags, if available and enabled.

    Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).

    -
    -pair_style lj/cut/coul/long 14.0
+
    pair_style lj/cut/coul/long 14.0
 if $(is_active(package,gpu)) then "suffix off"
 kspace_style pppm
-
    
+
    +

    Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step

    -
    -timestep $(2.0*(1.0+*is_active(pair,respa))
+
    timestep $(2.0*(1.0+*is_active(pair,respa))
 if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3"
-
    
+
    +

    The is_defined() function allows to query categories like compute, dump, fix, group, region, and variable whether an entry with the provided name or id is defined.

    @@ -1022,8 +1022,8 @@ reference means, since computes only produce either global or per-atom quantities, never both.

    ASPHERE
    --++ @@ -1046,9 +1046,9 @@ variable refers to a compute that produces both a global scalar and a global vector. Consider a compute with ID “foo” that does this, referenced as follows by variable “a”, where “myVec” is another vector-style variable:

    -
    -variable a vector c_foo*v_myVec
-
    +
    variable a vector c_foo*v_myVec
+
    +

    The reference “c_foo” could refer to either the global scalar or global vector produced by compute “foo”. In this case, “c_foo” will always refer to the global scalar, and “C_foo” can be used to @@ -1077,14 +1077,14 @@ vector values. A vector value can be a per-atom vector itself, or a column of an per-atom array. See the doc pages for individual fixes to see what kind of values they produce.

    The different kinds of fix references are exactly the same as the -compute references listed in the above table, where “c_” is replaced -by “f_”. Again, there is typically no ambiguity (see exception below) +compute references listed in the above table, where “c_” is replaced +by “f_”. Again, there is typically no ambiguity (see exception below) as to what a reference means, since fixes only produce either global or per-atom quantities, never both.

    c_ID
    --++ @@ -1152,8 +1152,8 @@ There is no ambiguity as to what a reference means, since variables produce only a global scalar or global vector or per-atom vector.

    f_ID
    --++ @@ -1188,7 +1188,7 @@ same syntax as equal-style variables described on this page. This effectively evaluates a formula immediately without using the variable command to define a named variable.

    More generally, there is a difference between referencing a variable -with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_” +with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_” (e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value @@ -1197,7 +1197,7 @@ un-named “immediate” variables for this purpose. For example, a string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates the string between the parenthesis as an equal-style variable formula.

    -

    Referencing a variable with a leading “v_” is an optional or required +

    Referencing a variable with a leading “v_” is an optional or required kind of argument for some commands (e.g. the fix ave/chunk or dump custom or thermo_style commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a @@ -1224,9 +1224,9 @@ variable v0 equal $v

    The second command will force “v” to be evaluated (yielding the initial volume) and assign that value to the variable “v0”. Thus the command

    -
    -thermo_style custom step v_v v_v0
-
    +
    thermo_style custom step v_v v_v0
+
    +

    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 @@ -1317,13 +1317,13 @@ a 0-timestep run before printing the variable has the desired effect.

    (3) The variable may be evaluated incorrectly and LAMMPS may have no way to detect this has occurred. Consider the following sequence of commands:

    -
    -pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-variable e equal pe
-print "Final potential energy = $e"
-
    +
    pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+variable e equal pe
+print "Final potential energy = $e"
+
    +

    The first run is performed using one setting for the pairwise potential defined by the pair_style and pair_coeff commands. The potential energy is @@ -1340,14 +1340,14 @@ perform a 0-timestep run before the variable is evaluated to insure the system is up-to-date. For example, this sequence of commands would print a potential energy that reflected the changed pairwise coefficient:

    -
    -pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-run 0
-variable e equal pe
-print "Final potential energy = $e"
-
    +
    pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+run 0
+variable e equal pe
+print "Final potential energy = $e"
+
    +
    diff --git a/doc/html/velocity.html b/doc/html/velocity.html index af9be7196c..06accf9593 100644 --- a/doc/html/velocity.html +++ b/doc/html/velocity.html @@ -172,13 +172,13 @@

    Examples

    -
    -velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 v_vz sum yes units box
-velocity flow scale 300.0
-velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
-velocity all zero linear
-
    +
    velocity all create 300.0 4928459 rot yes dist gaussian
+velocity border set NULL 4.0 v_vz sum yes units box
+velocity flow scale 300.0
+velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
+velocity all zero linear
+
    +

    Description

    @@ -244,7 +244,7 @@ replace them if sum = no.

    The mom and rot keywords are used by create. If mom = yes, the linear momentum of the newly created ensemble of velocities is zeroed; if rot = yes, the angular momentum is zeroed.

    -

    *line

    +

    *line

    If specified, the temp keyword is used by create and scale to specify a compute that calculates temperature in a desired way, e.g. by first subtracting out a velocity bias, as @@ -252,9 +252,9 @@ discussed in create and scale calculate temperature using a compute that is defined internally as follows:

    -
    -compute velocity_temp group-ID temp
-
    +
    compute velocity_temp group-ID temp
+
    +

    where group-ID is the same ID used in the velocity command. i.e. the group of atoms whose velocity is being altered. This compute is deleted when the velocity command is finished. See the compute temp command for details. If the calculated diff --git a/doc/html/write_coeff.html b/doc/html/write_coeff.html index d4d15e1ddf..1698ec2615 100644 --- a/doc/html/write_coeff.html +++ b/doc/html/write_coeff.html @@ -128,18 +128,18 @@

    write_coeff command

    Syntax

    -
    -write_coeff file
-
    +
    write_coeff file
+
    +
    file = name of data file to write out

    Examples

    -
    -write_coeff polymer.coeff
-
    +
    write_coeff polymer.coeff
+
    +

    Description

    diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ab82bb0716..e9e6cb9192 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 -7 Sep 2016 version :c,h4 +13 Sep 2016 version :c,h4 Version info: :h4 diff --git a/src/version.h b/src/version.h index 006495e9f1..60efccead2 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "7 Sep 2016" +#define LAMMPS_VERSION "13 Sep 2016"
    v_name