Description
diff --git a/doc/html/displace_atoms.html b/doc/html/displace_atoms.html
index 9208e97052..968c7345cd 100644
--- a/doc/html/displace_atoms.html
+++ b/doc/html/displace_atoms.html
@@ -128,9 +128,9 @@
displace_atoms command
Syntax
-
displace_atoms group-ID style args keyword value ...
-
-
+
+displace_atoms group-ID style args keyword value ...
+
- group-ID = ID of group of atoms to displace
- style = move or ramp or random or rotate
@@ -162,10 +162,10 @@ keyword = units
Examples
-
displace_atoms top move 0 -5 0 units box
-displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
-
-
+
+displace_atoms top move 0 -5 0 units box
+displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
+
Description
diff --git a/doc/html/dump.html b/doc/html/dump.html
index b47465bc33..d76697dbba 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 8bd838f671..b77890476a 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_h5md.html b/doc/html/dump_h5md.html
index 5980b4368d..e883ea5695 100644
--- a/doc/html/dump_h5md.html
+++ b/doc/html/dump_h5md.html
@@ -156,23 +156,23 @@ author value = quoted string
may specify a sub-interval to write the data only every N_element
iterations of the dump (i.e. every N*N_element time steps). This is
specified by the option
-
+
+every N_element
+
that follows directly the element declaration.
Examples
-
dump h5md1 all h5md 100 dump_h5md.h5 position image
-dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
-dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
-
-
+
+dump h5md1 all h5md 100 dump_h5md.h5 position image
+dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
+dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
+
Description
Dump a snapshot of atom coordinates every N timesteps in the
-HDF5 based H5MD file format (de Buyl).
+HDF5 based H5MD file format (de Buyl).
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.
Several dumps may write to the same file, by using file_from and
@@ -201,10 +201,10 @@ using the file_from keyword.
Typically, the species data is fixed. The following two commands
store the position data every 100 timesteps, with the image data, and
store once the species data in the same file.
-
dump h5md1 all h5md 100 dump.h5 position image
-write_dump all h5md dump.h5 file_from h5md1 species
-
-
+
+dump h5md1 all h5md 100 dump.h5 position image
+write_dump all h5md dump.h5 file_from h5md1 species
+
@@ -217,7 +217,7 @@ a limitation of the present dump h5md command and not of H5MD itself.
enabled if LAMMPS was built with that package. See the
Making LAMMPS section for more info. It also
requires (i) building the ch5md library provided with LAMMPS (See the
Making LAMMPS section for more info.) and
-(ii) having the
HDF5 library installed (C bindings are
+(ii) having the
HDF5 library installed (C bindings are
sufficient) on your system. The library ch5md is compiled with the
h5cc wrapper provided by the HDF5 library.
diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html
index 492ef0a5f5..08afa5c7c6 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 @@
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/dump_molfile.html b/doc/html/dump_molfile.html
index 7986ce9562..60ee56baf7 100644
--- a/doc/html/dump_molfile.html
+++ b/doc/html/dump_molfile.html
@@ -143,11 +143,11 @@
Examples
-
dump mf1 all molfile 10 melt1.xml hoomd
-dump mf2 all molfile 10 melt2-*.pdb pdb .
-dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
-
-
+
+dump mf1 all molfile 10 melt1.xml hoomd
+dump mf2 all molfile 10 melt2-*.pdb pdb .
+dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
+
Description
diff --git a/doc/html/fix_addforce.html b/doc/html/fix_addforce.html
index 2e773e8d92..68b8540f51 100644
--- a/doc/html/fix_addforce.html
+++ b/doc/html/fix_addforce.html
@@ -154,11 +154,11 @@
Examples
-
fix kick flow addforce 1.0 0.0 0.0
-fix kick flow addforce 1.0 0.0 v_oscillate
-fix ff boundary addforce 0.0 0.0 v_push energy v_espace
-
-
+
+fix kick flow addforce 1.0 0.0 0.0
+fix kick flow addforce 1.0 0.0 v_oscillate
+fix ff boundary addforce 0.0 0.0 v_push energy v_espace
+
Description
@@ -232,10 +232,8 @@ 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 potential “energy” inferred by the added force to the
diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html
index d53243c00f..c15d2330aa 100644
--- a/doc/html/fix_append_atoms.html
+++ b/doc/html/fix_append_atoms.html
@@ -197,10 +197,8 @@ A box value selects standard distance units as defined by the
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_atom_swap.html b/doc/html/fix_atom_swap.html
index 862d6932af..a56f3b4f8b 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
@@ -250,9 +250,7 @@ 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 b8459a1d96..72641a5006 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
@@ -246,15 +246,13 @@ 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.
-
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
@@ -502,10 +502,8 @@ 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 ccd754dbaf..a673143beb 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 @@
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
@@ -221,9 +221,7 @@ 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 e8291ddeb4..bb07687b4a 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 @@
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
@@ -399,10 +399,8 @@ 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 6c6744c5e6..2d41fdc0dc 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 @@
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
@@ -383,10 +383,8 @@ 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_aveforce.html b/doc/html/fix_aveforce.html
index b5d312fdc6..3a4daf418a 100644
--- a/doc/html/fix_aveforce.html
+++ b/doc/html/fix_aveforce.html
@@ -150,11 +150,11 @@
Examples
-
fix pressdown topwall aveforce 0.0 -1.0 0.0
-fix 2 bottomwall aveforce NULL -1.0 0.0 region top
-fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
-
-
+
+fix pressdown topwall aveforce 0.0 -1.0 0.0
+fix 2 bottomwall aveforce NULL -1.0 0.0 region top
+fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
+
Description
@@ -198,10 +198,8 @@ 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_balance.html b/doc/html/fix_balance.html
index 0415a0054b..56beb5da2b 100644
--- a/doc/html/fix_balance.html
+++ b/doc/html/fix_balance.html
@@ -432,10 +432,8 @@ will be duplicate nodes in the list.
rectangle for each processor (1 to 4).
For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and “SQUARES” replaced by “CUBES”.
-
-
-
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 is the imbalance factor
diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html
index 9be191ab77..ef0c90e2a9 100644
--- a/doc/html/fix_bond_break.html
+++ b/doc/html/fix_bond_break.html
@@ -224,10 +224,8 @@ 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).
-
![create_bonds command Syntax -create_bonds group-ID group2-ID btype rmin rmax - - + +create_bonds group-ID group2-ID btype rmin rmax + group-ID = ID of first group group2-ID = ID of second group, bonds will be between atoms in the 2 groups @@ -141,10 +141,10 @@ Examples -create_bonds all all 1 1.0 1.2 -create_bonds surf solvent 3 2.0 2.4 - - + +create_bonds all all 1 1.0 1.2 +create_bonds surf solvent 3 2.0 2.4 + Description diff --git a/doc/html/create_box.html b/doc/html/create_box.html index 27a19a1021..69c876edc3 100644 --- a/doc/html/create_box.html +++ b/doc/html/create_box.html @@ -128,9 +128,9 @@ create_box command Syntax -create_box N region-ID keyword value ... - - + +create_box N region-ID keyword value ... + N = # of atom types to use in this simulation region-ID = ID of region to use as simulation domain @@ -151,10 +151,10 @@ Examples -create_box 2 mybox -create_box 2 mybox bond/types 2 extra/bond/per/atom 1 - - + +create_box 2 mybox +create_box 2 mybox bond/types 2 extra/bond/per/atom 1 + Description diff --git a/doc/html/delete_atoms.html b/doc/html/delete_atoms.html index 63d2667cf6..cb151917cc 100644 --- a/doc/html/delete_atoms.html +++ b/doc/html/delete_atoms.html @@ -128,9 +128,9 @@ delete_atoms command Syntax -delete_atoms style args keyword value ... - - + +delete_atoms style args keyword value ... + style = group or region or overlap or porosity @@ -158,13 +158,13 @@ Examples -delete_atoms group edge -delete_atoms region sphere compress no -delete_atoms overlap 0.3 all all -delete_atoms overlap 0.5 solvent colloid -delete_atoms porosity cube 0.1 482793 bond yes - - + +delete_atoms group edge +delete_atoms region sphere compress no +delete_atoms overlap 0.3 all all +delete_atoms overlap 0.5 solvent colloid +delete_atoms porosity cube 0.1 482793 bond yes + Description diff --git a/doc/html/delete_bonds.html b/doc/html/delete_bonds.html index 18e52920f4..b10ff2515d 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 @@ 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_charmm.html b/doc/html/dihedral_charmm.html index 80c9b47043..9794ca050e 100644 --- a/doc/html/dihedral_charmm.html +++ b/doc/html/dihedral_charmm.html @@ -137,18 +137,18 @@ dihedral_style charmm/omp command Syntax -dihedral_style charmm - - + +dihedral_style charmm + Examples -dihedral_style charmm -dihedral_coeff 1 0.2 1 180 1.0 -dihedral_coeff 2 1.8 1 0 1.0 -dihedral_coeff 1 3.1 2 180 0.5 - - + +dihedral_style charmm +dihedral_coeff 1 0.2 1 180 1.0 +dihedral_coeff 2 1.8 1 0 1.0 +dihedral_coeff 1 3.1 2 180 0.5 + Description diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index 40f10f1e74..e9556733e2 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -131,21 +131,21 @@ dihedral_style class2/omp command Syntax -dihedral_style class2 - - + +dihedral_style class2 + Examples -dihedral_style class2 -dihedral_coeff 1 100 75 100 70 80 60 -dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 -dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 -dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 -dihedral_coeff * aat -13.5271 110.2453 105.1270 -dihedral_coeff * bb13 0.0 1.0119 1.1010 - - + +dihedral_style class2 +dihedral_coeff 1 100 75 100 70 80 60 +dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 +dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 +dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 +dihedral_coeff * aat -13.5271 110.2453 105.1270 +dihedral_coeff * bb13 0.0 1.0119 1.1010 + Description diff --git a/doc/html/dihedral_coeff.html b/doc/html/dihedral_coeff.html index c098bed43a..1c150bd7af 100644 --- a/doc/html/dihedral_coeff.html +++ b/doc/html/dihedral_coeff.html @@ -128,9 +128,9 @@ dihedral_coeff command Syntax -dihedral_coeff N args - - + +dihedral_coeff N args + N = dihedral type (see asterisk form below) args = coefficients for one or more dihedral types @@ -138,11 +138,11 @@ Examples -dihedral_coeff 1 80.0 1 3 -dihedral_coeff * 80.0 1 3 0.5 -dihedral_coeff 2* 80.0 1 3 0.5 - - + +dihedral_coeff 1 80.0 1 3 +dihedral_coeff * 80.0 1 3 0.5 +dihedral_coeff 2* 80.0 1 3 0.5 + Description @@ -154,7 +154,7 @@ Dihedral coefficients can also be set in the data file read by the N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple dihedral types. This takes the -form “*” or “n” or “n” or “m*n”. If N = the number of dihedral types, +form “*” or “*n” or “n*” or “m*n”. If N = the number of dihedral 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 @@ -162,10 +162,10 @@ means all types from m to n (inclusive). Note that using a dihedral_coeff command can override a previous setting for the same dihedral type. For example, these commands set the coeffs for all dihedral types, then overwrite the coeffs for just dihedral type 2: -dihedral_coeff * 80.0 1 3 -dihedral_coeff 2 200.0 1 3 - - + +dihedral_coeff * 80.0 1 3 +dihedral_coeff 2 200.0 1 3 + A line in a data file that specifies dihedral coefficients uses the exact same format as the arguments of the dihedral_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html index b6e718bce8..1cc73331be 100644 --- a/doc/html/dihedral_cosine_shift_exp.html +++ b/doc/html/dihedral_cosine_shift_exp.html @@ -131,16 +131,16 @@ dihedral_style cosine/shift/exp/omp command Syntax -dihedral_style cosine/shift/exp - - + +dihedral_style cosine/shift/exp + Examples -dihedral_style cosine/shift/exp -dihedral_coeff 1 10.0 45.0 2.0 - - + +dihedral_style cosine/shift/exp +dihedral_coeff 1 10.0 45.0 2.0 + Description diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html index 0feb09036b..1470ba7346 100644 --- a/doc/html/dihedral_fourier.html +++ b/doc/html/dihedral_fourier.html @@ -131,16 +131,16 @@ dihedral_style fourier/omp command Syntax -dihedral_style fourier - - + +dihedral_style fourier + Examples -dihedral_style fourier -dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 - - + +dihedral_style fourier +dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 + Description diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html index 14a06fac03..b8d5653099 100644 --- a/doc/html/dihedral_helix.html +++ b/doc/html/dihedral_helix.html @@ -131,16 +131,16 @@ dihedral_style helix/omp command Syntax -dihedral_style helix - - + +dihedral_style helix + Examples -dihedral_style helix -dihedral_coeff 1 80.0 100.0 40.0 - - + +dihedral_style helix +dihedral_coeff 1 80.0 100.0 40.0 + Description diff --git a/doc/html/dihedral_hybrid.html b/doc/html/dihedral_hybrid.html index 9b495bb81f..dc9383e3f2 100644 --- a/doc/html/dihedral_hybrid.html +++ b/doc/html/dihedral_hybrid.html @@ -128,20 +128,20 @@ dihedral_style hybrid command Syntax -dihedral_style hybrid style1 style2 ... - - + +dihedral_style hybrid style1 style2 ... + style1,style2 = list of one or more dihedral styles Examples -dihedral_style hybrid harmonic helix -dihedral_coeff 1 harmonic 6.0 1 3 -dihedral_coeff 2* helix 10 10 10 - - + +dihedral_style hybrid harmonic helix +dihedral_coeff 1 harmonic 6.0 1 3 +dihedral_coeff 2* helix 10 10 10 + Description diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html index c8f3b7b886..ec192b670e 100644 --- a/doc/html/dihedral_multi_harmonic.html +++ b/doc/html/dihedral_multi_harmonic.html @@ -131,16 +131,16 @@ dihedral_style multi/harmonic/omp command Syntax -dihedral_style multi/harmonic - - + +dihedral_style multi/harmonic + Examples -dihedral_style multi/harmonic -dihedral_coeff 1 20 20 20 20 20 - - + +dihedral_style multi/harmonic +dihedral_coeff 1 20 20 20 20 20 + Description diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html index eb35a50a58..eb59b45627 100644 --- a/doc/html/dihedral_nharmonic.html +++ b/doc/html/dihedral_nharmonic.html @@ -131,16 +131,16 @@ dihedral_style nharmonic/omp command Syntax -dihedral_style nharmonic - - + +dihedral_style nharmonic + Examples -dihedral_style nharmonic -dihedral_coeff 3 10.0 20.0 30.0 - - + +dihedral_style nharmonic +dihedral_coeff 3 10.0 20.0 30.0 + Description diff --git a/doc/html/dihedral_none.html b/doc/html/dihedral_none.html index 84f445b4da..c30711154a 100644 --- a/doc/html/dihedral_none.html +++ b/doc/html/dihedral_none.html @@ -128,15 +128,15 @@ dihedral_style none command Syntax -dihedral_style none - - + +dihedral_style none + Examples -dihedral_style none - - + +dihedral_style none + Description diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html index 2f73119b58..fd7c9f1e4f 100644 --- a/doc/html/dihedral_opls.html +++ b/doc/html/dihedral_opls.html @@ -137,18 +137,18 @@ dihedral_style opls/omp command Syntax -dihedral_style opls - - + +dihedral_style opls + Examples -dihedral_style opls -dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT -dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC -dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC - - + +dihedral_style opls +dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT +dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC +dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC + Description diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html index 3cc35b63dd..3b490ae5d6 100644 --- a/doc/html/dihedral_quadratic.html +++ b/doc/html/dihedral_quadratic.html @@ -131,16 +131,16 @@ dihedral_style quadratic/omp command Syntax -dihedral_style quadratic - - + +dihedral_style quadratic + Examples -dihedral_style quadratic -dihedral_coeff 100.0 80.0 - - + +dihedral_style quadratic +dihedral_coeff 100.0 80.0 + Description diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html index 1d9a9f7402..3e38d2d8ca 100644 --- a/doc/html/dihedral_spherical.html +++ b/doc/html/dihedral_spherical.html @@ -128,18 +128,18 @@ dihedral_style spherical command Syntax -dihedral_style spherical - - + +dihedral_style spherical + Examples -dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & - 17.3 0 0.0 0 1 158 1 0 0.0 0 & - 15.1 0 0.0 0 0 0.0 0 1 167.3 1 - - + +dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 +dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & + 17.3 0 0.0 0 1 158 1 0 0.0 0 & + 15.1 0 0.0 0 0 0.0 0 1 167.3 1 + Description diff --git a/doc/html/dihedral_style.html b/doc/html/dihedral_style.html index 9b21cd4640..c19d4a1a2e 100644 --- a/doc/html/dihedral_style.html +++ b/doc/html/dihedral_style.html @@ -128,20 +128,20 @@ dihedral_style command Syntax -dihedral_style style - - + +dihedral_style style + style = none or hybrid or charmm or class2 or harmonic or helix or multi/harmonic or opls Examples -dihedral_style harmonic -dihedral_style multi/harmonic -dihedral_style hybrid harmonic charmm - - + +dihedral_style harmonic +dihedral_style multi/harmonic +dihedral_style hybrid harmonic charmm + Description diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html index d967731158..fe30f6ab11 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 @@ 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/dihedral_zero.html b/doc/html/dihedral_zero.html index 99891fae28..9ff190c609 100644 --- a/doc/html/dihedral_zero.html +++ b/doc/html/dihedral_zero.html @@ -134,11 +134,11 @@ dihedral_style zero nocoeff Examples -dihedral_style zero -dihedral_style zero nocoeff -dihedral_coeff * - - + +dihedral_style zero +dihedral_style zero nocoeff +dihedral_coeff * + Description diff --git a/doc/html/displace_atoms.html b/doc/html/displace_atoms.html index 9208e97052..968c7345cd 100644 --- a/doc/html/displace_atoms.html +++ b/doc/html/displace_atoms.html @@ -128,9 +128,9 @@ displace_atoms command Syntax -displace_atoms group-ID style args keyword value ... - - + +displace_atoms group-ID style args keyword value ... + group-ID = ID of group of atoms to displace style = move or ramp or random or rotate @@ -162,10 +162,10 @@ keyword = units Examples -displace_atoms top move 0 -5 0 units box -displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 - - + +displace_atoms top move 0 -5 0 units box +displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 + Description diff --git a/doc/html/dump.html b/doc/html/dump.html index b47465bc33..d76697dbba 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 8bd838f671..b77890476a 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_h5md.html b/doc/html/dump_h5md.html index 5980b4368d..e883ea5695 100644 --- a/doc/html/dump_h5md.html +++ b/doc/html/dump_h5md.html @@ -156,23 +156,23 @@ author value = quoted string may specify a sub-interval to write the data only every N_element iterations of the dump (i.e. every N*N_element time steps). This is specified by the option -every N_element - - + +every N_element + that follows directly the element declaration. Examples -dump h5md1 all h5md 100 dump_h5md.h5 position image -dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 -dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" - - + +dump h5md1 all h5md 100 dump_h5md.h5 position image +dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 +dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" + Description Dump a snapshot of atom coordinates every N timesteps in the -HDF5 based H5MD file format (de Buyl). +HDF5 based H5MD file format (de Buyl). HDF5 files are binary, portable and self-describing. This dump style will write only one file, on the root node. Several dumps may write to the same file, by using file_from and @@ -201,10 +201,10 @@ using the file_from keyword. Typically, the species data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and store once the species data in the same file. -dump h5md1 all h5md 100 dump.h5 position image -write_dump all h5md dump.h5 file_from h5md1 species - - + +dump h5md1 all h5md 100 dump.h5 position image +write_dump all h5md dump.h5 file_from h5md1 species + @@ -217,7 +217,7 @@ a limitation of the present dump h5md command and not of H5MD itself. enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. It also requires (i) building the ch5md library provided with LAMMPS (See the Making LAMMPS section for more info.) and -(ii) having the HDF5 library installed (C bindings are +(ii) having the HDF5 library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html index 492ef0a5f5..08afa5c7c6 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 @@ 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/dump_molfile.html b/doc/html/dump_molfile.html index 7986ce9562..60ee56baf7 100644 --- a/doc/html/dump_molfile.html +++ b/doc/html/dump_molfile.html @@ -143,11 +143,11 @@ Examples -dump mf1 all molfile 10 melt1.xml hoomd -dump mf2 all molfile 10 melt2-*.pdb pdb . -dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile - - + +dump mf1 all molfile 10 melt1.xml hoomd +dump mf2 all molfile 10 melt2-*.pdb pdb . +dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile + Description diff --git a/doc/html/fix_addforce.html b/doc/html/fix_addforce.html index 2e773e8d92..68b8540f51 100644 --- a/doc/html/fix_addforce.html +++ b/doc/html/fix_addforce.html @@ -154,11 +154,11 @@ Examples -fix kick flow addforce 1.0 0.0 0.0 -fix kick flow addforce 1.0 0.0 v_oscillate -fix ff boundary addforce 0.0 0.0 v_push energy v_espace - - + +fix kick flow addforce 1.0 0.0 0.0 +fix kick flow addforce 1.0 0.0 v_oscillate +fix ff boundary addforce 0.0 0.0 v_push energy v_espace + Description @@ -232,10 +232,8 @@ 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 potential “energy” inferred by the added force to the diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html index d53243c00f..c15d2330aa 100644 --- a/doc/html/fix_append_atoms.html +++ b/doc/html/fix_append_atoms.html @@ -197,10 +197,8 @@ A box value selects standard distance units as defined by the 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_atom_swap.html b/doc/html/fix_atom_swap.html index 862d6932af..a56f3b4f8b 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 @@ -250,9 +250,7 @@ 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 b8459a1d96..72641a5006 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 @@ -246,15 +246,13 @@ 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 564b91e3ef..a6293fb62e 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 @@ 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 @@ -502,10 +502,8 @@ 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 ccd754dbaf..a673143beb 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 @@ 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 @@ -221,9 +221,7 @@ 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 e8291ddeb4..bb07687b4a 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 @@ 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 @@ -399,10 +399,8 @@ 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 6c6744c5e6..2d41fdc0dc 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 @@ 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 @@ -383,10 +383,8 @@ 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_aveforce.html b/doc/html/fix_aveforce.html index b5d312fdc6..3a4daf418a 100644 --- a/doc/html/fix_aveforce.html +++ b/doc/html/fix_aveforce.html @@ -150,11 +150,11 @@ Examples -fix pressdown topwall aveforce 0.0 -1.0 0.0 -fix 2 bottomwall aveforce NULL -1.0 0.0 region top -fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top - - + +fix pressdown topwall aveforce 0.0 -1.0 0.0 +fix 2 bottomwall aveforce NULL -1.0 0.0 region top +fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top + Description @@ -198,10 +198,8 @@ 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_balance.html b/doc/html/fix_balance.html index 0415a0054b..56beb5da2b 100644 --- a/doc/html/fix_balance.html +++ b/doc/html/fix_balance.html @@ -432,10 +432,8 @@ will be duplicate nodes in the list. rectangle for each processor (1 to 4). For a 3d problem, the syntax is similar with 8 vertices listed for each processor, instead of 4, and “SQUARES” replaced by “CUBES”. - - -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 is the imbalance factor diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html index 9be191ab77..ef0c90e2a9 100644 --- a/doc/html/fix_bond_break.html +++ b/doc/html/fix_bond_break.html @@ -224,10 +224,8 @@ 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 8ab79a00a5..8854f57578 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 @@ -320,10 +320,8 @@ 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_bond_swap.html b/doc/html/fix_bond_swap.html index 27a56cba19..a3ae59400a 100644 --- a/doc/html/fix_bond_swap.html +++ b/doc/html/fix_bond_swap.html @@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file. This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of style temp, as if this command had been issued: -compute fix-ID_temp all temp - - + +compute fix-ID_temp all temp + See the compute temp command for details. Note that the ID of the new compute is the fix-ID with underscore + “temp” appended and the group for the new compute is “all”, so that the diff --git a/doc/html/fix_box_relax.html b/doc/html/fix_box_relax.html index ea16211584..e81bc87098 100644 --- a/doc/html/fix_box_relax.html +++ b/doc/html/fix_box_relax.html @@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the pressure, even though this is subsequently ignored by default. 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 virial - - + +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp virial + 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”, and the group for the new computes is the same @@ -388,10 +388,8 @@ fix’s temperature or pressure via the or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this 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. The fix_modify temp and press options are supported by this fix. You can use them to assign a @@ -425,12 +423,12 @@ potential energy. This fix does not support the because that would result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants: -variable emin equal pe+f_1 - - -variable emin equal pe+f_1/atoms - - + +variable emin equal pe+f_1 + + +variable emin equal pe+f_1/atoms + No parameter of this fix can be used with the start/stop keywords of the run command. This fix is invoked during energy minimization, but diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html index 8ac1624b80..367d9b091c 100644 --- a/doc/html/fix_colvars.html +++ b/doc/html/fix_colvars.html @@ -200,9 +200,7 @@ 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_controller.html b/doc/html/fix_controller.html index e6608bc009..e9e662670c 100644 --- a/doc/html/fix_controller.html +++ b/doc/html/fix_controller.html @@ -141,13 +141,13 @@ Kd = derivative gain in PID equation (unitless) pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or 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 = 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 = value calculated by an equal-style variable with name + setpoint = desired value of process variable (same units as process variable) cvar = name of control variable @@ -155,11 +155,11 @@ Examples -fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol -fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall -fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol - - + +fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol +fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall +fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol + Description @@ -269,14 +269,14 @@ because the value of e_n-1 is not yet defined. compute or fix or the evaluation of a variable. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. -If pvar begins with “c_”, a compute ID must follow which has been +If pvar begins with “c_”, a compute ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual compute doc page for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. -If pvar begins with “f_”, a fix ID must follow which has been +If pvar begins with “f_”, a fix ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual fix doc page for details. Note that some fixes only produce their values on certain @@ -285,7 +285,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS. -If pvar begins with “v_”, a variable name must follow which has been +If pvar begins with “v_”, a variable name must follow which has been previously defined in the input script. Only equal-style variables can be referenced. See the variable command for details. Note that variables of style equal define a formula which @@ -296,14 +296,12 @@ variable. The target value setpoint for the process variable must be a numeric value, in whatever units pvar is defined for. The control variable cvar must be the name of an internal-style variable previously defined in the input script. Note -that it is not specified with a “v_” prefix, just the name of the +that it is not specified with a “v_” prefix, just the name of the variable. It must be an internal-style variable, because this fix updates its value directly. Note that other commands can use an equal-style versus internal-style variable interchangeably. - - -Restart, fix_modify, output, run start/stop, minimize info +Restart, fix_modify, output, run start/stop, minimize info: Currenlty, 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 with 3 values which can be accessed diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html index e8ad31ffb0..d23425a85b 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 @@ -633,9 +633,7 @@ 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 6e7e0be54f..566b353255 100644 --- a/doc/html/fix_deposit.html +++ b/doc/html/fix_deposit.html @@ -355,9 +355,7 @@ 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 c464c735a2..5864fe2ce5 100644 --- a/doc/html/fix_drag.html +++ b/doc/html/fix_drag.html @@ -156,9 +156,7 @@ 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 7134e2dbf5..6a078677dc 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 @@ -259,10 +259,8 @@ 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_dt_reset.html b/doc/html/fix_dt_reset.html index 9d7eaee03a..a6e011a7ac 100644 --- a/doc/html/fix_dt_reset.html +++ b/doc/html/fix_dt_reset.html @@ -182,9 +182,7 @@ outer loop (largest) timestep, which is the same timestep that the Note that the cumulative simulation time (in time units), which accounts for changes in the timestep size as a simulation proceeds, can be accessed by the thermo_style time keyword. - - -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_efield.html b/doc/html/fix_efield.html index c724217123..6ddd5f9067 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 @@ -218,10 +218,8 @@ 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_ehex.html b/doc/html/fix_ehex.html index f1cc66f404..a753adb554 100644 --- a/doc/html/fix_ehex.html +++ b/doc/html/fix_ehex.html @@ -262,10 +262,8 @@ be on the order of \(10^{-7}\) for relatively large temperature gradients. A higher precision can be achieved by decreasing the timestep. - - -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_enforce2d.html b/doc/html/fix_enforce2d.html index 3b70700e85..15595d17b3 100644 --- a/doc/html/fix_enforce2d.html +++ b/doc/html/fix_enforce2d.html @@ -162,10 +162,8 @@ 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_evaporate.html b/doc/html/fix_evaporate.html index 2f9d6f8aba..929f36c037 100644 --- a/doc/html/fix_evaporate.html +++ b/doc/html/fix_evaporate.html @@ -187,9 +187,7 @@ count is changing due to evaporation, 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: 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_external.html b/doc/html/fix_external.html index d2a176da50..264a4cf9ba 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. @@ -212,18 +212,16 @@ 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_flow_gauss.html b/doc/html/fix_flow_gauss.html index ca10c2d38d..7c5defac59 100644 --- a/doc/html/fix_flow_gauss.html +++ b/doc/html/fix_flow_gauss.html @@ -219,10 +219,8 @@ work on the system must have fix_modify energy yes set as well. This includes thermostat fixes and any constraints that hold the positions of wall atoms fixed, such as fix spring/self. - - -Restart, fix_modify, output, run start/stop, minimize info +Restart, fix_modify, output, run start/stop, minimize info: This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. No information about this fix is written to binary restart files. diff --git a/doc/html/fix_freeze.html b/doc/html/fix_freeze.html index 0d285a3709..66a6cb1629 100644 --- a/doc/html/fix_freeze.html +++ b/doc/html/fix_freeze.html @@ -166,10 +166,8 @@ 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. This fix computes a global 3-vector of forces, which can be accessed diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html index 02f1da98e6..2210a5c5c4 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 * @@ -375,9 +375,7 @@ 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_gld.html b/doc/html/fix_gld.html index aba80b6a9d..96beaab03f 100644 --- a/doc/html/fix_gld.html +++ b/doc/html/fix_gld.html @@ -128,9 +128,9 @@ fix gld command Syntax -fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... - - + +fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... + ID, group-ID are documented in fix command gld = style name of this fix command diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html index 9f9296aea3..e51ed41bf3 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. @@ -207,9 +207,7 @@ 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 e770f8e7fe..f10e0f3416 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 @@ -220,10 +220,8 @@ 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 fb5b0f55e7..2e88845d31 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 @@ -219,9 +219,7 @@ 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 5c92083e88..3245c8523d 100644 --- a/doc/html/fix_imd.html +++ b/doc/html/fix_imd.html @@ -237,9 +237,7 @@ they were real objects. See the -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_indent.html b/doc/html/fix_indent.html index 366694bd8a..92dafa1af5 100644 --- a/doc/html/fix_indent.html +++ b/doc/html/fix_indent.html @@ -163,11 +163,11 @@ Examples -fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0 -fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in -fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box - - + +fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0 +fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in +fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box + Description @@ -179,9 +179,9 @@ constraining wall around a simulation; see the discussion of the The indenter can either be spherical or cylindrical or planar. You must set one of those 3 keywords. A spherical indenter exerts a force of magnitude -F(r) = - K (r - R)^2 - - + +F(r) = - K (r - R)^2 + on each atom where K is the specified force constant, r is the distance from the atom to the center of the indenter, and R is the radius of the indenter. The force is repulsive and F(r) = 0 for r > @@ -226,23 +226,23 @@ fashion. For the latter, see the start and stop keywords of t then this variable definition will keep it’s center at a relative position in the simulation box, 1/4 of the way from the left edge to the right edge, even if the box size changes: -variable x equal "xlo + 0.25*lx" - - + +variable x equal "xlo + 0.25*lx" + Similarly, either of these variable definitions will move the indenter from an initial position at 2.5 at a constant velocity of 5: -variable x equal "2.5 + 5*elaplong*dt" -variable x equal vdisplace(2.5,5) - - + +variable x equal "2.5 + 5*elaplong*dt" +variable x equal vdisplace(2.5,5) + If a spherical indenter’s radius is specified as v_r, then these variable definitions will grow the size of the indenter at a specfied rate. -variable r0 equal 0.0 -variable rate equal 1.0 -variable r equal "v_r0 + step*dt*v_rate" - - + +variable r0 equal 0.0 +variable rate equal 1.0 +variable r equal "v_r0 + step*dt*v_rate" + If the side keyword is specified as out, which is the default, then particles outside the indenter are pushded away from its outer surface, as described above. This only applies to spherical or @@ -275,9 +275,7 @@ contains xlat, ylat, zlat keywords of the fix 1 all indent $k sphere ... - - -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 of interaction between atoms and the indenter to diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html index 615515d668..40917601b7 100644 --- a/doc/html/fix_ipi.html +++ b/doc/html/fix_ipi.html @@ -173,9 +173,7 @@ 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 40cfbcd9cc..bf67a0e983 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -375,10 +375,8 @@ 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 506e61e35c..dea014ff7b 100644 --- a/doc/html/fix_langevin_eff.html +++ b/doc/html/fix_langevin_eff.html @@ -178,9 +178,7 @@ interactions (fix langevin 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_fluid.html b/doc/html/fix_lb_fluid.html index 51eefacda2..fadee5ceb3 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -374,10 +374,8 @@ screen every N timesteps. test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid 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: Due to the large size of the fluid data, this fix writes it’s own binary restart files, if requested, independent of the main LAMMPS binary restart files; no information about lb_fluid diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html index aefe19517d..5ca4e990b6 100644 --- a/doc/html/fix_lb_momentum.html +++ b/doc/html/fix_lb_momentum.html @@ -167,9 +167,7 @@ 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 8a5281c6c3..8d27f6cd24 100644 --- a/doc/html/fix_lb_pc.html +++ b/doc/html/fix_lb_pc.html @@ -149,9 +149,7 @@ 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 ca3adc0748..8bda0b4a82 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -202,9 +202,7 @@ 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 efc00565c9..876c9eb1f0 100644 --- a/doc/html/fix_lb_viscous.html +++ b/doc/html/fix_lb_viscous.html @@ -164,10 +164,8 @@ 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 5ca8460a42..2734d0ff4e 100644 --- a/doc/html/fix_lineforce.html +++ b/doc/html/fix_lineforce.html @@ -151,9 +151,7 @@ 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_manifoldforce.html b/doc/html/fix_manifoldforce.html index bba7854a61..fa64343002 100644 --- a/doc/html/fix_manifoldforce.html +++ b/doc/html/fix_manifoldforce.html @@ -147,10 +147,8 @@ This can be used in combination with minimize to remove overlap between particles while keeping them (roughly) constrained to the given manifold, e.g. to set up a run with fix nve/manifold/rattle. I have found that only hftn and quickmin with a very small time step perform adequately though. - - -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_meso.html b/doc/html/fix_meso.html index a3727a2590..0ad7f8f622 100644 --- a/doc/html/fix_meso.html +++ b/doc/html/fix_meso.html @@ -150,9 +150,7 @@ needed to time-integrate mesoscopic systems where particles carry internal variables such as SPH or DPDE. See this PDF guide to using SPH in LAMMPS. - - -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_meso_stationary.html b/doc/html/fix_meso_stationary.html index 42106fb5c2..b4fb2d708c 100644 --- a/doc/html/fix_meso_stationary.html +++ b/doc/html/fix_meso_stationary.html @@ -151,9 +151,7 @@ fixed boundary particles which constrain a fluid to a given region in space. See this PDF guide to using SPH in LAMMPS. - - -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_modify.html b/doc/html/fix_modify.html index 7e3b41240e..2af8e6a5be 100644 --- a/doc/html/fix_modify.html +++ b/doc/html/fix_modify.html @@ -128,9 +128,9 @@ fix_modify command Syntax -fix_modify fix-ID keyword value ... - - + +fix_modify fix-ID keyword value ... + fix-ID = ID of the fix to modify one or more keyword/value pairs may be appended @@ -145,11 +145,11 @@ Examples -fix_modify 3 temp myTemp press myPress -fix_modify 1 energy yes -fix_modify tether respa 2 - - + +fix_modify 3 temp myTemp press myPress +fix_modify 1 energy yes +fix_modify tether respa 2 + Description diff --git a/doc/html/fix_momentum.html b/doc/html/fix_momentum.html index 8329e21764..c5388609c5 100644 --- a/doc/html/fix_momentum.html +++ b/doc/html/fix_momentum.html @@ -175,9 +175,7 @@ thermostatting). of atoms by rescaling the velocities after the momentum was removed. Note that the velocity command can be used to create initial velocities with zero aggregate linear and/or angular momentum. - - -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 66cf61d80e..ad7177b2bd 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 @@ -302,10 +302,8 @@ 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 f5a8d09ba8..c54106e01e 100644 --- a/doc/html/fix_msst.html +++ b/doc/html/fix_msst.html @@ -197,16 +197,14 @@ 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 @@ -230,15 +228,15 @@ 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 4b5777e1e2..1e50f393e0 100644 --- a/doc/html/fix_neb.html +++ b/doc/html/fix_neb.html @@ -190,9 +190,7 @@ 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.html b/doc/html/fix_nh.html index ff55e4e302..8cbee0b46f 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -158,9 +158,9 @@ fix nph/omp command Syntax -fix ID group-ID style_name keyword value ... - - + +fix ID group-ID style_name keyword value ... + ID, group-ID are documented in fix command style_name = nvt or npt or nph @@ -508,14 +508,14 @@ thermostatting and barostatting. These fixes compute a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if one of these two sets of 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 all temp -compute fix-ID_press all pressure fix-ID_temp - - + +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp + + +compute fix-ID_temp all temp +compute fix-ID_press all 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”. For fix nvt, the group for the new computes @@ -606,10 +606,8 @@ 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: These fixes writes the state of all the thermostat and barostat variables to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html index 5e8d66853c..d11bbb105e 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 ... + ID, group-ID are documented in fix command style_name = nvt/eff or npt/eff or nph/eff @@ -223,9 +223,7 @@ degrees of freedom with the < the user must allow for these degrees of freedom to equilibrate (i.e. equi-partitioning of energy) through time integration. - - -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 d7c91846db..2c2d1a4d0a 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” @@ -207,9 +207,7 @@ 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_body.html b/doc/html/fix_nph_body.html index 891af950d5..f19aff76b1 100644 --- a/doc/html/fix_nph_body.html +++ b/doc/html/fix_nph_body.html @@ -172,10 +172,10 @@ 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” @@ -204,9 +204,7 @@ 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 0529dba9db..ec7a15a0cd 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” @@ -207,9 +207,7 @@ 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_nphug.html b/doc/html/fix_nphug.html index da32f6307b..85dd234fe3 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -229,14 +229,14 @@ controlled by another fix - e.g. by compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp - - -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp - - + +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp + + +compute fix-ID_temp all temp +compute fix-ID_press all 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 @@ -266,10 +266,8 @@ 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 values of E0, V0, and P0, as well as the state of all the thermostat and barostat variables to binary restart files. See the @@ -293,7 +291,7 @@ compute temperature on a subset of atoms. The fix_modify energy option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system’s potential energy as part of -thermodynamic output. Either way, this energy is not +thermodynamic output. Either way, this energy is *not* included in the definition of internal energy E when calculating the value of Delta in the above equation. These fixes compute a global scalar and a global vector of quantities, diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html index 203bb248e0..2216a34678 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” @@ -227,9 +227,7 @@ 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 7a21169513..b037898463 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” @@ -224,9 +224,7 @@ 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 1d5d6ed867..f05e786221 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” @@ -226,9 +226,7 @@ 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.html b/doc/html/fix_nve.html index bda99e1820..8427631928 100644 --- a/doc/html/fix_nve.html +++ b/doc/html/fix_nve.html @@ -173,10 +173,8 @@ 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_asphere.html b/doc/html/fix_nve_asphere.html index 435fea89b4..88dbabd521 100644 --- a/doc/html/fix_nve_asphere.html +++ b/doc/html/fix_nve_asphere.html @@ -153,9 +153,7 @@ 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 75760b0c6a..dd98e2ce40 100644 --- a/doc/html/fix_nve_asphere_noforce.html +++ b/doc/html/fix_nve_asphere_noforce.html @@ -150,10 +150,8 @@ 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 cd459a4379..45816df757 100644 --- a/doc/html/fix_nve_body.html +++ b/doc/html/fix_nve_body.html @@ -151,9 +151,7 @@ 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_eff.html b/doc/html/fix_nve_eff.html index d7e486fe39..cb8c7c772f 100644 --- a/doc/html/fix_nve_eff.html +++ b/doc/html/fix_nve_eff.html @@ -149,9 +149,7 @@ nuclei and electrons in the group for the fix nve command, except that the radius and radial velocity of electrons are also updated. - - -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_limit.html b/doc/html/fix_nve_limit.html index ede833982c..febff4c671 100644 --- a/doc/html/fix_nve_limit.html +++ b/doc/html/fix_nve_limit.html @@ -178,9 +178,7 @@ strategy is to turn off fix shake when performing initial dynamics that need this fix, then turn fix shake on when doing normal dynamics with a fixed-size timestep. - - -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_nve_line.html b/doc/html/fix_nve_line.html index 5168b08db0..5b6a9bb8ab 100644 --- a/doc/html/fix_nve_line.html +++ b/doc/html/fix_nve_line.html @@ -152,9 +152,7 @@ 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 06d68cd6ae..de2190636f 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -172,20 +172,18 @@ 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_noforce.html b/doc/html/fix_nve_noforce.html index 495a804493..ddde5961c0 100644 --- a/doc/html/fix_nve_noforce.html +++ b/doc/html/fix_nve_noforce.html @@ -155,9 +155,7 @@ command, but with fix nve/noforce, the forces on the wall atoms are unchanged, and can thus be printed by the dump command or queried with an equal-style variable that uses the fcm() group function to compute the total force on the group of atoms. - - -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 e0e8bf5189..2a70998598 100644 --- a/doc/html/fix_nve_sphere.html +++ b/doc/html/fix_nve_sphere.html @@ -189,10 +189,8 @@ 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 e707401c30..1462555ef2 100644 --- a/doc/html/fix_nve_tri.html +++ b/doc/html/fix_nve_tri.html @@ -152,9 +152,7 @@ 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 08a1bea12b..473db13d7f 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 @@ -213,9 +213,7 @@ 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 9fecb55fc4..57ba66659d 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 @@ -210,9 +210,7 @@ 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_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html index bcb049ebeb..d20d96a113 100644 --- a/doc/html/fix_nvt_manifold_rattle.html +++ b/doc/html/fix_nvt_manifold_rattle.html @@ -160,10 +160,8 @@ keyword = temp or tchain or every This fix combines the RATTLE-based (Andersen) time integrator of fix nve/manifold/rattle (Paquay) with a Nose-Hoover-chain thermostat to sample the canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt). For a list of currently supported manifolds and their parameters, see manifolds - - -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_sllod.html b/doc/html/fix_nvt_sllod.html index a2592ab7e7..09875bceb8 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 @@ -238,9 +238,7 @@ 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 8492983e42..c175a68bdc 100644 --- a/doc/html/fix_nvt_sllod_eff.html +++ b/doc/html/fix_nvt_sllod_eff.html @@ -157,9 +157,7 @@ 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 fc5b3ddab1..6a27b967ed 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 @@ -213,9 +213,7 @@ 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_oneway.html b/doc/html/fix_oneway.html index 8d22f6f62f..bb5b2a052e 100644 --- a/doc/html/fix_oneway.html +++ b/doc/html/fix_oneway.html @@ -156,10 +156,8 @@ dimension. The effect is that the particle moves in one direction only. This can be used, for example, as a simple model of a semi-permeable membrane, or as an implementation of Maxwell’s demon. - - -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_orient.html b/doc/html/fix_orient.html index 74dd4d3477..9b01605d28 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -232,9 +232,7 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are shown below. A tutorial that can help for writing the orientation files is given in (Wicaksono2) - - -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 of atom interactions with the grain diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html index 40d369afee..3094e830ae 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 @@ -239,9 +239,7 @@ 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_pimd.html b/doc/html/fix_pimd.html index 57ee90e294..545be26b57 100644 --- a/doc/html/fix_pimd.html +++ b/doc/html/fix_pimd.html @@ -232,9 +232,9 @@ ring. To run a PIMD simulation with M quasi-beads in each ring polymer using N MPI tasks for each partition’s domain-decomposition, you would use P = MxN processors (cores) and run the simulation as follows: -mpirun -np P lmp_mpi -partition MxN -in script - - + +mpirun -np P lmp_mpi -partition MxN -in script + Note that in the LAMMPS input script for a multi-partition simulation, it is often very useful to define a uloop-style variable such as variable ibead uloop M pad @@ -243,11 +243,11 @@ it is often very useful to define a dump dcd all dcd 10 system_${ibead}.dcd + +dump dcd all dcd 10 system_${ibead}.dcd restart 1000 system_${ibead}.restart1 system_${ibead}.restart2 read_restart system_${ibead}.restart2 - - + Restrictions diff --git a/doc/html/fix_planeforce.html b/doc/html/fix_planeforce.html index 9adcd39dda..83c023cc9e 100644 --- a/doc/html/fix_planeforce.html +++ b/doc/html/fix_planeforce.html @@ -151,9 +151,7 @@ components of force in the plane specified by the normal vector force perpendicular to the plane. If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane 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_poems.html b/doc/html/fix_poems.html index d7308971fb..f1dc2c297e 100644 --- a/doc/html/fix_poems.html +++ b/doc/html/fix_poems.html @@ -208,9 +208,7 @@ for in temperature and pressure computations. Similarly, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. - - -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_pour.html b/doc/html/fix_pour.html index ca471ec2c3..ee3f050be4 100644 --- a/doc/html/fix_pour.html +++ b/doc/html/fix_pour.html @@ -316,10 +316,8 @@ 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_press_berendsen.html b/doc/html/fix_press_berendsen.html index ffd58394b6..5afff5a4f3 100644 --- a/doc/html/fix_press_berendsen.html +++ b/doc/html/fix_press_berendsen.html @@ -275,10 +275,10 @@ these 4 keywords: 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”, and the group for the new computes is the same @@ -291,9 +291,7 @@ fix’s temperature or pressure via the or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this 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. The fix_modify temp and press options are supported by this fix. You can use them to assign a diff --git a/doc/html/fix_print.html b/doc/html/fix_print.html index 68739849fc..85cd254494 100644 --- a/doc/html/fix_print.html +++ b/doc/html/fix_print.html @@ -186,9 +186,7 @@ keyword was used. By default, the title line is as follows: where ID is replaced with the fix-ID. - - -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_property_atom.html b/doc/html/fix_property_atom.html index 474600ad06..81dc2b6611 100644 --- a/doc/html/fix_property_atom.html +++ b/doc/html/fix_property_atom.html @@ -153,11 +153,11 @@ Examples -fix 1 all property/atom mol -fix 1 all property/atom i_myflag1 i_myflag2 -fix 1 all property/atom d_sx d_sy d_sz - - + +fix 1 all property/atom mol +fix 1 all property/atom i_myflag1 i_myflag2 +fix 1 all property/atom d_sx d_sy d_sz + Description @@ -246,10 +246,10 @@ you need to initialize them explicitly. This can be done by the read_data command, using its fix keyword and passing it the fix-ID of this fix. Thus these commands: -fix prop all property/atom mol d_flag -read_data data.txt fix prop NULL Molecules - - + +fix prop all property/atom mol d_flag +read_data data.txt fix prop NULL Molecules + would allow a data file to have a section like this: Molecules @@ -271,11 +271,11 @@ per-atom properties can be in any order. set command. For example, if you wanted molecules defined for every set of 10 atoms, based on their atom-IDs, these commands could be used: -fix prop all property/atom mol -variable cluster atom ((id-1)/10)+1 -set id * mol v_cluster - - + +fix prop all property/atom mol +variable cluster atom ((id-1)/10)+1 +set id * mol v_cluster + The atom-style variable will create values for atoms with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the set commands assigns them to the molecule ID for each atom, @@ -292,11 +292,11 @@ properties in a completely general fashion. their values. This means that the values can be output via the dump custom command, accessed by fixes like fix ave/atom, accessed by other computes like compute reduce, or used in atom-style variables. For example, these commands will output two new properties to a custom dump file: -fix prop all property/atom i_flag1 d_flag2 -compute 1 all property/atom i_flag1 d_flag2 -dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] - - + +fix prop all property/atom i_flag1 d_flag2 +compute 1 all property/atom i_flag1 d_flag2 +dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] + If you wish to add new pair styles, fixes, or computes that use the per-atom @@ -324,10 +324,10 @@ command, there will be a new section named with the fix-ID existing data file and just add this Isotopes section with one line per atom containing atom-ID and mass. Either way, the extended data file can be read back with: -fix Isotopes all property/atom rmass ghost yes -read_data tip4p-isotopes.data fix Isotopes NULL Isotopes - - + +fix Isotopes all property/atom rmass ghost yes +read_data tip4p-isotopes.data fix Isotopes NULL Isotopes + Please note that the first Isotopes refers to the fix-ID and the second to the name of the section. The following input script code will now change the first 100 water molecules in this @@ -337,10 +337,8 @@ example to heavy water: set group hwat mass 2.0141018 - - -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_qbmsst.html b/doc/html/fix_qbmsst.html index 1fb67f4518..f3dca0ee47 100644 --- a/doc/html/fix_qbmsst.html +++ b/doc/html/fix_qbmsst.html @@ -157,10 +157,10 @@ Examples -fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) -fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) - - + +fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) +fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) + Two example input scripts are given, including shocked alpha quartz and shocked liquid methane. The input script first equilibrate an initial state with the quantum thermal bath at the target temperature @@ -242,10 +242,8 @@ thermal bath and the system before shock loading. For all pressure styles, the simulation box stays orthorhombic in shape. Parrinello-Rahman boundary conditions (tilted box) are supported by LAMMPS, but are not implemented for QBMSST. - - -Restart, fix_modify, output, run start/stop, minimize info +Restart, fix_modify, output, run start/stop, minimize info: Because the state of the random number generator is not written to binary restart files, this fix cannot be restarted “exactly” in an uninterrupted fashion. However, in a statistical @@ -271,16 +269,16 @@ headers, the following LAMMPS commands are suggested. Here the fix_modify energy command is also enabled to allow the thermo keyword etotal to print the quantity <i>etot</i>. See also the thermo_style command. -fix fix_id all msst z -fix_modify fix_id energy yes -variable dhug equal f_fix_id[1] -variable dray equal f_fix_id[2] -variable lgr_vel equal f_fix_id[3] -variable lgr_pos equal f_fix_id[4] -variable T_qm equal f_fix_id[5] -thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id - - + +fix fix_id all msst z +fix_modify fix_id energy yes +variable dhug equal f_fix_id[1] +variable dray equal f_fix_id[2] +variable lgr_vel equal f_fix_id[3] +variable lgr_pos equal f_fix_id[4] +variable T_qm equal f_fix_id[5] +thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id + The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of <i>etot</i>. This global scalar and the vector of 5 quantities can be accessed by various output commands. It is worth noting that the diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html index addd4b9ecf..05e428f671 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 @@ -292,9 +292,7 @@ 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 c7382d021d..3bf7a12a5c 100644 --- a/doc/html/fix_qeq_comb.html +++ b/doc/html/fix_qeq_comb.html @@ -195,10 +195,8 @@ 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 cc02c2516a..665de2e845 100644 --- a/doc/html/fix_qeq_reax.html +++ b/doc/html/fix_qeq_reax.html @@ -180,9 +180,7 @@ 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 1adbcf6567..fa8cf47576 100644 --- a/doc/html/fix_qmmm.html +++ b/doc/html/fix_qmmm.html @@ -156,9 +156,7 @@ 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 2f8934ddd0..cffd9b2764 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 Δ<i>t</i> as the time interval for the MD integration, f_max is always reset by the code to make -<i>α</i> = (int)(2f_maxΔ<i>t</i>)<sup><i>-1</i></sup> a +<i>α</i> = (int)(2*f_max*Δ<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 0275b0ad0e..e8c6d12136 100644 --- a/doc/html/fix_reax_bonds.html +++ b/doc/html/fix_reax_bonds.html @@ -157,10 +157,8 @@ 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 d4f4f182bd..fb72dd69c4 100644 --- a/doc/html/fix_reaxc_species.html +++ b/doc/html/fix_reaxc_species.html @@ -215,10 +215,8 @@ 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_recenter.html b/doc/html/fix_recenter.html index 6428f2b3a3..59a3c11e74 100644 --- a/doc/html/fix_recenter.html +++ b/doc/html/fix_recenter.html @@ -208,9 +208,7 @@ solvent would be cooled to compensate. A better solution for this simulation scenario is to use the fix spring command to tether the molecule in place. - - -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_rx.html b/doc/html/fix_rx.html index b39fe17f46..6d337133f8 100644 --- a/doc/html/fix_rx.html +++ b/doc/html/fix_rx.html @@ -147,13 +147,13 @@ Examples -fix 1 all rx kinetics.rx none dense lammps_rk4 -fix 1 all rx kinetics.rx none sparse lammps_rk4 1 -fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 - - + +fix 1 all rx kinetics.rx none dense lammps_rk4 +fix 1 all rx kinetics.rx none sparse lammps_rk4 1 +fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 + Description @@ -271,7 +271,7 @@ temperature exponent n, and the activation energy Ea. are used by the fix eos/table/rx command to define the thermodynamic properties of each species. Furthermore, the number of species molecules (i.e., concentration) can be specified -either with the set command using the “d_” prefix or by +either with the set command using the “d_” prefix or by reading directly the concentrations from a data file. For the latter case, the read_data command with the fix keyword should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g. diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html index 29f7570dc9..08de66a8eb 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. @@ -264,9 +264,7 @@ 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_setforce.html b/doc/html/fix_setforce.html index 35b7f76194..3d3ee5d72f 100644 --- a/doc/html/fix_setforce.html +++ b/doc/html/fix_setforce.html @@ -149,11 +149,11 @@ Examples -fix freeze indenter setforce 0.0 0.0 0.0 -fix 2 edge setforce NULL 0.0 0.0 -fix 2 edge setforce NULL 0.0 v_oscillate - - + +fix freeze indenter setforce 0.0 0.0 0.0 +fix 2 edge setforce NULL 0.0 0.0 +fix 2 edge setforce NULL 0.0 v_oscillate + Description @@ -200,10 +200,8 @@ 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_shake.html b/doc/html/fix_shake.html index 7cfb03e019..6c279062d0 100644 --- a/doc/html/fix_shake.html +++ b/doc/html/fix_shake.html @@ -289,10 +289,8 @@ the RATTLE constraints. You can check whether the constraints work correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp to 1 and recompiling LAMMPS. - - -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. None of the fix_modify options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various output commands. No parameter of these fixes diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html index 5be23f5d7b..0c2d9bc519 100644 --- a/doc/html/fix_smd.html +++ b/doc/html/fix_smd.html @@ -212,9 +212,7 @@ 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 ebf49b94ca..734c433f36 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 @@ Examples -fix 1 all smd/adjust_dt 0.1 - - + +fix 1 all smd/adjust_dt 0.1 + Description @@ -157,9 +157,7 @@ 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 194f99be37..04c9db062a 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 @@ 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 @@ -155,9 +155,7 @@ 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 e45d7d3f31..58bd9fda2c 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 @@ -161,12 +161,10 @@ max_nn = maximum number of neighbors 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 689017806f..e3c04397e7 100644 --- a/doc/html/fix_smd_move_triangulated_surface.html +++ b/doc/html/fix_smd_move_triangulated_surface.html @@ -128,55 +128,53 @@ 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 cb8449f1c0..16fc5abc50 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 @@ -174,10 +174,8 @@ 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 92d197d542..f51d51f6a6 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 @@ Examples -fix stl_surf all smd/wall_surface tool.stl 2 65535 - - + +fix stl_surf all smd/wall_surface tool.stl 2 65535 + Description @@ -160,9 +160,7 @@ 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 a1d40fbf68..413066a788 100644 --- a/doc/html/fix_spring.html +++ b/doc/html/fix_spring.html @@ -215,9 +215,7 @@ 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 7373fd8e56..5ea20d8a43 100644 --- a/doc/html/fix_spring_chunk.html +++ b/doc/html/fix_spring_chunk.html @@ -166,9 +166,7 @@ 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_rg.html b/doc/html/fix_spring_rg.html index aeaa3bece4..8cb641326c 100644 --- a/doc/html/fix_spring_rg.html +++ b/doc/html/fix_spring_rg.html @@ -166,9 +166,7 @@ the mass of the entire group. Note that K is thus a force constant for the aggregate force on the group of atoms, not a per-atom force. If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. - - -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_spring_self.html b/doc/html/fix_spring_self.html index dbc542e600..28e33fc5ed 100644 --- a/doc/html/fix_spring_self.html +++ b/doc/html/fix_spring_self.html @@ -160,9 +160,7 @@ 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_srd.html b/doc/html/fix_srd.html index 10de92548e..8ee372d9d4 100644 --- a/doc/html/fix_srd.html +++ b/doc/html/fix_srd.html @@ -207,9 +207,9 @@ rotations every N timesteps. SRD particles have a mass, temperature, characteristic timestep dt_SRD, and mean free path between collisions (lamda). The fundamental equation relating these 4 quantities is -lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) - - + +lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) + The mass of SRD particles is set by the mass command elsewhere in the input script. The SRD timestep dt_SRD is N times the step dt defined by the timestep command. Big @@ -419,10 +419,8 @@ epsilon or cutoff length to 0.0. The “delete_atoms overlap” command may be useful in setting up an SRD simulation to insure there are no initial overlaps between big and SRD 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. None of the fix_modify options are relevant to this fix. This fix tabulates several SRD statistics which are stored in a vector diff --git a/doc/html/fix_store_force.html b/doc/html/fix_store_force.html index 30ced5f810..43d5848e79 100644 --- a/doc/html/fix_store_force.html +++ b/doc/html/fix_store_force.html @@ -168,9 +168,7 @@ i.e. before other fixes that apply constraints. However, if you wish to include certain constraints (e.g. fix shake) in the stored force, then it could be specified after some fixes and before others. - - -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 per-atom array which can be accessed by various diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html index 9d236aa13f..0a885ed683 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 @@ -217,9 +217,7 @@ 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 826fcfb6f4..4a5b09b42a 100644 --- a/doc/html/fix_temp_rescale_eff.html +++ b/doc/html/fix_temp_rescale_eff.html @@ -154,9 +154,7 @@ 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 1fa84393e7..32b9de3cbb 100644 --- a/doc/html/fix_tfmc.html +++ b/doc/html/fix_tfmc.html @@ -228,10 +228,8 @@ 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 97325bd91e..05f63ab2de 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 @@ -221,9 +221,7 @@ 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_ti_rs.html b/doc/html/fix_ti_rs.html index 311cabb702..f298fc952d 100644 --- a/doc/html/fix_ti_rs.html +++ b/doc/html/fix_ti_rs.html @@ -128,9 +128,9 @@ fix ti/rs command Syntax -fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... - - + +fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... + ID, group-ID are documented in fix command ti/rs = style name of this fix command @@ -198,9 +198,7 @@ scaling is faster at temperatures closer to the initial temperature of the procedure. An example script using this command is provided in the examples/USER/misc/ti directory. - - -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 fix computes a global vector quantitie which can be accessed by various output commands. The vector has diff --git a/doc/html/fix_ti_spring.html b/doc/html/fix_ti_spring.html index a0a3a6db23..e7d63d947a 100644 --- a/doc/html/fix_ti_spring.html +++ b/doc/html/fix_ti_spring.html @@ -128,9 +128,9 @@ fix ti/spring command Syntax -fix ID group-ID ti/spring K t_switch t_equil keyword value ... - - + +fix ID group-ID ti/spring K t_switch t_equil keyword value ... + ID, group-ID are documented in fix command ti/spring = style name of this fix command @@ -205,9 +205,7 @@ issues with the canonical sampling of harmonic degrees of freedom (notice that the chain option will NOT solve this problem). The Langevin thermostat (fix langevin) works fine. - - -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 a fix in an input script that reads a restart file, so that the operation of diff --git a/doc/html/fix_tmd.html b/doc/html/fix_tmd.html index c8e628825e..a6a826dd62 100644 --- a/doc/html/fix_tmd.html +++ b/doc/html/fix_tmd.html @@ -128,9 +128,9 @@ fix tmd command Syntax -fix ID group-ID tmd rho_final file1 N file2 - - + +fix ID group-ID tmd rho_final file1 N file2 + ID, group-ID are documented in fix command tmd = style name of this fix command @@ -142,10 +142,10 @@ Examples -fix 1 all nve -fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file - - + +fix 1 all nve +fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file + Description @@ -199,9 +199,7 @@ restarted runs, the name of the TMD statistics file should be changed to prevent it being overwritten. For more information about TMD, see (Schlitter1) and (Schlitter2). - - -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_ttm.html b/doc/html/fix_ttm.html index af630d2964..1b12323895 100644 --- a/doc/html/fix_ttm.html +++ b/doc/html/fix_ttm.html @@ -131,50 +131,50 @@ fix ttm/mod command Syntax -fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile -fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile - - + +fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile +fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile + ID, group-ID are documented in fix command style = ttm or ttm_mod seed = random number seed to use for white noise (positive integer) remaining arguments for fix ttm: -C_e = electronic specific heat (energy/(electron*temperature) units) -rho_e = electronic density (electrons/volume units) -kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) -gamma_p = friction coefficient due to electron-ion interactions (mass/time units) -gamma_s = friction coefficient due to electronic stopping (mass/time units) -v_0 = electronic stopping critical velocity (velocity units) -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) - - + +C_e = electronic specific heat (energy/(electron*temperature) units) +rho_e = electronic density (electrons/volume units) +kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) +gamma_p = friction coefficient due to electron-ion interactions (mass/time units) +gamma_s = friction coefficient due to electronic stopping (mass/time units) +v_0 = electronic stopping critical velocity (velocity units) +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) + remaining arguments for fix ttm/mod: -init_file = file with the parameters to TTM -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) - - + +init_file = file with the parameters to TTM +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) + Examples -fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out -fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out -fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out - - + +fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out +fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out +fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out + Description @@ -330,34 +330,32 @@ is calculated as The fix ttm/mod parameter file init_file has the following syntax/ Every line with the odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows: -a_0, energy/(temperature*electron) units -a_1, energy/(temperature^2*electron) units -a_2, energy/(temperature^3*electron) units -a_3, energy/(temperature^4*electron) units -a_4, energy/(temperature^5*electron) units -C_0, energy/(temperature*electron) units -A, 1/temperature units -rho_e, electrons/volume units -D_e, length^2/time units -gamma_p, mass/time units -gamma_s, mass/time units -v_0, length/time units -I_0, energy/(time*length^2) units -lsurface, electron grid units (positive integer) -rsurface, electron grid units (positive integer) -l_skin, length units -tau, time units -B, dimensionless -lambda, length units -n_ion, ions/volume units -surface_movement: 0 to disable tracking of surface motion, 1 to enable -T_e_min, temperature units - - - + +a_0, energy/(temperature*electron) units +a_1, energy/(temperature^2*electron) units +a_2, energy/(temperature^3*electron) units +a_3, energy/(temperature^4*electron) units +a_4, energy/(temperature^5*electron) units +C_0, energy/(temperature*electron) units +A, 1/temperature units +rho_e, electrons/volume units +D_e, length^2/time units +gamma_p, mass/time units +gamma_s, mass/time units +v_0, length/time units +I_0, energy/(time*length^2) units +lsurface, electron grid units (positive integer) +rsurface, electron grid units (positive integer) +l_skin, length units +tau, time units +B, dimensionless +lambda, length units +n_ion, ions/volume units +surface_movement: 0 to disable tracking of surface motion, 1 to enable +T_e_min, temperature units + - -Restart, fix_modify, output, run start/stop, minimize info +Restart, fix_modify, output, run start/stop, minimize info: These fixes write the state of the electronic subsystem and the energy exchange between the subsystems 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 diff --git a/doc/html/fix_vector.html b/doc/html/fix_vector.html index 87d0a0ebd7..17b80b0202 100644 --- a/doc/html/fix_vector.html +++ b/doc/html/fix_vector.html @@ -138,21 +138,21 @@ 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 = value calculated by an equal-style variable with name -v_name[I] = Ith component of vector-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 = value calculated by an equal-style variable with name +v_name[I] = Ith component of vector-style variable with name + Examples -fix 1 all vector 100 c_myTemp -fix 1 all vector 5 c_myTemp v_integral - - + +fix 1 all vector 100 c_myTemp +fix 1 all vector 5 c_myTemp v_integral + Description @@ -166,12 +166,12 @@ rows is growing. The resulting vector or array can be used by other time-integrated using the variable trap() function. For example the velocity auto-correlation function (VACF) can be time-integrated, to yield a diffusion coefficient, as follows: -compute 2 all vacf -fix 5 all vector 1 c_2[4] -variable diff equal dt*trap(f_5) -thermo_style custom step v_diff - - + +compute 2 all vacf +fix 5 all vector 1 c_2[4] +variable diff equal dt*trap(f_5) +thermo_style custom step v_diff + The group specified with this command is ignored. However, note that specified values may represent calculations performed by computes and fixes which store their own “group” definitions. @@ -197,7 +197,7 @@ command with a timestep value that encompasses all the runs. This is so that the vector or array stored by this fix can be allocated to a sufficient size. -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 global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector @@ -209,7 +209,7 @@ not in your input script, but by 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 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 global vector @@ -217,7 +217,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error 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. An equal-style or vector-style variable can be referenced; the latter requires a bracketed term to specify the Ith element of the vector calculated by @@ -227,10 +227,8 @@ which can reference individual atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to be stored by fix vector. - - -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 or global array which can be diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html index 03773104e4..16fa977a8f 100644 --- a/doc/html/fix_viscosity.html +++ b/doc/html/fix_viscosity.html @@ -226,9 +226,7 @@ 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 5bf3e54e0a..e63286eaeb 100644 --- a/doc/html/fix_viscous.html +++ b/doc/html/fix_viscous.html @@ -194,10 +194,8 @@ 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.html b/doc/html/fix_wall.html index 8f3ac46551..0a1d123b92 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff Examples -fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box -fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 -fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 -fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 - - + +fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box +fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 +fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 +fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 + Description @@ -321,22 +321,22 @@ want. in a time-dependent fashion using equal-style variables. The wall interaction parameters (epsilon, sigma) could be varied with additional variable definitions. -variable ramp equal ramp(0,10) -fix 1 all wall xlo v_ramp 1.0 1.0 2.5 - - -variable linear equal vdisplace(0,20) -fix 1 all wall xlo v_linear 1.0 1.0 2.5 - - -variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 - - -variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 - - + +variable ramp equal ramp(0,10) +fix 1 all wall xlo v_ramp 1.0 1.0 2.5 + + +variable linear equal vdisplace(0,20) +fix 1 all wall xlo v_linear 1.0 1.0 2.5 + + +variable wiggle equal swiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + + +variable wiggle equal cwiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + 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, @@ -344,20 +344,18 @@ 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)) + - -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 of interaction between atoms and each wall to diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html index 08178f888a..b6360f4ffb 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 @@ -257,9 +257,7 @@ 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 ade80b4497..baed71d961 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -199,10 +199,8 @@ 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 4c6467cd42..9df5dfe8ef 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. @@ -264,10 +264,8 @@ 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_wall_region.html b/doc/html/fix_wall_region.html index 4f24bee99a..ba645d66ef 100644 --- a/doc/html/fix_wall_region.html +++ b/doc/html/fix_wall_region.html @@ -280,9 +280,7 @@ and does not blow up as r -> 0, but you must use a large enough epsilon that particles always reamin on the correct side of the region surface (r > 0). - - -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 of interaction between atoms and the wall to the diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html index c72f90b6bb..d244f4b0cb 100644 --- a/doc/html/fix_wall_srd.html +++ b/doc/html/fix_wall_srd.html @@ -159,11 +159,11 @@ Examples -fix xwalls all wall/srd xlo EDGE xhi EDGE -fix walls all wall/srd xlo 0.0 ylo 10.0 units box -fix top all wall/srd zhi v_pressdown - - + +fix xwalls all wall/srd xlo EDGE xhi EDGE +fix walls all wall/srd xlo 0.0 ylo 10.0 units box +fix top all wall/srd zhi v_pressdown + Description @@ -249,22 +249,22 @@ 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/srd xlo v_ramp - - -variable linear equal vdisplace(0,20) -fix 1 all wall/srd xlo v_linear - - -variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall/srd xlo v_wiggle - - -variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall/srd xlo v_wiggle - - + +variable ramp equal ramp(0,10) +fix 1 all wall/srd xlo v_ramp + + +variable linear equal vdisplace(0,20) +fix 1 all wall/srd xlo v_linear + + +variable wiggle equal swiggle(0.0,5.0,3.0) +fix 1 all wall/srd xlo v_wiggle + + +variable wiggle equal cwiggle(0.0,5.0,3.0) +fix 1 all wall/srd xlo v_wiggle + The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The displace(c0,velocity) function does something similar using the equation position = c0 + velocity*delta, @@ -272,20 +272,18 @@ 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)) + - -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/genindex.html b/doc/html/genindex.html index b625eb13f3..b40e27bf00 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -156,93 +156,93 @@ - angle_coeff + angle\_coeff - angle_style + angle\_style - angle_style charmm + angle\_style charmm - angle_style class2 + angle\_style class2 - angle_style cosine + angle\_style cosine - angle_style cosine/delta + angle\_style cosine/delta - angle_style cosine/periodic + angle\_style cosine/periodic - angle_style cosine/shift + angle\_style cosine/shift - angle_style cosine/shift/exp + angle\_style cosine/shift/exp - angle_style cosine/squared + angle\_style cosine/squared - angle_style dipole + angle\_style dipole - angle_style fourier + angle\_style fourier - angle_style fourier/simple + angle\_style fourier/simple - angle_style harmonic + angle\_style harmonic - angle_style hybrid + angle\_style hybrid - angle_style none + angle\_style none - angle_style quartic + angle\_style quartic - angle_style sdk + angle\_style sdk - angle_style table + angle\_style table - angle_style zero + angle\_style zero - atom_modify + atom\_modify - atom_style + atom\_style @@ -256,69 +256,69 @@ - bond_coeff + bond\_coeff - bond_style + bond\_style - bond_style class2 + bond\_style class2 - bond_style fene + bond\_style fene - bond_style fene/expand + bond\_style fene/expand - bond_style harmonic + bond\_style harmonic - bond_style harmonic/shift + bond\_style harmonic/shift - bond_style harmonic/shift/cut + bond\_style harmonic/shift/cut - bond_style hybrid + bond\_style hybrid - bond_style morse + bond\_style morse - bond_style none + bond\_style none - bond_style nonlinear + bond\_style nonlinear - bond_style quartic + bond\_style quartic - bond_style table + bond\_style table - bond_style zero + bond\_style zero - bond_write + bond\_write @@ -336,7 +336,7 @@ - change_box + change\_box @@ -348,7 +348,7 @@ - comm_style + comm\_style @@ -798,19 +798,19 @@ - compute_modify + compute\_modify - create_atoms + create\_atoms - create_bonds + create\_bonds - create_box + create\_box @@ -820,11 +820,11 @@ - delete_atoms + delete\_atoms - delete_bonds + delete\_bonds @@ -832,73 +832,73 @@ + dihedral\_coeff + + + + dihedral\_style + + + + dihedral\_style charmm + + + + dihedral\_style class2 + + + + dihedral\_style cosine/shift/exp + + + + dihedral\_style fourier + + + dihedral\_style harmonic - dihedral_coeff + dihedral\_style helix - dihedral_style + dihedral\_style hybrid - dihedral_style charmm + dihedral\_style multi/harmonic - dihedral_style class2 - - - - dihedral_style cosine/shift/exp - - - - dihedral_style fourier - - - - dihedral_style helix - - - - dihedral_style hybrid - - - - dihedral_style multi/harmonic - - - - dihedral_style nharmonic + dihedral\_style nharmonic - dihedral_style none + dihedral\_style none - dihedral_style opls + dihedral\_style opls - dihedral_style quadratic + dihedral\_style quadratic - dihedral_style spherical + dihedral\_style spherical - dihedral_style table + dihedral\_style table - dihedral_style zero + dihedral\_style zero @@ -906,7 +906,7 @@ - displace_atoms + displace\_atoms @@ -930,7 +930,7 @@ - dump_modify + dump\_modify @@ -1408,19 +1408,19 @@ - fix smd/adjust_dt + fix smd/adjust\_dt - fix smd/integrate_tlsph + fix smd/integrate\_tlsph - fix smd/integrate_ulsph + fix smd/integrate\_ulsph - fix smd/move_tri_surf + fix smd/move\_tri\_surf @@ -1428,7 +1428,7 @@ - fix smd/wall_surface + fix smd/wall\_surface @@ -1540,7 +1540,7 @@ - fix_modify + fix\_modify @@ -1570,57 +1570,57 @@ - improper_coeff + improper\_coeff - improper_style + improper\_style - improper_style class2 + improper\_style class2 - improper_style cossq + improper\_style cossq - improper_style cvff + improper\_style cvff - improper_style distance + improper\_style distance - improper_style fourier + improper\_style fourier - improper_style harmonic + improper\_style harmonic - improper_style hybrid + improper\_style hybrid - improper_style none + improper\_style none - improper_style ring + improper\_style ring - improper_style umbrella + improper\_style umbrella - improper_style zero + improper\_style zero @@ -1648,13 +1648,13 @@ - kspace_modify + kspace\_modify - kspace_style + kspace\_style @@ -1688,11 +1688,11 @@ - min_modify + min\_modify - min_style + min\_style @@ -1744,22 +1744,336 @@ + pair\_coeff + + + pair\_modify + pair\_style + + + + pair\_style adp + + + + pair\_style airebo + + + + pair\_style awpmd/cut + + + + pair\_style beck + + + + pair\_style body + + + pair\_style bop + pair\_style born + + + + pair\_style born/coul/long/cs + + + + pair\_style brownian + + + + pair\_style buck + + + pair\_style buck/long/coul/long + pair\_style colloid + + + + pair\_style comb + + + + pair\_style coul/cut + + + + pair\_style coul/diel + + + + pair\_style dpd + + + + pair\_style dpd/fdt + + + + pair\_style dsmc + + + + pair\_style eam + + + + pair\_style edip + + + + pair\_style eff/cut + + + + pair\_style eim + + + + pair\_style exp6/rx + + + + pair\_style gauss + + + + pair\_style gayberne + + + pair\_style gran/hooke + pair\_style hbond/dreiding/lj + + + + pair\_style hybrid + + + + pair\_style kim + + + + pair\_style lcbop + + + + pair\_style line/lj + + + + pair\_style list + + + + pair\_style lj/charmm/coul/charmm + + + + pair\_style lj/class2 + + + + pair\_style lj/cubic + + + + pair\_style lj/cut + + + + pair\_style lj/cut/dipole/cut + + + + pair\_style lj/cut/soft + + + + pair\_style lj/expand + + + + pair\_style lj/gromacs + + + + pair\_style lj/long/coul/long + + + + pair\_style lj/mdf + + + + pair\_style lj/sdk + + + + pair\_style lj/sf + + + + pair\_style lj/smooth + + + + pair\_style lj/smooth/linear + + + + pair\_style lj96/cut + + + + + + pair\_style lubricate + + + + pair\_style lubricateU + + + + pair\_style meam + + + + pair\_style mgpt + + + + pair\_style mie/cut + + + + pair\_style morse + + + + pair\_style multi/lucy + + + + pair\_style multi/lucy/rx + + + + pair\_style nb3b/harmonic + + + + pair\_style nm/cut + + + + pair\_style none + + + + pair\_style peri/pmb + + + + pair\_style polymorphic + + + + pair\_style quip + + + + pair\_style reax + + + + pair\_style reax/c + + + + pair\_style resquared + + + + pair\_style smd/hertz + + + + pair\_style smd/tlsph + + + + pair\_style smd/tri\_surface + + + + pair\_style smd/ulsph + + + + pair\_style smtbq + + + + pair\_style snap + + + + pair\_style soft + + + + pair\_style sph/heatconduction + + + + pair\_style sph/idealgas + + + + pair\_style sph/lj + + + + pair\_style sph/rhosum + + + + pair\_style sph/taitwater + + + + pair\_style sph/taitwater/morris + + + + pair\_style srp + + + + pair\_style sw + + + pair\_style table @@ -1768,361 +2082,47 @@ + pair\_style tersoff + + + + pair\_style tersoff/mod + + + + pair\_style tersoff/zbl + + + + pair\_style thole + + + + pair\_style tri/lj + + + pair\_style vashishta - pair_coeff + pair\_style yukawa - pair_style + pair\_style yukawa/colloid - pair_style adp + pair\_style zbl - pair_style airebo + pair\_style zero - pair_style awpmd/cut - - - - pair_style beck - - - - pair_style body - - - - pair_style born - - - - pair_style born/coul/long/cs - - - - pair_style brownian - - - - pair_style buck - - - - pair_style colloid - - - - pair_style comb - - - - pair_style coul/cut - - - - pair_style coul/diel - - - - pair_style dpd - - - - pair_style dpd/fdt - - - - pair_style dsmc - - - - pair_style eam - - - - pair_style edip - - - - pair_style eff/cut - - - - pair_style eim - - - - pair_style exp6/rx - - - - pair_style gauss - - - - pair_style gayberne - - - - pair_style hbond/dreiding/lj - - - - pair_style hybrid - - - - pair_style kim - - - - pair_style lcbop - - - - pair_style line/lj - - - - pair_style list - - - - pair_style lj/charmm/coul/charmm - - - - pair_style lj/class2 - - - - pair_style lj/cubic - - - - pair_style lj/cut - - - - pair_style lj/cut/dipole/cut - - - - pair_style lj/cut/soft - - - - pair_style lj/expand - - - - pair_style lj/gromacs - - - - pair_style lj/long/coul/long - - - - pair_style lj/mdf - - - - pair_style lj/sdk - - - - pair_style lj/sf - - - - - - pair_style lj/smooth - - - - pair_style lj/smooth/linear - - - - pair_style lj96/cut - - - - pair_style lubricate - - - - pair_style lubricateU - - - - pair_style meam - - - - pair_style mgpt - - - - pair_style mie/cut - - - - pair_style morse - - - - pair_style multi/lucy - - - - pair_style multi/lucy/rx - - - - pair_style nb3b/harmonic - - - - pair_style nm/cut - - - - pair_style none - - - - pair_style peri/pmb - - - - pair_style polymorphic - - - - pair_style quip - - - - pair_style reax - - - - pair_style reax/c - - - - pair_style resquared - - - - pair_style smd/hertz - - - - pair_style smd/tlsph - - - - pair_style smd/tri_surface - - - - pair_style smd/ulsph - - - - pair_style smtbq - - - - pair_style snap - - - - pair_style soft - - - - pair_style sph/heatconduction - - - - pair_style sph/idealgas - - - - pair_style sph/lj - - - - pair_style sph/rhosum - - - - pair_style sph/taitwater - - - - pair_style sph/taitwater/morris - - - - pair_style srp - - - - pair_style sw - - - - pair_style tersoff - - - - pair_style tersoff/mod - - - - pair_style tersoff/zbl - - - - pair_style thole - - - - pair_style tri/lj - - - - pair_style yukawa - - - - pair_style yukawa/colloid - - - - pair_style zbl - - - - pair_style zero - - - - pair_write + pair\_write @@ -2166,11 +2166,11 @@ - read_dump + read\_dump - read_restart + read\_restart @@ -2188,7 +2188,7 @@ - reset_timestep + reset\_timestep @@ -2200,7 +2200,7 @@ - run_style + run\_style @@ -2220,7 +2220,7 @@ - special_bonds + special\_bonds @@ -2246,13 +2246,13 @@ - thermo_modify + thermo\_modify - thermo_style + thermo\_style @@ -2310,21 +2310,21 @@ - write\_dump + write\_coeff - write_coeff + write\_data - write_data + write\_dump - write_restart + write\_restart diff --git a/doc/html/group.html b/doc/html/group.html index d21faf214a..009ce0deea 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 @@ -353,7 +353,8 @@ 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 @@ -361,8 +362,7 @@ fix 1 mobile nve run ${nsteps} group mobile static run ${nsteps} - - + Note All fixes and computes take a group ID as an argument, but they diff --git a/doc/html/if.html b/doc/html/if.html index f2ba9d34e7..fe0350f9d5 100644 --- a/doc/html/if.html +++ b/doc/html/if.html @@ -143,7 +143,8 @@ Examples -if "${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 & @@ -152,10 +153,9 @@ 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/improper_class2.html b/doc/html/improper_class2.html index c6758cff97..0d39e5935a 100644 --- a/doc/html/improper_class2.html +++ b/doc/html/improper_class2.html @@ -131,17 +131,17 @@ improper_style class2/omp command Syntax -improper_style class2 - - + +improper_style class2 + Examples -improper_style class2 -improper_coeff 1 100.0 0 -improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 - - + +improper_style class2 +improper_coeff 1 100.0 0 +improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 + Description diff --git a/doc/html/improper_coeff.html b/doc/html/improper_coeff.html index bad06f5d5e..a457db6736 100644 --- a/doc/html/improper_coeff.html +++ b/doc/html/improper_coeff.html @@ -128,9 +128,9 @@ improper_coeff command Syntax -improper_coeff N args - - + +improper_coeff N args + N = improper type (see asterisk form below) args = coefficients for one or more improper types @@ -138,11 +138,11 @@ Examples -improper_coeff 1 300.0 0.0 -improper_coeff * 80.2 -1 2 -improper_coeff *4 80.2 -1 2 - - + +improper_coeff 1 300.0 0.0 +improper_coeff * 80.2 -1 2 +improper_coeff *4 80.2 -1 2 + Description @@ -154,7 +154,7 @@ file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple improper types. This takes -the form “*” or “n” or “n” or “m*n”. If N = the number of improper +the form “*” or “*n” or “n*” or “m*n”. If N = the number of improper 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 @@ -163,10 +163,10 @@ asterisk means all types from m to n (inclusive). setting for the same improper type. For example, these commands set the coeffs for all improper types, then overwrite the coeffs for just improper type 2: -improper_coeff * 300.0 0.0 -improper_coeff 2 50.0 0.0 - - + +improper_coeff * 300.0 0.0 +improper_coeff 2 50.0 0.0 + A line in a data file that specifies improper coefficients uses the exact same format as the arguments of the improper_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html index 9a7aa85c8d..28c2370f09 100644 --- a/doc/html/improper_cossq.html +++ b/doc/html/improper_cossq.html @@ -131,16 +131,16 @@ improper_style cossq/omp command Syntax -improper_style cossq - - + +improper_style cossq + Examples -improper_style cossq -improper_coeff 1 4.0 0.0 - - + +improper_style cossq +improper_coeff 1 4.0 0.0 + Description diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html index 186c5aa3e1..461f02eeab 100644 --- a/doc/html/improper_cvff.html +++ b/doc/html/improper_cvff.html @@ -134,16 +134,16 @@ improper_style cvff/omp command Syntax -improper_style cvff - - + +improper_style cvff + Examples -improper_style cvff -improper_coeff 1 80.0 -1 4 - - + +improper_style cvff +improper_coeff 1 80.0 -1 4 + Description diff --git a/doc/html/improper_distance.html b/doc/html/improper_distance.html index 69718ece9a..3f42cef8d0 100644 --- a/doc/html/improper_distance.html +++ b/doc/html/improper_distance.html @@ -132,10 +132,10 @@ Examples -improper_style distance -improper_coeff 1 80.0 100.0 - - + +improper_style distance +improper_coeff 1 80.0 100.0 + Description diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html index 545282aa2a..be22144ccf 100644 --- a/doc/html/improper_fourier.html +++ b/doc/html/improper_fourier.html @@ -131,16 +131,16 @@ improper_style fourier/omp command Syntax -improper_style fourier - - + +improper_style fourier + Examples -improper_style fourier -improper_coeff 1 100.0 180.0 - - + +improper_style fourier +improper_coeff 1 100.0 180.0 + Description diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html index d268c62014..11553c0187 100644 --- a/doc/html/improper_harmonic.html +++ b/doc/html/improper_harmonic.html @@ -137,16 +137,16 @@ improper_style harmonic/omp command Syntax -improper_style harmonic - - + +improper_style harmonic + Examples -improper_style harmonic -improper_coeff 1 100.0 0 - - + +improper_style harmonic +improper_coeff 1 100.0 0 + Description diff --git a/doc/html/improper_hybrid.html b/doc/html/improper_hybrid.html index 438f01c690..742c0c785e 100644 --- a/doc/html/improper_hybrid.html +++ b/doc/html/improper_hybrid.html @@ -128,20 +128,20 @@ improper_style hybrid command Syntax -improper_style hybrid style1 style2 ... - - + +improper_style hybrid style1 style2 ... + style1,style2 = list of one or more improper styles Examples -improper_style hybrid harmonic helix -improper_coeff 1 harmonic 120.0 30 -improper_coeff 2 cvff 20.0 -1 2 - - + +improper_style hybrid harmonic helix +improper_coeff 1 harmonic 120.0 30 +improper_coeff 2 cvff 20.0 -1 2 + Description diff --git a/doc/html/improper_none.html b/doc/html/improper_none.html index 5b3ddfa062..daeabe5196 100644 --- a/doc/html/improper_none.html +++ b/doc/html/improper_none.html @@ -128,15 +128,15 @@ improper_style none command Syntax -improper_style none - - + +improper_style none + Examples -improper_style none - - + +improper_style none + Description diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html index aa3b557a57..0e7e4330b0 100644 --- a/doc/html/improper_ring.html +++ b/doc/html/improper_ring.html @@ -131,16 +131,16 @@ improper_style ring/omp command Syntax -improper_style ring - - + +improper_style ring + Examples -improper_style ring -improper_coeff 1 8000 70.5 - - + +improper_style ring +improper_coeff 1 8000 70.5 + Description @@ -150,8 +150,8 @@ specified by (i,j,k,l) indices and theta0 its equilibrium value. If the 4 atoms in an improper quadruplet (listed in the data file read by the read_data command) are ordered i,j,k,l then -theta_ijl is the angle between atoms i,j and l, theta_ijk is the -angle between atoms i,j and k, theta_kjl is the angle between atoms +theta_ijl is the angle between atoms i,j and l, theta_ijk is the +angle between atoms i,j and k, theta_kjl is the angle between atoms j,k, and l. The “ring” improper style implements the improper potential introduced by Destree et al., in Equation (9) of (Destree). This diff --git a/doc/html/improper_style.html b/doc/html/improper_style.html index b21d0199f5..cd71f9a567 100644 --- a/doc/html/improper_style.html +++ b/doc/html/improper_style.html @@ -128,20 +128,20 @@ improper_style command Syntax -improper_style style - - + +improper_style style + style = none or hybrid or class2 or cvff or harmonic Examples -improper_style harmonic -improper_style cvff -improper_style hybrid cvff harmonic - - + +improper_style harmonic +improper_style cvff +improper_style hybrid cvff harmonic + Description @@ -208,9 +208,9 @@ a package. Default -improper_style none - - + +improper_style none + diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html index f1fb943d5e..de79db67ef 100644 --- a/doc/html/improper_umbrella.html +++ b/doc/html/improper_umbrella.html @@ -131,16 +131,16 @@ improper_style umbrella/omp command Syntax -improper_style umbrella - - + +improper_style umbrella + Examples -improper_style umbrella -improper_coeff 1 100.0 180.0 - - + +improper_style umbrella +improper_coeff 1 100.0 180.0 + Description diff --git a/doc/html/improper_zero.html b/doc/html/improper_zero.html index 35365943bc..8fcf52d50c 100644 --- a/doc/html/improper_zero.html +++ b/doc/html/improper_zero.html @@ -134,11 +134,11 @@ improper_style zero nocoeff Examples -improper_style zero -improper_style zero nocoeff -improper_coeff * - - + +improper_style zero +improper_style zero nocoeff +improper_coeff * + Description diff --git a/doc/html/jump.html b/doc/html/jump.html index a87db9100d..8b2f4578a4 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 961ea342d6..2019d48cff 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 53a0c22ce2..5cecc5b41d 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 @@ 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 636cba7437..07d659915c 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 @@ -349,20 +349,21 @@ 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 & @@ -374,17 +375,16 @@ variable c equal $a*sqrt(8.0/3.0) 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/manifolds.html b/doc/html/manifolds.html index 73f57ef600..5fec3a287f 100644 --- a/doc/html/manifolds.html +++ b/doc/html/manifolds.html @@ -139,9 +139,9 @@ to the relevant fixes. - - - + + + @@ -159,7 +159,7 @@ to the relevant fixes. cylinder_dent R l a -x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise +x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise A cylinder with a dent around z = 0 @@ -195,7 +195,7 @@ to the relevant fixes. supersphere R q -|x|^q + |y|^q + |z|^q - R^q = 0 +|x|^q + |y|^q + |z|^q - R^q = 0 A supersphere of hyperradius R diff --git a/doc/html/mass.html b/doc/html/mass.html index b52482445a..45725432bf 100644 --- a/doc/html/mass.html +++ b/doc/html/mass.html @@ -138,11 +138,11 @@ Examples -mass 1 1.0 -mass * 62.5 -mass 2* 62.5 - - + +mass 1 1.0 +mass * 62.5 +mass 2* 62.5 + Description @@ -153,7 +153,7 @@ what mass units to use. The I index can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the mass for multiple atom types. This -takes the form “*” or “n” or “n” or “m*n”. If N = the number of +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 diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html index 5434586014..bd9a1f285f 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 + Description diff --git a/doc/html/min_style.html b/doc/html/min_style.html index 158cf94d45..c2c66e37b9 100644 --- a/doc/html/min_style.html +++ b/doc/html/min_style.html @@ -128,19 +128,19 @@ min_style command Syntax -min_style style - - + +min_style style + style = cg or hftn or sd or quickmin or fire Examples -min_style cg -min_style fire - - + +min_style cg +min_style fire + Description @@ -206,9 +206,9 @@ involving the electron radius in Default -min_style cg - - + +min_style cg + (Sheppard) Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008). See ref 1 in this paper for original reference to Qmin in diff --git a/doc/html/next.html b/doc/html/next.html index 91a180f677..e8b2338450 100644 --- a/doc/html/next.html +++ b/doc/html/next.html @@ -196,7 +196,8 @@ see in your directory during and after such a LAMMPS run. command with an index-style variable. If this input script is named in.polymer, 8 simulations would be run using data files from directories run1 thru run8. -variable d index run1 run2 run3 run4 run5 run6 run7 run8 + +variable d index run1 run2 run3 run4 run5 run6 run7 run8 shell cd $d read_data data.polymer run 10000 @@ -204,8 +205,7 @@ shell cd .. clear next d jump in.polymer - - + 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 @@ -214,7 +214,8 @@ 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 ... @@ -225,8 +226,7 @@ For example, this script will run 15 simulations in a double loop. 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 90477fc5ec..7146faef4d 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_adp.html b/doc/html/pair_adp.html index c38bbab6b5..5bc88ab7d0 100644 --- a/doc/html/pair_adp.html +++ b/doc/html/pair_adp.html @@ -131,17 +131,17 @@ pair_style adp/omp command Syntax -pair_style adp - - + +pair_style adp + Examples -pair_style adp -pair_coeff * * Ta.adp Ta -pair_coeff * * ../potentials/AlCu.adp Al Al Cu - - + +pair_style adp +pair_coeff * * Ta.adp Ta +pair_coeff * * ../potentials/AlCu.adp Al Al Cu + Description @@ -188,9 +188,9 @@ file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use the following pair_coeff command: -pair_coeff * * AlCu.adp Al Al Al Cu - - + +pair_coeff * * AlCu.adp Al Al Al Cu + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Al arguments map LAMMPS atom types 1,2,3 to the Al element in the extended setfl file. The final Cu argument maps diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html index 503da5ef6a..6827568073 100644 --- a/doc/html/pair_airebo.html +++ b/doc/html/pair_airebo.html @@ -143,9 +143,9 @@ pair_style rebo/omp command Syntax -pair_style style cutoff LJ_flag TORSION_flag - - + +pair_style style cutoff LJ_flag TORSION_flag + style = airebo or airebo/morse or rebo cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only) @@ -155,19 +155,19 @@ Examples -pair_style airebo 3.0 -pair_style airebo 2.5 1 0 -pair_coeff * * ../potentials/CH.airebo H C - - -pair_style airebo/morse 3.0 -pair_coeff * * ../potentials/CH.airebo-m H C - - -pair_style rebo -pair_coeff * * ../potentials/CH.airebo H C - - + +pair_style airebo 3.0 +pair_style airebo 2.5 1 0 +pair_coeff * * ../potentials/CH.airebo H C + + +pair_style airebo/morse 3.0 +pair_coeff * * ../potentials/CH.airebo-m H C + + +pair_style rebo +pair_coeff * * ../potentials/CH.airebo H C + Description @@ -242,9 +242,9 @@ to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C, and the 4th to be H, you would use the following pair_coeff command: -pair_coeff * * CH.airebo C C C H - - + +pair_coeff * * CH.airebo C C C H + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three C arguments map LAMMPS atom types 1,2,3 to the C element in the AIREBO file. The final H argument maps LAMMPS atom @@ -273,13 +273,13 @@ The 3 values correspond to the following sub-categories: To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: -compute 0 all pair airebo -variable REBO equal c_0[1] -variable LJ equal c_0[2] -variable TORSION equal c_0[3] -thermo_style custom step temp epair v_REBO v_LJ v_TORSION - - + +compute 0 all pair airebo +variable REBO equal c_0[1] +variable LJ equal c_0[2] +variable TORSION equal c_0[3] +thermo_style custom step temp epair v_REBO v_LJ v_TORSION + Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. diff --git a/doc/html/pair_awpmd.html b/doc/html/pair_awpmd.html index 5fb4a74c41..4b2dc24da3 100644 --- a/doc/html/pair_awpmd.html +++ b/doc/html/pair_awpmd.html @@ -128,9 +128,9 @@ pair_style awpmd/cut command Syntax -pair_style awpmd/cut Rc keyword value ... - - + +pair_style awpmd/cut Rc keyword value ... + Rc = global cutoff, -1 means cutoff of half the shortest box length zero or more keyword/value pairs may be appended @@ -154,12 +154,12 @@ Examples -pair_style awpmd/cut -1 -pair_style awpmd/cut 40.0 uhf free -pair_coeff * * -pair_coeff 2 2 20.0 - - + +pair_style awpmd/cut -1 +pair_style awpmd/cut 40.0 uhf free +pair_coeff * * +pair_coeff 2 2 20.0 + Description diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html index 10325668e8..baf69eecfa 100644 --- a/doc/html/pair_beck.html +++ b/doc/html/pair_beck.html @@ -134,20 +134,20 @@ pair_style beck/omp command Syntax -pair_style beck Rc - - + +pair_style beck Rc + Rc = cutoff for interactions (distance units) Examples -pair_style beck 8.0 -pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 -pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 - - + +pair_style beck 8.0 +pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 +pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 + Description diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html index 5f4df83aa4..5f623fb0b7 100644 --- a/doc/html/pair_body.html +++ b/doc/html/pair_body.html @@ -128,18 +128,18 @@ pair_style body command Syntax -pair_style body cutoff - - + +pair_style body cutoff + cutoff = global cutoff for interactions (distance units) Examples -pair_style body 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 - - + +pair_style body 3.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.5 2.5 + Description diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html index 3740bb4699..c73ca9761f 100644 --- a/doc/html/pair_born.html +++ b/doc/html/pair_born.html @@ -161,9 +161,9 @@ pair_style born/coul/wolf/omp command Syntax -pair_style style args - - + +pair_style style args + style = born or born/coul/long or born/coul/long/cs or born/coul/msm or born/coul/wolf args = list of arguments for a particular style @@ -185,31 +185,31 @@ Examples -pair_style born 10.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/long 10.0 -pair_style born/coul/long/cs 10.0 -pair_style born/coul/long 10.0 8.0 -pair_style born/coul/long/cs 10.0 8.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/msm 10.0 -pair_style born/coul/msm 10.0 8.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/wolf 0.25 10.0 -pair_style born/coul/wolf 0.25 10.0 9.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - + +pair_style born 10.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/long 10.0 +pair_style born/coul/long/cs 10.0 +pair_style born/coul/long 10.0 8.0 +pair_style born/coul/long/cs 10.0 8.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/msm 10.0 +pair_style born/coul/msm 10.0 8.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/wolf 0.25 10.0 +pair_style born/coul/wolf 0.25 10.0 9.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + Description diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html index eaf0a723c3..777cb46f10 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 @@ 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_buck.html b/doc/html/pair_buck.html index 58eccb8ce8..fa537931bf 100644 --- a/doc/html/pair_buck.html +++ b/doc/html/pair_buck.html @@ -179,9 +179,9 @@ pair_style buck/coul/msm/omp command Syntax -pair_style style args - - + +pair_style style args + style = buck or buck/coul/cut or buck/coul/long or buck/coul/long/cs or buck/coul/msm args = list of arguments for a particular style @@ -202,32 +202,32 @@ Examples -pair_style buck 2.5 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 - - -pair_style buck/coul/cut 10.0 -pair_style buck/coul/cut 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 - - -pair_style buck/coul/long 10.0 -pair_style buck/coul/long/cs 10.0 -pair_style buck/coul/long 10.0 8.0 -pair_style buck/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - - -pair_style buck/coul/msm 10.0 -pair_style buck/coul/msm 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - - + +pair_style buck 2.5 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 3.0 + + +pair_style buck/coul/cut 10.0 +pair_style buck/coul/cut 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 + + +pair_style buck/coul/long 10.0 +pair_style buck/coul/long/cs 10.0 +pair_style buck/coul/long 10.0 8.0 +pair_style buck/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + + +pair_style buck/coul/msm 10.0 +pair_style buck/coul/msm 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + Description diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html index 75994eddd2..93e44709ce 100644 --- a/doc/html/pair_charmm.html +++ b/doc/html/pair_charmm.html @@ -158,9 +158,9 @@ pair_style lj/charmm/coul/msm/omp command Syntax -pair_style style args - - + +pair_style style args + style = lj/charmm/coul/charmm or lj/charmm/coul/charmm/implicit or lj/charmm/coul/long or lj/charmm/coul/msm args = list of arguments for a particular style @@ -182,30 +182,30 @@ Examples -pair_style lj/charmm/coul/charmm 8.0 10.0 -pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/long 8.0 10.0 -pair_style lj/charmm/coul/long 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/msm 8.0 10.0 -pair_style lj/charmm/coul/msm 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - + +pair_style lj/charmm/coul/charmm 8.0 10.0 +pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 +pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/long 8.0 10.0 +pair_style lj/charmm/coul/long 8.0 10.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/msm 8.0 10.0 +pair_style lj/charmm/coul/msm 8.0 10.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + Description diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html index 5e62dd99ef..a2dee8a442 100644 --- a/doc/html/pair_class2.html +++ b/doc/html/pair_class2.html @@ -158,9 +158,9 @@ pair_style lj/class2/coul/long/omp command Syntax -pair_style style args - - + +pair_style style args + style = lj/class2 or lj/class2/coul/cut or lj/class2/coul/long args = list of arguments for a particular style @@ -178,24 +178,24 @@ Examples -pair_style lj/class2 10.0 -pair_coeff * * 100.0 2.5 -pair_coeff 1 2* 100.0 2.5 9.0 - - -pair_style lj/class2/coul/cut 10.0 -pair_style lj/class2/coul/cut 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 -pair_coeff 1 1 100.0 3.5 9.0 9.0 - - -pair_style lj/class2/coul/long 10.0 -pair_style lj/class2/coul/long 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - + +pair_style lj/class2 10.0 +pair_coeff * * 100.0 2.5 +pair_coeff 1 2* 100.0 2.5 9.0 + + +pair_style lj/class2/coul/cut 10.0 +pair_style lj/class2/coul/cut 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 +pair_coeff 1 1 100.0 3.5 9.0 9.0 + + +pair_style lj/class2/coul/long 10.0 +pair_style lj/class2/coul/long 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + Description diff --git a/doc/html/pair_coeff.html b/doc/html/pair_coeff.html index 1689bf6047..c5bb770a91 100644 --- a/doc/html/pair_coeff.html +++ b/doc/html/pair_coeff.html @@ -128,9 +128,9 @@ pair_coeff command Syntax -pair_coeff I J args - - + +pair_coeff I J args + I,J = atom types (see asterisk form below) args = coefficients for one or more pairs of atom types @@ -138,15 +138,15 @@ Examples -pair_coeff 1 2 1.0 1.0 2.5 -pair_coeff 2 * 1.0 1.0 -pair_coeff 3* 1*2 1.0 1.0 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff * * nialhjea 1 1 2 -pair_coeff * 3 morse.table ENTRY1 -pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) - - + +pair_coeff 1 2 1.0 1.0 2.5 +pair_coeff 2 * 1.0 1.0 +pair_coeff 3* 1*2 1.0 1.0 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff * * nialhjea 1 1 2 +pair_coeff * 3 morse.table ENTRY1 +pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) + Description @@ -160,7 +160,7 @@ required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. A wildcard asterisk can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs 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 @@ -170,10 +170,10 @@ asterisks imply type pairs where J < I, they are ignored. Note that a pair_coeff command can override a previous setting for the same I,J pair. For example, these commands set the coeffs for all I,J pairs, then overwrite the coeffs for just the I,J = 2,3 pair: -pair_coeff * * 1.0 1.0 2.5 -pair_coeff 2 3 2.0 1.0 1.12 - - + +pair_coeff * * 1.0 1.0 2.5 +pair_coeff 2 3 2.0 1.0 1.12 + A line in a data file that specifies pair coefficients uses the exact same format as the arguments of the pair_coeff command in an input script, with the exception of the I,J type arguments. In each line of @@ -214,13 +214,13 @@ copying them into your working directory. Environment variables are set in different ways for different shells. Here are example settings for csh, tcsh: -% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials - - + +% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials + bash: -% export LAMMPS_POTENTIALS=/path/to/lammps/potentials - - + +% export LAMMPS_POTENTIALS=/path/to/lammps/potentials + Windows: % set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials" diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html index c4254f1606..a1520bc730 100644 --- a/doc/html/pair_colloid.html +++ b/doc/html/pair_colloid.html @@ -134,22 +134,22 @@ pair_style colloid/omp command Syntax -pair_style colloid cutoff - - + +pair_style colloid cutoff + cutoff = global cutoff for colloidal interactions (distance units) Examples -pair_style colloid 10.0 -pair_coeff * * 25 1.0 10.0 10.0 -pair_coeff 1 1 144 1.0 0.0 0.0 3.0 -pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 -pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 - - + +pair_style colloid 10.0 +pair_coeff * * 25 1.0 10.0 10.0 +pair_coeff 1 1 144 1.0 0.0 0.0 3.0 +pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 +pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 + Description diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html index d7ca86f242..c0768ee36a 100644 --- a/doc/html/pair_comb.html +++ b/doc/html/pair_comb.html @@ -134,10 +134,10 @@ pair_style comb3 command Syntax -pair_style comb -pair_style comb3 keyword - - + +pair_style comb +pair_style comb3 keyword + keyword = polar polar value = polar_on or polar_off = whether or not to include atomic polarization @@ -145,15 +145,15 @@ keyword = polar Examples -pair_style comb -pair_coeff * * ../potentials/ffield.comb Si -pair_coeff * * ../potentials/ffield.comb Hf Si O - - -pair_style comb3 polar_off -pair_coeff * * ../potentials/ffield.comb3 O Cu N C O - - + +pair_style comb +pair_coeff * * ../potentials/ffield.comb Si +pair_coeff * * ../potentials/ffield.comb Hf Si O + + +pair_style comb3 polar_off +pair_coeff * * ../potentials/ffield.comb3 O Cu N C O + Description @@ -191,9 +191,9 @@ command, where N is the number of LAMMPS atom types. HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would use the following pair_coeff command: -pair_coeff * * ../potentials/ffield.comb Si Hf O Si - - + +pair_coeff * * ../potentials/ffield.comb Si Hf O Si + The first two arguments must be * * so as to span all LAMMPS atom types. The first and last Si arguments map LAMMPS atom types 1 and 4 to the Si element in the ffield.comb file. The second Hf argument diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html index 1df9e6791a..98cba31724 100644 --- a/doc/html/pair_coul.html +++ b/doc/html/pair_coul.html @@ -206,18 +206,18 @@ pair_style tip4p/long/omp command Syntax -pair_style coul/cut cutoff -pair_style coul/debye kappa cutoff -pair_style coul/dsf alpha cutoff -pair_style coul/long cutoff -pair_style coul/long/cs cutoff -pair_style coul/long/gpu cutoff -pair_style coul/wolf alpha cutoff -pair_style coul/streitz cutoff keyword alpha -pair_style tip4p/cut otype htype btype atype qdist cutoff -pair_style tip4p/long otype htype btype atype qdist cutoff - - + +pair_style coul/cut cutoff +pair_style coul/debye kappa cutoff +pair_style coul/dsf alpha cutoff +pair_style coul/long cutoff +pair_style coul/long/cs cutoff +pair_style coul/long/gpu cutoff +pair_style coul/wolf alpha cutoff +pair_style coul/streitz cutoff keyword alpha +pair_style tip4p/cut otype htype btype atype qdist cutoff +pair_style tip4p/long otype htype btype atype qdist cutoff + cutoff = global cutoff for Coulombic interactions kappa = Debye length (inverse distance units) @@ -226,46 +226,46 @@ Examples -pair_style coul/cut 2.5 -pair_coeff * * -pair_coeff 2 2 3.5 - - -pair_style coul/debye 1.4 3.0 -pair_coeff * * -pair_coeff 2 2 3.5 - - -pair_style coul/dsf 0.05 10.0 -pair_coeff * * - - -pair_style coul/long 10.0 -pair_style coul/long/cs 10.0 -pair_coeff * * - - -pair_style coul/msm 10.0 -pair_coeff * * - - -pair_style coul/wolf 0.2 9.0 -pair_coeff * * - - -pair_style coul/streitz 12.0 ewald -pair_style coul/streitz 12.0 wolf 0.30 -pair_coeff * * AlO.streitz Al O - - -pair_style tip4p/cut 1 2 7 8 0.15 12.0 -pair_coeff * * - - -pair_style tip4p/long 1 2 7 8 0.15 10.0 -pair_coeff * * - - + +pair_style coul/cut 2.5 +pair_coeff * * +pair_coeff 2 2 3.5 + + +pair_style coul/debye 1.4 3.0 +pair_coeff * * +pair_coeff 2 2 3.5 + + +pair_style coul/dsf 0.05 10.0 +pair_coeff * * + + +pair_style coul/long 10.0 +pair_style coul/long/cs 10.0 +pair_coeff * * + + +pair_style coul/msm 10.0 +pair_coeff * * + + +pair_style coul/wolf 0.2 9.0 +pair_coeff * * + + +pair_style coul/streitz 12.0 ewald +pair_style coul/streitz 12.0 wolf 0.30 +pair_coeff * * AlO.streitz Al O + + +pair_style tip4p/cut 1 2 7 8 0.15 12.0 +pair_coeff * * + + +pair_style tip4p/long 1 2 7 8 0.15 10.0 +pair_coeff * * + Description @@ -317,21 +317,21 @@ used with p short-range potential that has been parameterized appropriately) via the pair_style hybrid/overlay command. Likewise, charge equilibration must be performed via the fix qeq/slater command. For example: -pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz - - + +pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy +pair_coeff * * coul/streitz AlO.streitz Al O +pair_coeff * * eam/alloy AlO.eam.alloy Al O +fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz + The keyword wolf in the coul/streitz command denotes computing Coulombic interactions via Wolf summation. An additional damping parameter is required for the Wolf summation, as described for the coul/wolf potential above. Alternatively, Coulombic interactions can be computed via an Ewald summation. For example: -pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -kspace_style ewald 1e-6 - - + +pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy +kspace_style ewald 1e-6 + Keyword ewald does not need a damping parameter, but a kspace_style must be defined, which can be style ewald or pppm. The Ewald method was used in Streitz and diff --git a/doc/html/pair_coul_diel.html b/doc/html/pair_coul_diel.html index 1f7d3e04af..88e078dfd5 100644 --- a/doc/html/pair_coul_diel.html +++ b/doc/html/pair_coul_diel.html @@ -131,17 +131,17 @@ pair_style coul/diel/omp command Syntax -pair_style coul/diel cutoff - - + +pair_style coul/diel cutoff + cutoff = global cutoff (distance units) Examples -pair_style coul/diel 3.5 -pair_coeff 1 4 78. 1.375 0.112 - - + +pair_style coul/diel 3.5 +pair_coeff 1 4 78. 1.375 0.112 + Description diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html index 75b462f741..12d0c515ef 100644 --- a/doc/html/pair_cs.html +++ b/doc/html/pair_cs.html @@ -131,9 +131,9 @@ pair_style buck/coul/long/cs command Syntax -pair_style style args - - + +pair_style style args + style = born/coul/long/cs or buck/coul/long/cs args = list of arguments for a particular style @@ -149,16 +149,16 @@ Examples -pair_style born/coul/long/cs 10.0 8.0 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style buck/coul/long/cs 10.0 -pair_style buck/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - - + +pair_style born/coul/long/cs 10.0 8.0 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style buck/coul/long/cs 10.0 +pair_style buck/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + Description diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html index f605baaa87..1275469c41 100644 --- a/doc/html/pair_dpd.html +++ b/doc/html/pair_dpd.html @@ -143,10 +143,10 @@ pair_style dpd/tstat/omp command Syntax -pair_style dpd T cutoff seed -pair_style dpd/tstat Tstart Tstop cutoff seed - - + +pair_style dpd T cutoff seed +pair_style dpd/tstat Tstart Tstop cutoff seed + T = temperature (temperature units) Tstart,Tstop = desired temperature at start/end of run (temperature units) @@ -156,16 +156,16 @@ Examples -pair_style dpd 1.0 2.5 34387 -pair_coeff * * 3.0 1.0 -pair_coeff 1 1 3.0 1.0 1.0 - - -pair_style dpd/tstat 1.0 1.0 2.5 34387 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 1.0 - - + +pair_style dpd 1.0 2.5 34387 +pair_coeff * * 3.0 1.0 +pair_coeff 1 1 3.0 1.0 1.0 + + +pair_style dpd/tstat 1.0 1.0 2.5 34387 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 1.0 + Description diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html index cd8033694c..e6132b19d2 100644 --- a/doc/html/pair_dpd_fdt.html +++ b/doc/html/pair_dpd_fdt.html @@ -131,9 +131,9 @@ pair_style dpd/fdt/energy command Syntax -pair_style style args - - + +pair_style style args + style = dpd/fdt or dpd/fdt/energy args = list of arguments for a particular style @@ -150,14 +150,14 @@ Examples -pair_style dpd/fdt 300.0 2.5 34387 -pair_coeff * * 3.0 1.0 2.5 - - -pair_style dpd/fdt/energy 2.5 34387 -pair_coeff * * 3.0 1.0 0.1 2.5 - - + +pair_style dpd/fdt 300.0 2.5 34387 +pair_coeff * * 3.0 1.0 2.5 + + +pair_style dpd/fdt/energy 2.5 34387 +pair_coeff * * 3.0 1.0 0.1 2.5 + Description diff --git a/doc/html/pair_dsmc.html b/doc/html/pair_dsmc.html index 5f8ddd5600..4c971f1dd1 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 @@ 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_eam.html b/doc/html/pair_eam.html index 81abf57a5a..62a0305a0c 100644 --- a/doc/html/pair_eam.html +++ b/doc/html/pair_eam.html @@ -176,32 +176,32 @@ pair_style eam/fs/opt command Syntax -pair_style style - - + +pair_style style + style = eam or eam/alloy or eam/cd or eam/fs Examples -pair_style eam -pair_coeff * * cuu3 -pair_coeff 1*3 1*3 niu3.eam - - -pair_style eam/alloy -pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni - - -pair_style eam/cd -pair_coeff * * ../potentials/FeCr.cdeam Fe Cr - - -pair_style eam/fs -pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni - - + +pair_style eam +pair_coeff * * cuu3 +pair_coeff 1*3 1*3 niu3.eam + + +pair_style eam/alloy +pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni + + +pair_style eam/cd +pair_coeff * * ../potentials/FeCr.cdeam Fe Cr + + +pair_style eam/fs +pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni + Description @@ -270,9 +270,9 @@ single argument: filename Thus the following command -pair_coeff *2 1*2 cuu3.eam - - + +pair_coeff *2 1*2 cuu3.eam + will read the cuu3 potential file and use the tabulated Cu values for F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs 1,2 and 2,1 are ignored). See the pair_coeff doc @@ -315,9 +315,9 @@ density). The units for the effective charge Z are “atomic charge” sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used by LAMMPS to compute the pair potential term in the EAM energy expression as r*phi, in units of eV-Angstroms, via the formula -r*phi = 27.2 * 0.529 * Zi * Zj - - + +r*phi = 27.2 * 0.529 * Zi * Zj + where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. Style eam/alloy computes pairwise interactions using the same @@ -350,9 +350,9 @@ page for alternate ways to specify the path for the potential file. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Ni, and the 4th to be Al, you would use the following pair_coeff command: -pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al - - + +pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni element in the setfl file. The final Al argument maps LAMMPS atom @@ -446,9 +446,9 @@ require that; the user can tabulate any functional form desired in the FS potential files. For style eam/fs, the form of the pair_coeff command is exactly the same as for style eam/alloy, e.g. -pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al - - + +pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al + where there are N additional arguments after the filename, where N is the number of LAMMPS atom types. See the pair_coeff doc page for alternate ways to specify the path for the potential diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html index 8c9d9ccdee..54a690dde1 100644 --- a/doc/html/pair_edip.html +++ b/doc/html/pair_edip.html @@ -128,12 +128,12 @@ pair_style edip command Syntax -pair_style edip - - -pair_style edip/omp - - + +pair_style edip + + +pair_style edip/omp + Examples diff --git a/doc/html/pair_eff.html b/doc/html/pair_eff.html index 6bcd28cef2..939cdbbf5c 100644 --- a/doc/html/pair_eff.html +++ b/doc/html/pair_eff.html @@ -128,9 +128,9 @@ pair_style eff/cut command Syntax -pair_style eff/cut cutoff keyword args ... - - + +pair_style eff/cut cutoff keyword args ... + cutoff = global cutoff for Coulombic interactions zero or more keyword/value pairs may be appended @@ -146,16 +146,16 @@ keyword = limit/eradius or pressure/evirials or ecp Examples -pair_style eff/cut 39.7 -pair_style eff/cut 40.0 limit/eradius -pair_style eff/cut 40.0 limit/eradius pressure/evirials -pair_style eff/cut 40.0 ecp 1 Si 3 C -pair_coeff * * -pair_coeff 2 2 20.0 -pair_coeff 1 s 0.320852 2.283269 0.814857 -pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 - - + +pair_style eff/cut 39.7 +pair_style eff/cut 40.0 limit/eradius +pair_style eff/cut 40.0 limit/eradius pressure/evirials +pair_style eff/cut 40.0 ecp 1 Si 3 C +pair_coeff * * +pair_coeff 2 2 20.0 +pair_coeff 1 s 0.320852 2.283269 0.814857 +pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 + Description diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html index 62c5a4a918..831c9f00dc 100644 --- a/doc/html/pair_eim.html +++ b/doc/html/pair_eim.html @@ -131,21 +131,21 @@ pair_style eim/omp command Syntax -pair_style style - - + +pair_style style + style = eim Examples -pair_style eim -pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl -pair_coeff * * Na Cl ffield.eim Na Na Na Cl -pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na - - + +pair_style eim +pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl +pair_coeff * * Na Cl ffield.eim Na Na Na Cl +pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na + Description @@ -207,9 +207,9 @@ to specify the path for the potential file. system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Na, and the 4th to be Cl, you would use the following pair_coeff command: -pair_coeff * * Na Cl ffield.eim Na Na Na Cl - - + +pair_coeff * * Na Cl ffield.eim Na Na Na Cl + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The filename is the EIM potential file. The Na and Cl arguments (before the file name) are the two elements for which info will be diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html index 6bd4ae6865..79f0a9b4ae 100644 --- a/doc/html/pair_exp6_rx.html +++ b/doc/html/pair_exp6_rx.html @@ -128,21 +128,21 @@ pair_style exp6/rx command Syntax -pair_style exp6/rx cutoff - - + +pair_style exp6/rx cutoff + cutoff = global cutoff for DPD interactions (distance units) Examples -pair_style exp6/rx 10.0 -pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 -pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 -pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 - - + +pair_style exp6/rx 10.0 +pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 +pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 +pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 + Description diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html index 2f167476f8..d90d449b83 100644 --- a/doc/html/pair_gauss.html +++ b/doc/html/pair_gauss.html @@ -140,25 +140,25 @@ pair_style gauss/cut/omp command Syntax -pair_style gauss cutoff -pair_style gauss/cut cutoff - - + +pair_style gauss cutoff +pair_style gauss/cut cutoff + cutoff = global cutoff for Gauss interactions (distance units) Examples -pair_style gauss 12.0 -pair_coeff * * 1.0 0.9 -pair_coeff 1 4 1.0 0.9 10.0 - - -pair_style gauss/cut 3.5 -pair_coeff 1 4 0.2805 1.45 0.112 - - + +pair_style gauss 12.0 +pair_coeff * * 1.0 0.9 +pair_coeff 1 4 1.0 0.9 10.0 + + +pair_style gauss/cut 3.5 +pair_coeff 1 4 0.2805 1.45 0.112 + Description @@ -239,11 +239,11 @@ sites have an atom within the distance at which the force is a maximum = sqrt(0.5/b). This quantity can be accessed via the compute pair command as a vector of values of length 1. To print this quantity to the log file (with a descriptive column heading) the following commands could be included in an input script: -compute gauss all pair gauss -variable occ equal c_gauss[1] -thermo_style custom step temp epair v_occ - - + +compute gauss all pair gauss +variable occ equal c_gauss[1] +thermo_style custom step temp epair v_occ + diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html index 0b02a49a51..68e46bd2d8 100644 --- a/doc/html/pair_gayberne.html +++ b/doc/html/pair_gayberne.html @@ -137,9 +137,9 @@ pair_style gayberne/omp command Syntax -pair_style gayberne gamma upsilon mu cutoff - - + +pair_style gayberne gamma upsilon mu cutoff + gamma = shift for potential minimum (typically 1) upsilon = exponent for eta orientation-dependent energy function @@ -149,10 +149,10 @@ Examples -pair_style gayberne 1.0 1.0 1.0 10.0 -pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 - - + +pair_style gayberne 1.0 1.0 1.0 10.0 +pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 + Description diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html index 7cc3aee2ce..a58a10912a 100644 --- a/doc/html/pair_gromacs.html +++ b/doc/html/pair_gromacs.html @@ -140,9 +140,9 @@ pair_style lj/gromacs/coul/gromacs/omp command Syntax -pair_style style args - - + +pair_style style args + style = lj/gromacs or lj/gromacs/coul/gromacs args = list of arguments for a particular style @@ -157,16 +157,16 @@ Examples -pair_style lj/gromacs 9.0 12.0 -pair_coeff * * 100.0 2.0 -pair_coeff 2 2 100.0 2.0 8.0 10.0 - - -pair_style lj/gromacs/coul/gromacs 9.0 12.0 -pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 - - + +pair_style lj/gromacs 9.0 12.0 +pair_coeff * * 100.0 2.0 +pair_coeff 2 2 100.0 2.0 8.0 10.0 + + +pair_style lj/gromacs/coul/gromacs 9.0 12.0 +pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 + Description diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html index 659f637dec..e639ba34e8 100644 --- a/doc/html/pair_hbond_dreiding.html +++ b/doc/html/pair_hbond_dreiding.html @@ -137,9 +137,9 @@ pair_style hbond/dreiding/morse/omp command Syntax -pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof - - + +pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof + style = hbond/dreiding/lj or hbond/dreiding/morse n = cosine angle periodicity @@ -151,14 +151,14 @@ Examples -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 - - -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 - - + +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 +pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 + + +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 +pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 + Description @@ -265,7 +265,7 @@ follows: A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogens. This takes the form -“*” or “n” or “n” or “m*n”. See the pair_coeff command +“*” or “*n” or “n*” or “m*n”. See the pair_coeff command doc page for details. If the donor flag is i, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor @@ -321,12 +321,12 @@ quantities can be accessed via the compute hb all pair hbond/dreiding/lj -variable n_hbond equal c_hb[1] #number hbonds -variable E_hbond equal c_hb[2] #hbond energy -thermo_style custom step temp epair v_E_hbond - - + +compute hb all pair hbond/dreiding/lj +variable n_hbond equal c_hb[1] #number hbonds +variable E_hbond equal c_hb[2] #hbond energy +thermo_style custom step temp epair v_E_hbond + diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html index afe0cebcd6..60044d0faf 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_kim.html b/doc/html/pair_kim.html index 0465abb269..b3dd8684cb 100644 --- a/doc/html/pair_kim.html +++ b/doc/html/pair_kim.html @@ -128,9 +128,9 @@ pair_style kim command Syntax -pair_style kim virialmode model printflag - - + +pair_style kim virialmode model printflag + virialmode = KIMvirial or LAMMPSvirial model = name of KIM model (potential) @@ -139,14 +139,14 @@ Examples -pair_style kim KIMvirial model_Ar_P_Morse -pair_coeff * * Ar Ar - - -pair_style kim KIMvirial model_Ar_P_Morse 1 -pair_coeff * * Ar Ar - - + +pair_style kim KIMvirial model_Ar_P_Morse +pair_coeff * * Ar Ar + + +pair_style kim KIMvirial model_Ar_P_Morse 1 +pair_coeff * * Ar Ar + Description @@ -177,9 +177,9 @@ pair_coeff command, where N is the number of LAMMPS atom types: As an example, imagine the KIM model supports Si and C atoms. If your LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * Si Si Si C - - + +pair_coeff * * Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to Si as defined within KIM. The final C argument maps LAMMPS atom type 4 to C diff --git a/doc/html/pair_lcbop.html b/doc/html/pair_lcbop.html index 7e2e82ff4a..9f3f225455 100644 --- a/doc/html/pair_lcbop.html +++ b/doc/html/pair_lcbop.html @@ -128,16 +128,16 @@ pair_style lcbop command Syntax -pair_style lcbop - - + +pair_style lcbop + Examples -pair_style lcbop -pair_coeff * * ../potentials/C.lcbop C - - + +pair_style lcbop +pair_coeff * * ../potentials/C.lcbop C + Description @@ -157,9 +157,9 @@ where N is the number of LAMMPS atom types: to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C you would use the following pair_coeff command: -pair_coeff * * C.lcbop C C C NULL - - + +pair_coeff * * C.lcbop C C C NULL + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first C argument maps LAMMPS atom type 1 to the C element in the LCBOP file. If a mapping value is specified as NULL, the mapping is diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html index f36f573822..c79f73301e 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_list.html b/doc/html/pair_list.html index f7d59aba21..2897df868b 100644 --- a/doc/html/pair_list.html +++ b/doc/html/pair_list.html @@ -128,9 +128,9 @@ pair_style list command Syntax -pair_style list listfile cutoff keyword - - + +pair_style list listfile cutoff keyword + listfile = name of file with list of pairwise interactions cutoff = global cutoff (distance units) @@ -139,15 +139,15 @@ Examples -pair_style list restraints.txt 200.0 -pair_coeff * * - - -pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 3* 3* list - - + +pair_style list restraints.txt 200.0 +pair_coeff * * + + +pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff 3* 3* list + Description diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html index fd46ab5d3b..73f9948c27 100644 --- a/doc/html/pair_lj.html +++ b/doc/html/pair_lj.html @@ -218,9 +218,9 @@ pair_style lj/cut/tip4p/long/opt command Syntax -pair_style style args - - + +pair_style style args + style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/long/cs or lj/cut/coul/msm or lj/cut/tip4p/long args = list of arguments for a particular style @@ -261,56 +261,56 @@ Examples -pair_style lj/cut 2.5 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 - - -pair_style lj/cut/coul/cut 10.0 -pair_style lj/cut/coul/cut 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 -pair_coeff 1 1 100.0 3.5 9.0 9.0 - - -pair_style lj/cut/coul/debye 1.5 3.0 -pair_style lj/cut/coul/debye 1.5 2.5 5.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 -pair_coeff 1 1 1.0 1.5 2.5 5.0 - - -pair_style lj/cut/coul/dsf 0.05 2.5 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 2.5 - - -pair_style lj/cut/coul/long 10.0 -pair_style lj/cut/coul/long/cs 10.0 -pair_style lj/cut/coul/long 10.0 8.0 -pair_style lj/cut/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/coul/msm 10.0 -pair_style lj/cut/coul/msm 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 -pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 -pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - + +pair_style lj/cut 2.5 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 + + +pair_style lj/cut/coul/cut 10.0 +pair_style lj/cut/coul/cut 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 +pair_coeff 1 1 100.0 3.5 9.0 9.0 + + +pair_style lj/cut/coul/debye 1.5 3.0 +pair_style lj/cut/coul/debye 1.5 2.5 5.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.5 2.5 +pair_coeff 1 1 1.0 1.5 2.5 5.0 + + +pair_style lj/cut/coul/dsf 0.05 2.5 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 2.5 + + +pair_style lj/cut/coul/long 10.0 +pair_style lj/cut/coul/long/cs 10.0 +pair_style lj/cut/coul/long 10.0 8.0 +pair_style lj/cut/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/coul/msm 10.0 +pair_style lj/cut/coul/msm 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 +pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 +pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + Description diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html index 25b68df4b4..3f7e8fdd9b 100644 --- a/doc/html/pair_lj96.html +++ b/doc/html/pair_lj96.html @@ -134,20 +134,20 @@ pair_style lj96/cut/omp command Syntax -pair_style lj96/cut cutoff - - + +pair_style lj96/cut cutoff + cutoff = global cutoff for lj96/cut interactions (distance units) Examples -pair_style lj96/cut 2.5 -pair_coeff * * 1.0 1.0 4.0 -pair_coeff 1 1 1.0 1.0 - - + +pair_style lj96/cut 2.5 +pair_coeff * * 1.0 1.0 4.0 +pair_coeff 1 1 1.0 1.0 + Description diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html index 6032650397..6dad5de332 100644 --- a/doc/html/pair_lj_cubic.html +++ b/doc/html/pair_lj_cubic.html @@ -134,16 +134,16 @@ pair_style lj/cubic/omp command Syntax -pair_style lj/cubic - - + +pair_style lj/cubic + Examples -pair_style lj/cubic -pair_coeff * * 1.0 0.8908987 - - + +pair_style lj/cubic +pair_coeff * * 1.0 0.8908987 + Description diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html index fef3f21c46..69fc39c046 100644 --- a/doc/html/pair_lj_expand.html +++ b/doc/html/pair_lj_expand.html @@ -134,20 +134,20 @@ pair_style lj/expand/omp command Syntax -pair_style lj/expand cutoff - - + +pair_style lj/expand cutoff + cutoff = global cutoff for lj/expand interactions (distance units) Examples -pair_style lj/expand 2.5 -pair_coeff * * 1.0 1.0 0.5 -pair_coeff 1 1 1.0 1.0 -0.2 2.0 - - + +pair_style lj/expand 2.5 +pair_coeff * * 1.0 1.0 0.5 +pair_coeff 1 1 1.0 1.0 -0.2 2.0 + Description diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html index fd2fa29241..2256d2d48e 100644 --- a/doc/html/pair_lj_long.html +++ b/doc/html/pair_lj_long.html @@ -137,9 +137,9 @@ pair_style lj/long/tip4p/long command Syntax -pair_style style args - - + +pair_style style args + style = lj/long/coul/long or lj/long/tip4p/long args = list of arguments for a particular style @@ -171,19 +171,19 @@ Examples -pair_style lj/long/coul/long cut off 2.5 -pair_style lj/long/coul/long cut long 2.5 4.0 -pair_style lj/long/coul/long long long 2.5 4.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 3 4 - - -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - + +pair_style lj/long/coul/long cut off 2.5 +pair_style lj/long/coul/long cut long 2.5 4.0 +pair_style lj/long/coul/long long long 2.5 4.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 3 4 + + +pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 +pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + Description diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html index 8505d91cf5..b09ff7e036 100644 --- a/doc/html/pair_lj_sf.html +++ b/doc/html/pair_lj_sf.html @@ -131,20 +131,20 @@ pair_style lj/sf/omp command Syntax -pair_style lj/sf cutoff - - + +pair_style lj/sf cutoff + cutoff = global cutoff for Lennard-Jones interactions (distance units) Examples -pair_style lj/sf 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 3.0 - - + +pair_style lj/sf 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 3.0 + Description diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html index 22565da2d7..0973d95ff9 100644 --- a/doc/html/pair_lj_smooth.html +++ b/doc/html/pair_lj_smooth.html @@ -131,9 +131,9 @@ pair_style lj/smooth/omp command Syntax -pair_style lj/smooth Rin Rc - - + +pair_style lj/smooth Rin Rc + Rin = inner cutoff beyond which force smoothing will be applied (distance units) Rc = outer cutoff for lj/smooth interactions (distance units) @@ -141,11 +141,11 @@ Examples -pair_style lj/smooth 8.0 10.0 -pair_coeff * * 10.0 1.5 -pair_coeff 1 1 20.0 1.3 7.0 9.0 - - + +pair_style lj/smooth 8.0 10.0 +pair_coeff * * 10.0 1.5 +pair_coeff 1 1 20.0 1.3 7.0 9.0 + Description diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html index f19e28551e..edd6d68386 100644 --- a/doc/html/pair_lj_smooth_linear.html +++ b/doc/html/pair_lj_smooth_linear.html @@ -131,20 +131,20 @@ pair_style lj/smooth/linear/omp command Syntax -pair_style lj/smooth/linear Rc - - + +pair_style lj/smooth/linear Rc + Rc = cutoff for lj/smooth/linear interactions (distance units) Examples -pair_style lj/smooth/linear 5.456108274435118 -pair_coeff * * 0.7242785984051078 2.598146797350056 -pair_coeff 1 1 20.0 1.3 9.0 - - + +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +pair_coeff 1 1 20.0 1.3 9.0 + Description diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html index e253536083..f67e200935 100644 --- a/doc/html/pair_lj_soft.html +++ b/doc/html/pair_lj_soft.html @@ -173,9 +173,9 @@ pair_style tip4p/long/soft/omp command Syntax -pair_style style args - - + +pair_style style args + style = lj/cut/soft or lj/cut/coul/cut/soft or lj/cut/coul/long/soft or lj/cut/tip4p/long/soft or lj/charmm/coul/long/soft or coul/cut/soft or coul/long/soft or tip4p/long/soft args = list of arguments for a particular style @@ -219,47 +219,47 @@ Examples -pair_style lj/cut/soft 2.0 0.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 9.5 - - -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 - - -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 - - -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 -pair_coeff * * 0.155 3.1536 1.0 -pair_coeff 1 1 0.155 3.1536 1.0 9.5 - - -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 - - -pair_style coul/long/soft 1.0 10.0 9.5 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 - - -pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 - - + +pair_style lj/cut/soft 2.0 0.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 1.0 9.5 + + +pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 +pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 0.5 10.0 +pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 + + +pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 +pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 + + +pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 +pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 +pair_coeff * * 0.155 3.1536 1.0 +pair_coeff 1 1 0.155 3.1536 1.0 9.5 + + +pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 +pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 + + +pair_style coul/long/soft 1.0 10.0 9.5 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 9.5 + + +pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 9.5 + Description diff --git a/doc/html/pair_lubricate.html b/doc/html/pair_lubricate.html index 2cae3906c3..b415ee6c3a 100644 --- a/doc/html/pair_lubricate.html +++ b/doc/html/pair_lubricate.html @@ -137,9 +137,9 @@ pair_style lubricate/poly/omp command Syntax -pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF - - + +pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF + style = lubricate or lubricate/poly mu = dynamic viscosity (dynamic viscosity units) @@ -151,17 +151,17 @@ flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms Examples: (all assume radius = 1) -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * - - -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff * * -variable mu equal ramp(1,2) -fix 1 all adapt 1 pair lubricate mu * * v_mu - - + +pair_style lubricate 1.5 1 1 2.01 2.5 +pair_coeff 1 1 2.05 2.8 +pair_coeff * * + + +pair_style lubricate 1.5 1 1 2.01 2.5 +pair_coeff * * +variable mu equal ramp(1,2) +fix 1 all adapt 1 pair lubricate mu * * v_mu + Description diff --git a/doc/html/pair_lubricateU.html b/doc/html/pair_lubricateU.html index 4d518c72e8..deca70058e 100644 --- a/doc/html/pair_lubricateU.html +++ b/doc/html/pair_lubricateU.html @@ -131,9 +131,9 @@ pair_style lubricateU/poly command Syntax -pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF - - + +pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF + style = lubricateU or lubricateU/poly mu = dynamic viscosity (dynamic viscosity units) @@ -145,11 +145,11 @@ flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms Examples: (all assume radius = 1) -pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * - - + +pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 +pair_coeff 1 1 2.05 2.8 +pair_coeff * * + Description diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html index 9f78149009..477829e523 100644 --- a/doc/html/pair_mdf.html +++ b/doc/html/pair_mdf.html @@ -134,9 +134,9 @@ pair_style lennard/mdf command Syntax -pair_style style args - - + +pair_style style args + style = lj/mdf or buck/mdf or lennard/mdf args = list of arguments for a particular style @@ -155,21 +155,21 @@ Examples -pair_style lj/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 - - -pair_style buck 2.5 3.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 3.5 - - -pair_style lennard/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 - - + +pair_style lj/mdf 2.5 3.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 3.0 3.2 + + +pair_style buck 2.5 3.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 3.0 3.5 + + +pair_style lennard/mdf 2.5 3.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 3.0 3.2 + Description @@ -198,7 +198,7 @@ below: epsilon (energy units) sigma (distance units) r_m (distance units) -r_cut (distance units) +r_cut (distance units) For the buck/mdf pair_style, the potential energy, E(r), is the @@ -209,7 +209,7 @@ standard Buckingham potential: rho (distance units) C (energy-distance^6 units) r_m (distance units) -r_cut$ (distance units) +r_cut$ (distance units) For the lennard/mdf pair_style, the potential energy, E(r), is the @@ -223,7 +223,7 @@ commands, or by mixing as described below: A (energy-distance^12 units) B (energy-distance^6 units) r_m (distance units) -r_cut (distance units) +r_cut (distance units) Mixing, shift, table, tail correction, restart, rRESPA info: diff --git a/doc/html/pair_meam.html b/doc/html/pair_meam.html index 4c704bc583..e9ec4ac13b 100644 --- a/doc/html/pair_meam.html +++ b/doc/html/pair_meam.html @@ -128,17 +128,17 @@ pair_style meam command Syntax -pair_style meam - - + +pair_style meam + Examples -pair_style meam -pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si -pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni - - + +pair_style meam +pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si +pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni + Description @@ -194,9 +194,9 @@ settings for a variety of elements. The potentials/sic.meam file has specific parameter settings for a Si and C alloy system. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * library.meam Si C sic.meam Si Si Si C - - + +pair_coeff * * library.meam Si C sic.meam Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The two filenames are for the library and parameter file respectively. The Si and C arguments (between the file names) are the two elements @@ -390,14 +390,14 @@ parameter erose_form, can be used to modify the Rose energy function used to compute the pair potential. This function gives the energy of the reference state as a function of interatomic spacing. The form of this function is: -astar = alpha * (r/re - 1.d0) -if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) -if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) -if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) -a3 = repuls, astar < 0 -a3 = attrac, astar >= 0 - - + +astar = alpha * (r/re - 1.d0) +if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) +if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) +if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) +a3 = repuls, astar < 0 +a3 = attrac, astar >= 0 + Most published MEAM parameter sets use the default values attrac=repulse=0. Setting repuls=attrac=delta corresponds to the form used in several recent published MEAM parameter sets, such as (Valone) diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html index 04957d08ca..d0f57e43cb 100644 --- a/doc/html/pair_meam_spline.html +++ b/doc/html/pair_meam_spline.html @@ -131,17 +131,17 @@ pair_style meam/spline/omp Syntax -pair_style meam/spline - - + +pair_style meam/spline + Examples -pair_style meam/spline -pair_coeff * * Ti.meam.spline Ti -pair_coeff * * Ti.meam.spline Ti Ti Ti - - + +pair_style meam/spline +pair_coeff * * Ti.meam.spline Ti +pair_coeff * * Ti.meam.spline Ti Ti Ti + Description @@ -180,9 +180,9 @@ to specify the path for the potential file. your LAMMPS simulation has 3 atoms types and they are all to be treated with this potentials, you would use the following pair_coeff command: -pair_coeff * * Ti.meam.spline Ti Ti Ti - - + +pair_coeff * * Ti.meam.spline Ti Ti Ti + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element in the potential file. If a mapping value is specified as NULL, the diff --git a/doc/html/pair_meam_sw_spline.html b/doc/html/pair_meam_sw_spline.html index 2608d4c901..f3b221fef6 100644 --- a/doc/html/pair_meam_sw_spline.html +++ b/doc/html/pair_meam_sw_spline.html @@ -131,17 +131,17 @@ pair_style meam/sw/spline/omp Syntax -pair_style meam/sw/spline - - + +pair_style meam/sw/spline + Examples -pair_style meam/sw/spline -pair_coeff * * Ti.meam.sw.spline Ti -pair_coeff * * Ti.meam.sw.spline Ti Ti Ti - - + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +pair_coeff * * Ti.meam.sw.spline Ti Ti Ti + Description diff --git a/doc/html/pair_mgpt.html b/doc/html/pair_mgpt.html index b014cdeb42..9ac4b2224d 100644 --- a/doc/html/pair_mgpt.html +++ b/doc/html/pair_mgpt.html @@ -128,20 +128,20 @@ pair_style mgpt command Syntax -pair_style mgpt - - + +pair_style mgpt + Examples -pair_style mgpt -pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega -cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin -cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin -pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double -pair_coeff * * parmin potin Omega volpress yes nbody 12 - - + +pair_style mgpt +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega +cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin +cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin +pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double +pair_coeff * * parmin potin Omega volpress yes nbody 12 + Description diff --git a/doc/html/pair_mie.html b/doc/html/pair_mie.html index cdab3eaf53..517b4bbec6 100644 --- a/doc/html/pair_mie.html +++ b/doc/html/pair_mie.html @@ -131,21 +131,21 @@ pair_style mie/cut/gpu command Syntax -pair_style mie/cut cutoff - - + +pair_style mie/cut cutoff + cutoff = global cutoff for mie/cut interactions (distance units) Examples -pair_style mie/cut 10.0 -pair_coeff 1 1 0.72 3.40 23.00 6.66 -pair_coeff 2 2 0.30 3.55 12.65 6.00 -pair_coeff 1 2 0.46 3.32 16.90 6.31 - - + +pair_style mie/cut 10.0 +pair_coeff 1 1 0.72 3.40 23.00 6.66 +pair_coeff 2 2 0.30 3.55 12.65 6.00 +pair_coeff 1 2 0.46 3.32 16.90 6.31 + Description diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html index bac9a4aa44..bcf7271af0 100644 --- a/doc/html/pair_morse.html +++ b/doc/html/pair_morse.html @@ -146,9 +146,9 @@ pair_style morse/soft command Syntax -pair_style style args - - + +pair_style style args + style = morse or morse/smooth/linear or morse/soft args = list of arguments for a particular style @@ -170,11 +170,11 @@ pair_style morse/smooth/linear 2.5 pair_coeff * * 100.0 2.0 1.5 pair_coeff 1 1 100.0 2.0 1.5 3.0 -pair_style morse/soft 4 0.9 10.0 -pair_coeff * * 100.0 2.0 1.5 1.0 -pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 - - + +pair_style morse/soft 4 0.9 10.0 +pair_coeff * * 100.0 2.0 1.5 1.0 +pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 + Description diff --git a/doc/html/pair_multi_lucy.html b/doc/html/pair_multi_lucy.html index 6835ef752e..4a16b32697 100644 --- a/doc/html/pair_multi_lucy.html +++ b/doc/html/pair_multi_lucy.html @@ -128,9 +128,9 @@ pair_style multi/lucy command Syntax -pair_style multi/lucy style N keyword ... - - + +pair_style multi/lucy style N keyword ... + style = lookup or linear = method of interpolation N = use N values in lookup, linear tables @@ -138,10 +138,10 @@ Examples -pair_style multi/lucy linear 1000 -pair_coeff * * multibody.table ENTRY1 7.0 - - + +pair_style multi/lucy linear 1000 +pair_coeff * * multibody.table ENTRY1 7.0 + Description @@ -196,15 +196,15 @@ defined as follows (without the parenthesized comments): # Density-dependent function (one or more comment or blank lines) -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 - - + +DD-FUNCTION (keyword is first text on line) +N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) +1 1.0 25.5 102.34 (index, density, energy/r^4, force) +2 1.02 23.4 98.5 +... +500 10.0 0.001 0.003 + A section begins with a non-blank line whose 1st character is not a “#”; blank lines or lines starting with “#” can be used as comments between sections. The first line begins with a keyword which diff --git a/doc/html/pair_multi_lucy_rx.html b/doc/html/pair_multi_lucy_rx.html index 380cdc22fa..ca4b859cdd 100644 --- a/doc/html/pair_multi_lucy_rx.html +++ b/doc/html/pair_multi_lucy_rx.html @@ -128,9 +128,9 @@ pair_style multi/lucy/rx command Syntax -pair_style multi/lucy/rx style N keyword ... - - + +pair_style multi/lucy/rx style N keyword ... + style = lookup or linear = method of interpolation N = use N values in lookup, linear tables @@ -138,11 +138,11 @@ Examples -pair_style multi/lucy/rx linear 1000 -pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 -pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 - - + +pair_style multi/lucy/rx linear 1000 +pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 +pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 + Description @@ -215,15 +215,15 @@ defined as follows (without the parenthesized comments): # Density-dependent function (one or more comment or blank lines) -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 - - + +DD-FUNCTION (keyword is first text on line) +N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) +1 1.0 25.5 102.34 (index, density, energy/r^4, force) +2 1.02 23.4 98.5 +... +500 10.0 0.001 0.003 + A section begins with a non-blank line whose 1st character is not a “#”; blank lines or lines starting with “#” can be used as comments between sections. The first line begins with a keyword which diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html index 59fe5effb2..a24bb092e7 100644 --- a/doc/html/pair_nb3b_harmonic.html +++ b/doc/html/pair_nb3b_harmonic.html @@ -131,16 +131,16 @@ pair_style nb3b/harmonic/omp command Syntax -pair_style nb3b/harmonic - - + +pair_style nb3b/harmonic + Examples -pair_style nb3b/harmonic -pair_coeff * * MgOH.nb3bharmonic Mg O H - - + +pair_style nb3b/harmonic +pair_coeff * * MgOH.nb3bharmonic Mg O H + Description @@ -166,9 +166,9 @@ to specify the path for the potential file. for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * SiC.nb3b.harmonic Si Si Si C - - + +pair_coeff * * SiC.nb3b.harmonic Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the potential file. The final C argument maps LAMMPS atom diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html index 10052c9d20..c7759721cf 100644 --- a/doc/html/pair_nm.html +++ b/doc/html/pair_nm.html @@ -143,9 +143,9 @@ pair_style nm/cut/coul/long/omp command Syntax -pair_style style args - - + +pair_style style args + style = nm/cut or nm/cut/coul/cut or nm/cut/coul/long args = list of arguments for a particular style @@ -163,21 +163,21 @@ Examples -pair_style nm/cut 12.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - - -pair_style nm/cut/coul/cut 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - - -pair_style nm/cut/coul/long 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - - + +pair_style nm/cut 12.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + + +pair_style nm/cut/coul/cut 12.0 15.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + + +pair_style nm/cut/coul/long 12.0 15.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + Description diff --git a/doc/html/pair_none.html b/doc/html/pair_none.html index 1b294a15f5..84a0e71b67 100644 --- a/doc/html/pair_none.html +++ b/doc/html/pair_none.html @@ -128,15 +128,15 @@ pair_style none command Syntax -pair_style none - - + +pair_style none + Examples -pair_style none - - + +pair_style none + Description diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html index a57e98bbb1..c2fa31cce8 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_polymorphic.html b/doc/html/pair_polymorphic.html index 550805f4da..017a5148d0 100644 --- a/doc/html/pair_polymorphic.html +++ b/doc/html/pair_polymorphic.html @@ -128,20 +128,20 @@ pair_style polymorphic command Syntax -pair_style polymorphic - - + +pair_style polymorphic + style = polymorphic Examples -pair_style polymorphic -pair_coeff * * TlBr_msw.polymorphic Tl Br -pair_coeff * * AlCu_eam.polymorphic Al Cu -pair_coeff * * GaN_tersoff.polymorphic Ga N -pair_coeff * * GaN_sw.polymorphic GaN - - + +pair_style polymorphic +pair_coeff * * TlBr_msw.polymorphic Tl Br +pair_coeff * * AlCu_eam.polymorphic Al Cu +pair_coeff * * GaN_tersoff.polymorphic Ga N +pair_coeff * * GaN_sw.polymorphic GaN + Description @@ -210,9 +210,9 @@ included in the potentials dir of the LAMMPS distro. They have a functions for Si-C tersoff potential. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * SiC_tersoff.polymorphic Si Si Si C - - + +pair_coeff * * SiC_tersoff.polymorphic Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the polymorphic file. The final C argument maps LAMMPS @@ -235,19 +235,19 @@ eta_ij defined in the potential functions above is set to 1 - delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines each lists two numbers and a character string representing atomic number, atomic mass, and name of the species of the ntypes elements: -atomic_number atomic-mass element (1) -atomic_number atomic-mass element (2) -... -atomic_number atomic-mass element (ntypes) - - + +atomic_number atomic-mass element (1) +atomic_number atomic-mass element (2) +... +atomic_number atomic-mass element (ntypes) + The next ntypes*(ntypes+1)/2 lines contain two numbers: -cut xi (1) -cut xi (2) -... -cut xi (ntypes*(ntypes+1)/2) - - + +cut xi (1) +cut xi (2) +... +cut xi (ntypes*(ntypes+1)/2) + Here cut means the cutoff distance of the pair functions, xi is the same as defined in the potential functions above. The ntypes*(ntypes+1)/2 lines are related to the pairs according to the diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html index e2bae6d90b..91f1131efb 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 3093a0b62b..3929a8cd0d 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 @@ 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 bd96471c6b..38e27022b9 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_resquared.html b/doc/html/pair_resquared.html index edf33d6bdb..70c4fd0ba0 100644 --- a/doc/html/pair_resquared.html +++ b/doc/html/pair_resquared.html @@ -134,19 +134,19 @@ pair_style resquared/omp command Syntax -pair_style resquared cutoff - - + +pair_style resquared cutoff + cutoff = global cutoff for interactions (distance units) Examples -pair_style resquared 10.0 -pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 - - + +pair_style resquared 10.0 +pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 + Description diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html index a8cfc33d42..21a9ded1a5 100644 --- a/doc/html/pair_sdk.html +++ b/doc/html/pair_sdk.html @@ -146,9 +146,9 @@ pair_style lj/sdk/coul/long/omp command Syntax -pair_style style args - - + +pair_style style args + style = lj/sdk or lj/sdk/coul/long args = list of arguments for a particular style @@ -163,15 +163,15 @@ Examples -pair_style lj/sdk 2.5 -pair_coeff 1 1 lj12_6 1 1.1 2.8 - - -pair_style lj/sdk/coul/long 10.0 -pair_style lj/sdk/coul/long 10.0 12.0 -pair_coeff 1 1 lj9_6 100.0 3.5 12.0 - - + +pair_style lj/sdk 2.5 +pair_coeff 1 1 lj12_6 1 1.1 2.8 + + +pair_style lj/sdk/coul/long 10.0 +pair_style lj/sdk/coul/long 10.0 12.0 +pair_coeff 1 1 lj9_6 100.0 3.5 12.0 + Description diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html index 52dd7939f6..25cbc618da 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_tlsph.html b/doc/html/pair_smd_tlsph.html index 69ea38dfa4..330e3c56f2 100644 --- a/doc/html/pair_smd_tlsph.html +++ b/doc/html/pair_smd_tlsph.html @@ -128,9 +128,9 @@ pair_style smd/tlsph command Syntax -pair_style smd/tlsph args - - + +pair_style smd/tlsph args + Examples @@ -140,11 +140,11 @@ Description The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm. This pair style is invoked with the following command: -pair_style smd/tlsph -pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp & - *END - - + +pair_style smd/tlsph +pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp & + *END + Here, i and j denote the LAMMPS particle types for which this pair style is defined. Note that i and j must be equal, i.e., no tlsph cross interactions between different particle types are allowed. @@ -152,7 +152,7 @@ In contrast to the usual LAMMPS pair coeff definitions, which number of floats and integers, the tlsph pair coeff definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The pair coeff line must be terminated with -the **END* keyword. The use the line continuation operator & is recommended. A typical +the *END keyword. The use the line continuation operator & is recommended. A typical invocation of the tlsph for a solid body would consist of an equation of state for computing the pressure (the diagonal components of the stress tensor), and a material model to compute shear stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added. diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html index 9f4ba0991d..428893dfc3 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_smd_ulsph.html b/doc/html/pair_smd_ulsph.html index a838c63e41..1e21539e51 100644 --- a/doc/html/pair_smd_ulsph.html +++ b/doc/html/pair_smd_ulsph.html @@ -128,27 +128,27 @@ pair_style smd/ulsph command Syntax -pair_style smd/ulsph args - - + +pair_style smd/ulsph args + these keywords must be given -keyword = **DENSITY_SUMMATION* or **DENSITY_CONTINUITY* and **VELOCITY_GRADIENT* or **NO_VELOCITY_GRADIENT* and **GRADIENT_CORRECTION* or **NO_GRADIENT_CORRECTION* +keyword = *DENSITY_SUMMATION or *DENSITY_CONTINUITY and *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT and *GRADIENT_CORRECTION or *NO_GRADIENT_CORRECTION Examples -pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION Description The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm. This pair style is invoked similar to the following command: -pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION -pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & - *END - - + +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION +pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & + *END + Here, i and j denote the LAMMPS particle types for which this pair style is defined. Note that i and j can be different, i.e., ulsph cross interactions between different particle types are allowed. However, i–i respectively j–j pair_coeff lines have to preceed a cross interaction. @@ -156,11 +156,11 @@ In contrast to the usual LAMMPS pair coeff definitions, which number of floats and integers, the ulsph pair coeff definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The pair coeff line must be terminated with -the **END* keyword. The use the line continuation operator & is recommended. A typical +the *END keyword. The use the line continuation operator & is recommended. A typical invocation of the ulsph for a solid body would consist of an equation of state for computing the pressure (the diagonal components of the stress tensor), and a material model to compute shear stresses (the off-diagonal components of the stress tensor). -Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended. +Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended. Please see the SMD user guide for a complete listing of the possible keywords and material models. Mixing, shift, table, tail correction, restart, rRESPA info: diff --git a/doc/html/pair_smtbq.html b/doc/html/pair_smtbq.html index 568539fd0c..f9b3de8f22 100644 --- a/doc/html/pair_smtbq.html +++ b/doc/html/pair_smtbq.html @@ -128,16 +128,16 @@ pair_style smtbq command Syntax -pair_style smtbq - - + +pair_style smtbq + Examples -pair_style smtbq -pair_coeff * * ffield.smtbq.Al2O3 O Al - - + +pair_style smtbq +pair_coeff * * ffield.smtbq.Al2O3 O Al + Description @@ -164,9 +164,9 @@ filename in the pair_coeff command. Note that atom type 1 must always correspond to oxygen atoms. As an example, to simulate a TiO2 system, atom type 1 has to be oxygen and atom type 2 Ti. The following pair_coeff command should then be used: -pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti - - + +pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti + The electrostatic part of the energy consists of two components self-energy of atom i in the form of a second order charge dependent polynomial and a long-range Coulombic electrostatic interaction. The @@ -271,7 +271,7 @@ quotation marks (‘’). Keyword for element1, element2 and interaction potential (‘second_moment’ or ‘buck’ or ‘buckPlusAttr’) between element 1 and 2. If the potential is ‘second_moment’, specify ‘oxide’ or ‘metal’ for metal-oxygen or metal-metal interactions respectively. -Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : A (eV), p, ξ<sup>0</sup> (eV) and q <br/> r<sub>c1</sub> (Å), r<sub>c2</sub> (Å) and r<sub>0</sub> (Å) <br/> If type of potential is ‘buck’ : C (eV) and ρ (Å) <br/> If type of potential is ‘buckPlusAttr’ : C (eV) and ρ (Å) <br/> D (eV), B (Å<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (Å) and r<sub>2</sub><sup>OO</sup> (Å) </pre> +Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : A (eV), p, ξ<sup>0</sup> (eV) and q <br/> r<sub>c1</sub> (Å), r<sub>c2</sub> (Å) and r<sub>0</sub> (Å) <br/> If type of potential is ‘buck’ : C (eV) and ρ (Å) <br/> If type of potential is ‘buckPlusAttr’ : C (eV) and ρ (Å) <br/> D (eV), B (Å<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (Å) and r<sub>2</sub><sup>OO</sup> (Å) </pre> Divided line diff --git a/doc/html/pair_snap.html b/doc/html/pair_snap.html index bc82ce506e..0589cb40a5 100644 --- a/doc/html/pair_snap.html +++ b/doc/html/pair_snap.html @@ -128,16 +128,16 @@ pair_style snap command Syntax -pair_style snap - - + +pair_style snap + Examples -pair_style snap -pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P - - + +pair_style snap +pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P + Description @@ -180,9 +180,9 @@ command, where N is the number of LAMMPS atom types: As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the 3rd and 4th being phophorous, the pair_coeff command would look like this: -pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P - - + +pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The two filenames are for the element and parameter files, respectively. The ‘In’ and ‘P’ arguments (between the file names) are the two elements @@ -210,7 +210,8 @@ using the hybrid/overlay pair style. As an example, the SNAP tantalum potential provided in the LAMMPS potentials directory combines the snap and zbl pair styles. It is invoked by the following commands: -variable zblcutinner equal 4 + +variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 73 pair_style hybrid/overlay & @@ -219,8 +220,7 @@ pair_coeff * * zbl 0.0 pair_coeff 1 1 zbl ${zblz} pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta & ../potentials/Ta06A.snapparam Ta - - + It is convenient to keep these commands in a separate file that can be inserted in any LAMMPS input script using the include command. diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html index 0929a1f6af..3443927106 100644 --- a/doc/html/pair_soft.html +++ b/doc/html/pair_soft.html @@ -134,26 +134,26 @@ pair_style soft/omp command Syntax -pair_style soft cutoff - - + +pair_style soft cutoff + cutoff = global cutoff for soft interactions (distance units) Examples -pair_style soft 1.0 -pair_coeff * * 10.0 -pair_coeff 1 1 10.0 3.0 - - -pair_style soft 1.0 -pair_coeff * * 0.0 -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor - - + +pair_style soft 1.0 +pair_coeff * * 10.0 +pair_coeff 1 1 10.0 3.0 + + +pair_style soft 1.0 +pair_coeff * * 0.0 +variable prefactor equal ramp(0,30) +fix 1 all adapt 1 pair soft a * * v_prefactor + Description @@ -193,10 +193,10 @@ pair_coeff settings for A must still be specified, but will be overridden. For example these commands will vary the prefactor A for all pairwise interactions from 0.0 at the beginning to 30.0 at the end of a run: -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor - - + +variable prefactor equal ramp(0,30) +fix 1 all adapt 1 pair soft a * * v_prefactor + Note that a formula defined by an equal-style variable can use the current timestep, elapsed time in the current run, elapsed time since the beginning of a series of runs, as well as access other diff --git a/doc/html/pair_sph_heatconduction.html b/doc/html/pair_sph_heatconduction.html index b864553905..d4161616a4 100644 --- a/doc/html/pair_sph_heatconduction.html +++ b/doc/html/pair_sph_heatconduction.html @@ -128,16 +128,16 @@ pair_style sph/heatconduction command Syntax -pair_style sph/heatconduction - - + +pair_style sph/heatconduction + Examples -pair_style sph/heatconduction -pair_coeff * * 1.0 2.4 - - + +pair_style sph/heatconduction +pair_coeff * * 1.0 2.4 + Description diff --git a/doc/html/pair_sph_idealgas.html b/doc/html/pair_sph_idealgas.html index 130c193d90..602e66a277 100644 --- a/doc/html/pair_sph_idealgas.html +++ b/doc/html/pair_sph_idealgas.html @@ -128,16 +128,16 @@ pair_style sph/idealgas command Syntax -pair_style sph/idealgas - - + +pair_style sph/idealgas + Examples -pair_style sph/idealgas -pair_coeff * * 1.0 2.4 - - + +pair_style sph/idealgas +pair_coeff * * 1.0 2.4 + Description diff --git a/doc/html/pair_sph_lj.html b/doc/html/pair_sph_lj.html index ffc548c39f..78b5ba0a20 100644 --- a/doc/html/pair_sph_lj.html +++ b/doc/html/pair_sph_lj.html @@ -128,16 +128,16 @@ pair_style sph/lj command Syntax -pair_style sph/lj - - + +pair_style sph/lj + Examples -pair_style sph/lj -pair_coeff * * 1.0 2.4 - - + +pair_style sph/lj +pair_coeff * * 1.0 2.4 + Description diff --git a/doc/html/pair_sph_rhosum.html b/doc/html/pair_sph_rhosum.html index 77029fa778..358b99eaf7 100644 --- a/doc/html/pair_sph_rhosum.html +++ b/doc/html/pair_sph_rhosum.html @@ -128,19 +128,19 @@ pair_style sph/rhosum command Syntax -pair_style sph/rhosum Nstep - - + +pair_style sph/rhosum Nstep + Nstep = timestep interval Examples -pair_style sph/rhosum 10 -pair_coeff * * 2.4 - - + +pair_style sph/rhosum 10 +pair_coeff * * 2.4 + Description diff --git a/doc/html/pair_sph_taitwater.html b/doc/html/pair_sph_taitwater.html index 0d56ce2bdd..0ce7b08918 100644 --- a/doc/html/pair_sph_taitwater.html +++ b/doc/html/pair_sph_taitwater.html @@ -128,16 +128,16 @@ pair_style sph/taitwater command Syntax -pair_style sph/taitwater - - + +pair_style sph/taitwater + Examples -pair_style sph/taitwater -pair_coeff * * 1000.0 1430.0 1.0 2.4 - - + +pair_style sph/taitwater +pair_coeff * * 1000.0 1430.0 1.0 2.4 + Description diff --git a/doc/html/pair_sph_taitwater_morris.html b/doc/html/pair_sph_taitwater_morris.html index 8c6f8c913a..fda93bd07c 100644 --- a/doc/html/pair_sph_taitwater_morris.html +++ b/doc/html/pair_sph_taitwater_morris.html @@ -128,16 +128,16 @@ pair_style sph/taitwater/morris command Syntax -pair_style sph/taitwater/morris - - + +pair_style sph/taitwater/morris + Examples -pair_style sph/taitwater/morris -pair_coeff * * 1000.0 1430.0 1.0 2.4 - - + +pair_style sph/taitwater/morris +pair_coeff * * 1000.0 1430.0 1.0 2.4 + Description diff --git a/doc/html/pair_srp.html b/doc/html/pair_srp.html index caddb4012a..a9e1607ab8 100644 --- a/doc/html/pair_srp.html +++ b/doc/html/pair_srp.html @@ -143,24 +143,24 @@ Examples -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes -pair_coeff 1 1 dpd 60.0 4.5 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 - - -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes -pair_coeff 1 1 dpd 60.0 50 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 40.0 - - -pair_style hybrid srp 0.8 2 mid -pair_coeff 1 1 none -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 - - + +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes +pair_coeff 1 1 dpd 60.0 4.5 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 + + +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes +pair_coeff 1 1 dpd 60.0 50 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 40.0 + + +pair_style hybrid srp 0.8 2 mid +pair_coeff 1 1 none +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 + Description diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html index 4dc6adc479..86a80963cc 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 @@ 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_sw.html b/doc/html/pair_sw.html index 099d2de727..687c162b34 100644 --- a/doc/html/pair_sw.html +++ b/doc/html/pair_sw.html @@ -140,17 +140,17 @@ pair_style sw/omp command Syntax -pair_style sw - - + +pair_style sw + Examples -pair_style sw -pair_coeff * * si.sw Si -pair_coeff * * GaN.sw Ga N Ga - - + +pair_style sw +pair_coeff * * si.sw Si +pair_coeff * * GaN.sw Ga N Ga + Description @@ -175,9 +175,9 @@ to specify the path for the potential file. Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * SiC.sw Si Si Si C - - + +pair_coeff * * SiC.sw Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the SW file. The final C argument maps LAMMPS atom type 4 diff --git a/doc/html/pair_tersoff.html b/doc/html/pair_tersoff.html index 6ea2a43607..8345a1c90b 100644 --- a/doc/html/pair_tersoff.html +++ b/doc/html/pair_tersoff.html @@ -146,22 +146,22 @@ pair_style tersoff/table/omp command Syntax -pair_style style - - + +pair_style style + style = tersoff or tersoff/table or tersoff/gpu or tersoff/omp or tersoff/table/omp Examples -pair_style tersoff -pair_coeff * * Si.tersoff Si -pair_coeff * * SiC.tersoff Si C Si - - -pair_style tersoff/table -pair_coeff * * SiCGe.tersoff Si(D) - - + +pair_style tersoff +pair_coeff * * Si.tersoff Si +pair_coeff * * SiC.tersoff Si C Si + + +pair_style tersoff/table +pair_coeff * * SiCGe.tersoff Si(D) + Description @@ -191,9 +191,9 @@ to specify the path for the potential file. and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * SiC.tersoff Si Si Si C - - + +pair_coeff * * SiC.tersoff Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff file. The final C argument maps LAMMPS atom diff --git a/doc/html/pair_tersoff_mod.html b/doc/html/pair_tersoff_mod.html index b88d02ee18..34a2120f67 100644 --- a/doc/html/pair_tersoff_mod.html +++ b/doc/html/pair_tersoff_mod.html @@ -137,16 +137,16 @@ pair_style tersoff/mod/omp command Syntax -pair_style tersoff/mod - - + +pair_style tersoff/mod + Examples -pair_style tersoff/mod -pair_coeff * * Si.tersoff.mod Si Si - - + +pair_style tersoff/mod +pair_coeff * * Si.tersoff.mod Si Si + Description @@ -180,9 +180,9 @@ where N is the number of LAMMPS atom types: As an example, imagine the Si.tersoff_mod file has Tersoff values for Si. If your LAMMPS simulation has 3 Si atoms types, you would use the following pair_coeff command: -pair_coeff * * Si.tersoff_mod Si Si Si - - + +pair_coeff * * Si.tersoff_mod Si Si Si + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff/MOD file. If a mapping value is specified as NULL, the diff --git a/doc/html/pair_tersoff_zbl.html b/doc/html/pair_tersoff_zbl.html index 90e840acc3..694938f86e 100644 --- a/doc/html/pair_tersoff_zbl.html +++ b/doc/html/pair_tersoff_zbl.html @@ -137,16 +137,16 @@ pair_style tersoff/zbl/omp command Syntax -pair_style tersoff/zbl - - + +pair_style tersoff/zbl + Examples -pair_style tersoff/zbl -pair_coeff * * SiC.tersoff.zbl Si C Si - - + +pair_style tersoff/zbl +pair_coeff * * SiC.tersoff.zbl Si C Si + Description @@ -188,9 +188,9 @@ to specify the path for the potential file. for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: -pair_coeff * * SiC.tersoff Si Si Si C - - + +pair_coeff * * SiC.tersoff Si Si Si C + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff/ZBL file. The final C argument maps LAMMPS diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html index b2742247f9..8e8f15daf2 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 @@ 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 e6c6b24ddd..bdda14e2e2 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/pair_write.html b/doc/html/pair_write.html index 3b82d7c51d..f9dfa7d90d 100644 --- a/doc/html/pair_write.html +++ b/doc/html/pair_write.html @@ -128,9 +128,9 @@ pair_write command Syntax -pair_write itype jtype N style inner outer file keyword Qi Qj - - + +pair_write itype jtype N style inner outer file keyword Qi Qj + itype,jtype = 2 atom types N = # of values @@ -143,10 +143,10 @@ Examples -pair_write 1 3 500 r 1.0 10.0 table.txt LJ -pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5 - - + +pair_write 1 3 500 r 1.0 10.0 table.txt LJ +pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5 + Description diff --git a/doc/html/pair_yukawa.html b/doc/html/pair_yukawa.html index 826c7de7ff..3f0d3b3e2c 100644 --- a/doc/html/pair_yukawa.html +++ b/doc/html/pair_yukawa.html @@ -134,9 +134,9 @@ pair_style yukawa/omp command Syntax -pair_style yukawa kappa cutoff - - + +pair_style yukawa kappa cutoff + kappa = screening length (inverse distance units) cutoff = global cutoff for Yukawa interactions (distance units) @@ -144,11 +144,11 @@ Examples -pair_style yukawa 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 - - + +pair_style yukawa 2.0 2.5 +pair_coeff 1 1 100.0 2.3 +pair_coeff * * 100.0 + Description diff --git a/doc/html/pair_yukawa_colloid.html b/doc/html/pair_yukawa_colloid.html index 560d253325..0c16f65c1d 100644 --- a/doc/html/pair_yukawa_colloid.html +++ b/doc/html/pair_yukawa_colloid.html @@ -134,9 +134,9 @@ pair_style yukawa/colloid/omp command Syntax -pair_style yukawa/colloid kappa cutoff - - + +pair_style yukawa/colloid kappa cutoff + kappa = screening length (inverse distance units) cutoff = global cutoff for colloidal Yukawa interactions (distance units) @@ -144,11 +144,11 @@ Examples -pair_style yukawa/colloid 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 - - + +pair_style yukawa/colloid 2.0 2.5 +pair_coeff 1 1 100.0 2.3 +pair_coeff * * 100.0 + Description @@ -182,9 +182,9 @@ charge and surface potential due to the presence of electrolyte. Note that the A for this potential style has different units than the A used in pair_style yukawa. For low surface potentials, i.e. less than about 25 mV, A can be written as: -A = 2 * PI * R*eps*eps0 * kappa * psi^2 - - + +A = 2 * PI * R*eps*eps0 * kappa * psi^2 + where R = colloid radius (distance units) diff --git a/doc/html/pair_zbl.html b/doc/html/pair_zbl.html index 71b3bea35c..54ad6b5344 100644 --- a/doc/html/pair_zbl.html +++ b/doc/html/pair_zbl.html @@ -134,9 +134,9 @@ pair_style zbl/omp command Syntax -pair_style zbl inner outer - - + +pair_style zbl inner outer + inner = distance where switching function begins outer = global cutoff for ZBL interaction @@ -144,11 +144,11 @@ Examples -pair_style zbl 3.0 4.0 -pair_coeff * * 73.0 73.0 -pair_coeff 1 1 14.0 14.0 - - + +pair_style zbl 3.0 4.0 +pair_coeff * * 73.0 73.0 +pair_coeff 1 1 14.0 14.0 + Description diff --git a/doc/html/pair_zero.html b/doc/html/pair_zero.html index b0605c1fce..e64a46c138 100644 --- a/doc/html/pair_zero.html +++ b/doc/html/pair_zero.html @@ -139,12 +139,12 @@ nocoeff = ignore all pair_coeff parameters (optional) Examples -pair_style zero 10.0 -pair_style zero 5.0 nocoeff -pair_coeff * * -pair_coeff 1 2*4 3.0 - - + +pair_style zero 10.0 +pair_style zero 5.0 nocoeff +pair_coeff * * +pair_coeff 1 2*4 3.0 + Description diff --git a/doc/html/partition.html b/doc/html/partition.html index 858da5aef8..9b26e1252f 100644 --- a/doc/html/partition.html +++ b/doc/html/partition.html @@ -142,8 +142,8 @@ partition yes 1 processors 4 10 6 partition no 5 print "Active partition" -partition yes 5 fix all nve -partition yes 6 fix all nvt temp 1.0 1.0 0.1 +partition yes *5 fix all nve +partition yes 6* fix all nvt temp 1.0 1.0 0.1 @@ -171,7 +171,7 @@ partitions specified by the 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 f0feeb91ba..15f24d6340 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 f78a9df834..6700435a9f 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 603ab46785..5e2e9f96eb 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/read_restart.html b/doc/html/read_restart.html index 5a2e8099fa..ca1284f6aa 100644 --- a/doc/html/read_restart.html +++ b/doc/html/read_restart.html @@ -128,9 +128,9 @@ read_restart command Syntax -read_restart file flag - - + +read_restart file flag + file = name of binary restart file to read in flag = remap (optional) @@ -138,13 +138,13 @@ Examples -read_restart save.10000 -read_restart save.10000 remap -read_restart restart.* -read_restart restart.*.mpiio -read_restart poly.*.% remap - - + +read_restart save.10000 +read_restart save.10000 remap +read_restart restart.* +read_restart restart.*.mpiio +read_restart poly.*.% remap + Description diff --git a/doc/html/reset_timestep.html b/doc/html/reset_timestep.html index 9a274dfb77..b261a67791 100644 --- a/doc/html/reset_timestep.html +++ b/doc/html/reset_timestep.html @@ -128,19 +128,19 @@ reset_timestep command Syntax -reset_timestep N - - + +reset_timestep N + N = timestep number Examples -reset_timestep 0 -reset_timestep 4000000 - - + +reset_timestep 0 +reset_timestep 4000000 + Description diff --git a/doc/html/restart.html b/doc/html/restart.html index d6fc25f246..3f169da485 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 9ef0e69f67..b00835c7e1 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 @@ 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 89ea2eb1ff..075dbb3510 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/shell.html b/doc/html/shell.html index 732af4e4f4..c4ed4806b4 100644 --- a/doc/html/shell.html +++ b/doc/html/shell.html @@ -153,17 +153,17 @@ anything else is passed as a command to the shell for direct execution Examples -shell cd sub1 -shell cd .. -shell mkdir tmp1 tmp2 tmp3 -shell rmdir tmp1 -shell mv log.lammps hold/log.1 -shell rm TMP/file1 TMP/file2 -shell putenv LAMMPS_POTENTIALS=../../potentials -shell my_setup file1 10 file2 -shell my_post_process 100 dump.out - - + +shell cd sub1 +shell cd .. +shell mkdir tmp1 tmp2 tmp3 +shell rmdir tmp1 +shell mv log.lammps hold/log.1 +shell rm TMP/file1 TMP/file2 +shell putenv LAMMPS_POTENTIALS=../../potentials +shell my_setup file1 10 file2 +shell my_post_process 100 dump.out + Description @@ -199,15 +199,15 @@ performed. The resulting string is then used literally. Any other cmd is passed as-is to the shell along with its arguments as one string, invoked by the C-library system() call. For example, these lines in your input script: -variable n equal 10 + +variable n equal 10 variable foo string file2 shell my_setup file1 $n ${foo} - - + would be the same as invoking -% my_setup file1 10 file2 - - + +% my_setup file1 10 file2 + from a command-line prompt. The executable program “my_setup” is run with 3 arguments: file1 10 file2. diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html index 08a1e3f74c..d431cc49b3 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 @@ 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 d4f05d75ae..e4bab3f210 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 @@ 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. delt_lo is the time of each detected +entered, in units of timestep. del*t_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 8567a3fd63..7a5cb15c32 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_modify.html b/doc/html/thermo_modify.html index 403b94ca91..17118e5b21 100644 --- a/doc/html/thermo_modify.html +++ b/doc/html/thermo_modify.html @@ -128,9 +128,9 @@ thermo_modify command Syntax -thermo_modify keyword value ... - - + +thermo_modify keyword value ... + one or more keyword/value pairs may be listed @@ -150,12 +150,12 @@ keyword = lost or lost/bond or norm or flush Examples -thermo_modify lost ignore flush yes -thermo_modify temp myTemp format 3 %15.8g -thermo_modify temp myTemp format line "%ld %g %g %15.8g" -thermo_modify line multi format float %g - - + +thermo_modify lost ignore flush yes +thermo_modify temp myTemp format 3 %15.8g +thermo_modify temp myTemp format line "%ld %g %g %15.8g" +thermo_modify line multi format float %g + Description diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html index 5a6e41bfc9..4f0f68acae 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 @@ 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 9dc8285c6d..e80e207a23 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 2b9cdb1f79..3582bbab10 100644 --- a/doc/html/variable.html +++ b/doc/html/variable.html @@ -197,7 +197,8 @@ 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 @@ -214,8 +215,7 @@ 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. @@ -1035,8 +1035,8 @@ reference means, since computes only produce either global or per-atom quantities, never both. - - + + c_ID @@ -1059,9 +1059,9 @@ 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 @@ -1090,14 +1090,14 @@ 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. - - + + f_ID @@ -1165,8 +1165,8 @@ There is no ambiguity as to what a reference means, since variables produce only a global scalar or global vector or per-atom vector. - - + + v_name @@ -1201,7 +1201,7 @@ 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 @@ -1210,7 +1210,7 @@ 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 @@ -1237,9 +1237,9 @@ 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 @@ -1330,13 +1330,13 @@ 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 @@ -1353,14 +1353,14 @@ 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 06accf9593..af9be7196c 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 1698ec2615..d4d15e1ddf 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/html/write_data.html b/doc/html/write_data.html index d0d619bb4a..5e4286d69d 100644 --- a/doc/html/write_data.html +++ b/doc/html/write_data.html @@ -128,9 +128,9 @@ write_data command Syntax -write_data file keyword value ... - - + +write_data file keyword value ... + file = name of data file to write out zero or more keyword/value pairs may be appended @@ -145,10 +145,10 @@ Examples -write_data data.polymer -write_data data.* - - + +write_data data.polymer +write_data data.* + Description diff --git a/doc/html/write_restart.html b/doc/html/write_restart.html index b3403777c6..f1a7fba6bb 100644 --- a/doc/html/write_restart.html +++ b/doc/html/write_restart.html @@ -128,9 +128,9 @@ write_restart command Syntax -write_restart file keyword value ... - - + +write_restart file keyword value ... + file = name of file to write restart information to zero or more keyword/value pairs may be appended @@ -145,11 +145,11 @@ Examples -write_restart restart.equil -write_restart restart.equil.mpiio -write_restart poly.%.* nfile 10 - - + +write_restart restart.equil +write_restart restart.equil.mpiio +write_restart poly.%.* nfile 10 + Description](_images/sinusoid.jpg){kind=link}