- -
fix com command -
-Syntax: -
-fix ID group-ID com N file --
- ID, group-ID are documented in fix command -
- com = style name of this fix command -
- N = compute center-of-mass every this many timesteps -
- file = filename to write center-of-mass info to -
Examples: -
-fix 1 all com 100 com.out --
Description: -
-Compute the center-of-mass of the group of atoms every N steps, -including all effects due to atoms passing thru periodic boundaries. -Write the results to the specified file. -
-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 be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: none -
-Related commands: none -
-Default: none -
- diff --git a/doc/fix_com.txt b/doc/fix_com.txt deleted file mode 100644 index d252382fe1..0000000000 --- a/doc/fix_com.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix com command :h3 - -[Syntax:] - -fix ID group-ID com N file :pre - -ID, group-ID are documented in "fix"_fix.html command -com = style name of this fix command -N = compute center-of-mass every this many timesteps -file = filename to write center-of-mass info to :ul - -[Examples:] - -fix 1 all com 100 com.out :pre - -[Description:] - -Compute the center-of-mass of the group of atoms every N steps, -including all effects due to atoms passing thru periodic boundaries. -Write the results to the specified file. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none - - - - diff --git a/doc/fix_gyration.html b/doc/fix_gyration.html deleted file mode 100644 index dce19f1954..0000000000 --- a/doc/fix_gyration.html +++ /dev/null @@ -1,57 +0,0 @@ - -- -
fix gyration command -
-Syntax: -
-fix ID group-ID gyration N file --
- ID, group-ID are documented in fix command -
- gyration = style name of this fix command -
- N = compute radius-of-gyration every this many timesteps -
- file = filename to write gyration info to -
Examples: -
-fix 1 all gyration 100 molecule.out --
Description: -
-Compute the radius-of-gyration of the group of atoms every N steps, -including all effects due to atoms passing thru periodic boundaries. -Write the results to the specified file. -
-Rg is a measure of the size of the group of atoms, and is computed by -this formula -
-
-where M is the total mass of the group and Rcm is the center-of-mass -position of the group. -
-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 be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: none -
-Related commands: none -
-Default: none -
- diff --git a/doc/fix_gyration.txt b/doc/fix_gyration.txt deleted file mode 100644 index fa7cdfa193..0000000000 --- a/doc/fix_gyration.txt +++ /dev/null @@ -1,52 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix gyration command :h3 - -[Syntax:] - -fix ID group-ID gyration N file :pre - -ID, group-ID are documented in "fix"_fix.html command -gyration = style name of this fix command -N = compute radius-of-gyration every this many timesteps -file = filename to write gyration info to :ul - -[Examples:] - -fix 1 all gyration 100 molecule.out :pre - -[Description:] - -Compute the radius-of-gyration of the group of atoms every N steps, -including all effects due to atoms passing thru periodic boundaries. -Write the results to the specified file. - -Rg is a measure of the size of the group of atoms, and is computed by -this formula - -:c,image(Eqs/fix_gyration.jpg) - -where M is the total mass of the group and Rcm is the center-of-mass -position of the group. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/fix_msd.html b/doc/fix_msd.html deleted file mode 100644 index 14ffa3c397..0000000000 --- a/doc/fix_msd.html +++ /dev/null @@ -1,89 +0,0 @@ - -- -
fix msd command -
-Syntax: -
-fix ID group-ID msd N file keyword value ... --
- ID, group-ID are documented in fix command - -
- msd = style name of this fix command - -
- N = compute mean-squared displacement every this many timesteps - -
- file = filename to write mean-squared displacement info to - -
- zero or more keyword/value pairs may be appended - -
- keyword = com
-
-
com value = yes or no -
- -
Examples: -
-fix 1 all msd 100 diff.out -fix 1 all msd 1000 diff.out com yes --
Description: -
-Compute the mean-squared displacement (MSD) of the group of atoms -every N steps, including all effects due to atoms passing thru -periodic boundaries. The MSD is the square of the displacement of -each atom, averaged over all the atoms in the group. The displacement -of an atom is from its original position at the time the fix command -was issued. The slope of the mean-squared displacement versus time is -proportional to the diffusion coefficient of the diffusing atoms. -
-The MSD values versus time are written to the specified file. -
-IMPORTANT NOTE: If an atom is part of a rigid body (see the fix -rigid command), it's periodic image flags are altered, -and the computed MSD will not reflect its true displacement. See the -fix rigid command for details. Thus, to compute the -MSD of rigid bodies as they cross periodic boundaries, you will need -to post-process a dump file containing coordinates of the -atoms in the bodies. -
-If the com option is set to yes then the effect of any drift -in the center-of-mass of the group of atoms is subtracted out before -the displacment of each atom is calcluated. -
-Restart, fix_modify, output, run start/stop, minimize info: -
-This fix writes the original coordinates of diffusing atoms to binary -restart files, so that the mean-squared displacement -will be accurate 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 the fix continues in an uninterrupted fashion. -
-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 be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: none -
-Related commands: -
- -Default: -
-The option default is com = no. -
- diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt deleted file mode 100644 index cf0d82e9bf..0000000000 --- a/doc/fix_msd.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix msd command :h3 - -[Syntax:] - -fix ID group-ID msd N file keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -msd = style name of this fix command :l -N = compute mean-squared displacement every this many timesteps :l -file = filename to write mean-squared displacement info to :l -zero or more keyword/value pairs may be appended :l -keyword = {com} :l - {com} value = {yes} or {no} :pre -:ule - -[Examples:] - -fix 1 all msd 100 diff.out -fix 1 all msd 1000 diff.out com yes :pre - -[Description:] - -Compute the mean-squared displacement (MSD) of the group of atoms -every N steps, including all effects due to atoms passing thru -periodic boundaries. The MSD is the square of the displacement of -each atom, averaged over all the atoms in the group. The displacement -of an atom is from its original position at the time the fix command -was issued. The slope of the mean-squared displacement versus time is -proportional to the diffusion coefficient of the diffusing atoms. - -The MSD values versus time are written to the specified file. - -IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix -rigid"_fix_rigid.html command), it's periodic image flags are altered, -and the computed MSD will not reflect its true displacement. See the -"fix rigid"_fix_rigid.html command for details. Thus, to compute the -MSD of rigid bodies as they cross periodic boundaries, you will need -to post-process a "dump file"_dump.html containing coordinates of the -atoms in the bodies. - -If the {com} option is set to {yes} then the effect of any drift -in the center-of-mass of the group of atoms is subtracted out before -the displacment of each atom is calcluated. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the original coordinates of diffusing atoms to "binary -restart files"_restart.html, so that the mean-squared displacement -will be accurate in a restarted simulation. See the -"read_restart"_read_restart.html 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 uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html 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"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix coord/original"_fix_coord_original.html - -[Default:] - -The option default is com = no. diff --git a/doc/fix_rdf.html b/doc/fix_rdf.html deleted file mode 100644 index 4729297fbb..0000000000 --- a/doc/fix_rdf.html +++ /dev/null @@ -1,74 +0,0 @@ - -- -
fix rdf command -
-Syntax: -
-fix ID group-ID rdf N file Nbin itype1 jtype1 itype2 jtype2 ... --
- ID, group-ID are documented in fix command -
- rdf = style name of this fix command -
- N = compute radial distribution function (RDF) every this many timesteps -
- file = filename to write radial distribution function info to -
- Nbin = number of RDF bins -
- itypeN = central atom type for RDF pair N -
- jtypeN = distribution atom type for RDF pair N -
Examples: -
-fix 1 all rdf 500 rdf.out 100 1 1 -fix 1 fluid rdf 10000 rdf.out 100 1 1 1 2 2 1 2 2 --
Description: -
-Compute the radial distribution function (RDF), also known as g(r), -and coordination number every N steps. The RDF for each specified -atom type pair is histogrammed in Nbin bins from distance 0 to Rc, -where Rc = the maximum force cutoff for any pair of atom types. An -atom pair only contributes to the RDF if -
-- both atoms are in the fix group -
- the distance between them is within the maximum force cutoff -
- their interaction is stored in the neighbor list -
Bonded atoms (1-2, 1-3, 1-4 interactions within a molecular topology) -with a pairwise weighting factor of 0.0 are not included in the RDF; -pairs with a non-zero weighting factor are included. The weighting -factor is set by the special_bonds command. -
-The RDF statistics for each timestep are written to the specified -file, as are the RDF values averaged over all timesteps. -
-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 be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: -
-The RDF is not computed for distances longer than the force cutoff, -since processors (in parallel) don't know atom coordinates for atoms -further away than that distance. If you want an RDF for larger r, -you'll need to post-process a dump file. -
-Related commands: -
- -Default: none -
- diff --git a/doc/fix_rdf.txt b/doc/fix_rdf.txt deleted file mode 100644 index d854817373..0000000000 --- a/doc/fix_rdf.txt +++ /dev/null @@ -1,69 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix rdf command :h3 - -[Syntax:] - -fix ID group-ID rdf N file Nbin itype1 jtype1 itype2 jtype2 ... :pre - -ID, group-ID are documented in "fix"_fix.html command -rdf = style name of this fix command -N = compute radial distribution function (RDF) every this many timesteps -file = filename to write radial distribution function info to -Nbin = number of RDF bins -itypeN = central atom type for RDF pair N -jtypeN = distribution atom type for RDF pair N :ul - -[Examples:] - -fix 1 all rdf 500 rdf.out 100 1 1 -fix 1 fluid rdf 10000 rdf.out 100 1 1 1 2 2 1 2 2 :pre - -[Description:] - -Compute the radial distribution function (RDF), also known as g(r), -and coordination number every N steps. The RDF for each specified -atom type pair is histogrammed in Nbin bins from distance 0 to Rc, -where Rc = the maximum force cutoff for any pair of atom types. An -atom pair only contributes to the RDF if - -both atoms are in the fix group -the distance between them is within the maximum force cutoff -their interaction is stored in the neighbor list :ul - -Bonded atoms (1-2, 1-3, 1-4 interactions within a molecular topology) -with a pairwise weighting factor of 0.0 are not included in the RDF; -pairs with a non-zero weighting factor are included. The weighting -factor is set by the "special_bonds"_special_bonds.html command. - -The RDF statistics for each timestep are written to the specified -file, as are the RDF values averaged over all timesteps. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -The RDF is not computed for distances longer than the force cutoff, -since processors (in parallel) don't know atom coordinates for atoms -further away than that distance. If you want an RDF for larger {r}, -you'll need to post-process a dump file. - -[Related commands:] - -"pair_style"_pair_style.html - -[Default:] none