Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="21 Dec 2016 version"> <META NAME="docnumber" CONTENT="6 Jan 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 21 Dec 2016 version :c,h4 6 Jan 2017 version :c,h4 Version info: :h4 Loading doc/src/PDF/colvars-refman-lammps.pdf +1.89 KiB (553 KiB) File changed.No diff preview for this file type. View original file View changed file doc/src/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -581,7 +581,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, "lineforce"_fix_lineforce.html, "momentum"_fix_momentum.html, "momentum (k)"_fix_momentum.html, "move"_fix_move.html, "msst"_fix_msst.html, "neb"_fix_neb.html, Loading Loading @@ -702,6 +702,7 @@ package"_Section_start.html#start_3. "manifoldforce"_fix_manifoldforce.html, "meso/stationary"_fix_meso_stationary.html, "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nvk"_fix_nvk.html, "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "nph/eff"_fix_nh_eff.html, "npt/eff"_fix_nh_eff.html, Loading doc/src/fix_colvars.txt +5 −12 Original line number Diff line number Diff line Loading @@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre [Description:] This fix interfaces LAMMPS to a "collective variables" or "colvars" module library which allows to calculate potentials of mean force This fix interfaces LAMMPS to the collective variables "Colvars" library, which allows to calculate potentials of mean force (PMFs) for any set of colvars, using different sampling methods: currently implemented are the Adaptive Biasing Force (ABF) method, metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic restraint bias. The colvars library is hosted at "http://colvars.github.io/"_http://colvars.github.io/ (US) via a flexible harmonic restraint bias. This documentation describes only the fix colvars command itself and LAMMPS specific parts of the code. The full documentation of the colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf A detailed discussion of the implementation of the portable collective variable library is in "(Fiorin)"_#Fiorin. Additional information can be found in "(Henin)"_#Henin. The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin. There are some example scripts for using this package with LAMMPS in the examples/USER/colvars directory. Loading Loading @@ -129,8 +127,3 @@ and tstat = NULL. :link(Fiorin) [(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 :link(Henin) [(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, 35-47 (2010) doc/src/fix_eos_table_rx.txt +38 −4 Original line number Diff line number Diff line Loading @@ -10,7 +10,7 @@ fix eos/table/rx command :h3 [Syntax:] fix ID group-ID eos/table/rx style file1 N keyword file2 :pre fix ID group-ID eos/table/rx style file1 N keyword ... :pre ID, group-ID are documented in "fix"_fix.html command eos/table/rx = style name of this fix command Loading @@ -18,11 +18,16 @@ style = {linear} = method of interpolation file1 = filename containing the tabulated equation of state N = use N values in {linear} tables keyword = name of table keyword correponding to table file file2 = filename containing the heats of formation of each species :ul file2 = filename containing the heats of formation of each species (optional) deltaHf = heat of formation for a single species in energy units (optional) energyCorr = energy correction in energy units (optional) tempCorrCoeff = temperature correction coefficient (optional) :ul [Examples:] fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre [Description:] Loading @@ -39,7 +44,15 @@ where {m} is the number of species, {c_i,j} is the concentration of species {j} in particle {i}, {u_j} is the internal energy of species j, {DeltaH_f,j} is the heat of formation of species {j}, N is the number of molecules represented by the coarse-grained particle, kb is the Boltzmann constant, and T is the temperature of the system. Boltzmann constant, and T is the temperature of the system. Additionally, it is possible to modify the concentration-dependent particle internal energy relation by adding an energy correction, temperature-dependent correction, and/or a molecule-dependent correction. An energy correction can be specified as a constant (in energy units). A temperature correction can be specified by multiplying a temperature correction coefficient by the internal temperature. A molecular correction can be specified by by multiplying a molecule correction coefficient by the average number of product gas particles in the coarse-grain particle. Fix {eos/table/rx} creates interpolation tables of length {N} from {m} internal energy values of each species {u_j} listed in a file as a Loading @@ -58,6 +71,14 @@ file is described below. The second filename specifies a file containing heat of formation {DeltaH_f,j} for each species. In cases where the coarse-grain particle represents a single molecular species (i.e., no reactions occur and fix {rx} is not present in the input file), fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} within a non-reactive DPD simulation. In this case, the heat of formation filename is replaced with the heat of formation value for the single species. Additionally, the energy correction and temperature correction coefficients may also be specified as fix arguments. :line The format of a tabulated file is as follows (without the Loading Loading @@ -116,6 +137,19 @@ Note that the species can be listed in any order. The tag that is used as the species name must correspond with the tags used to define the reactions with the "fix rx"_fix_rx.html command. Alternatively, corrections to the EOS can be included by specifying three additional columns that correspond to the energy correction, the temperature correction coefficient and molecule correction coefficient. In this case, the format of the file is as follows: # HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre (blank) h2 0.00 1.23 0.025 0.0 (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient) no2 0.34 0.00 0.000 -1.76 n2 0.00 0.00 0.000 -1.76 ... no 0.93 0.00 0.000 -1.76 :pre :line [Restrictions:] Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="21 Dec 2016 version"> <META NAME="docnumber" CONTENT="6 Jan 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 21 Dec 2016 version :c,h4 6 Jan 2017 version :c,h4 Version info: :h4 Loading
doc/src/PDF/colvars-refman-lammps.pdf +1.89 KiB (553 KiB) File changed.No diff preview for this file type. View original file View changed file
doc/src/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -581,7 +581,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, "lineforce"_fix_lineforce.html, "momentum"_fix_momentum.html, "momentum (k)"_fix_momentum.html, "move"_fix_move.html, "msst"_fix_msst.html, "neb"_fix_neb.html, Loading Loading @@ -702,6 +702,7 @@ package"_Section_start.html#start_3. "manifoldforce"_fix_manifoldforce.html, "meso/stationary"_fix_meso_stationary.html, "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nvk"_fix_nvk.html, "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "nph/eff"_fix_nh_eff.html, "npt/eff"_fix_nh_eff.html, Loading
doc/src/fix_colvars.txt +5 −12 Original line number Diff line number Diff line Loading @@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre [Description:] This fix interfaces LAMMPS to a "collective variables" or "colvars" module library which allows to calculate potentials of mean force This fix interfaces LAMMPS to the collective variables "Colvars" library, which allows to calculate potentials of mean force (PMFs) for any set of colvars, using different sampling methods: currently implemented are the Adaptive Biasing Force (ABF) method, metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic restraint bias. The colvars library is hosted at "http://colvars.github.io/"_http://colvars.github.io/ (US) via a flexible harmonic restraint bias. This documentation describes only the fix colvars command itself and LAMMPS specific parts of the code. The full documentation of the colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf A detailed discussion of the implementation of the portable collective variable library is in "(Fiorin)"_#Fiorin. Additional information can be found in "(Henin)"_#Henin. The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin. There are some example scripts for using this package with LAMMPS in the examples/USER/colvars directory. Loading Loading @@ -129,8 +127,3 @@ and tstat = NULL. :link(Fiorin) [(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 :link(Henin) [(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, 35-47 (2010)
doc/src/fix_eos_table_rx.txt +38 −4 Original line number Diff line number Diff line Loading @@ -10,7 +10,7 @@ fix eos/table/rx command :h3 [Syntax:] fix ID group-ID eos/table/rx style file1 N keyword file2 :pre fix ID group-ID eos/table/rx style file1 N keyword ... :pre ID, group-ID are documented in "fix"_fix.html command eos/table/rx = style name of this fix command Loading @@ -18,11 +18,16 @@ style = {linear} = method of interpolation file1 = filename containing the tabulated equation of state N = use N values in {linear} tables keyword = name of table keyword correponding to table file file2 = filename containing the heats of formation of each species :ul file2 = filename containing the heats of formation of each species (optional) deltaHf = heat of formation for a single species in energy units (optional) energyCorr = energy correction in energy units (optional) tempCorrCoeff = temperature correction coefficient (optional) :ul [Examples:] fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre [Description:] Loading @@ -39,7 +44,15 @@ where {m} is the number of species, {c_i,j} is the concentration of species {j} in particle {i}, {u_j} is the internal energy of species j, {DeltaH_f,j} is the heat of formation of species {j}, N is the number of molecules represented by the coarse-grained particle, kb is the Boltzmann constant, and T is the temperature of the system. Boltzmann constant, and T is the temperature of the system. Additionally, it is possible to modify the concentration-dependent particle internal energy relation by adding an energy correction, temperature-dependent correction, and/or a molecule-dependent correction. An energy correction can be specified as a constant (in energy units). A temperature correction can be specified by multiplying a temperature correction coefficient by the internal temperature. A molecular correction can be specified by by multiplying a molecule correction coefficient by the average number of product gas particles in the coarse-grain particle. Fix {eos/table/rx} creates interpolation tables of length {N} from {m} internal energy values of each species {u_j} listed in a file as a Loading @@ -58,6 +71,14 @@ file is described below. The second filename specifies a file containing heat of formation {DeltaH_f,j} for each species. In cases where the coarse-grain particle represents a single molecular species (i.e., no reactions occur and fix {rx} is not present in the input file), fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} within a non-reactive DPD simulation. In this case, the heat of formation filename is replaced with the heat of formation value for the single species. Additionally, the energy correction and temperature correction coefficients may also be specified as fix arguments. :line The format of a tabulated file is as follows (without the Loading Loading @@ -116,6 +137,19 @@ Note that the species can be listed in any order. The tag that is used as the species name must correspond with the tags used to define the reactions with the "fix rx"_fix_rx.html command. Alternatively, corrections to the EOS can be included by specifying three additional columns that correspond to the energy correction, the temperature correction coefficient and molecule correction coefficient. In this case, the format of the file is as follows: # HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre (blank) h2 0.00 1.23 0.025 0.0 (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient) no2 0.34 0.00 0.000 -1.76 n2 0.00 0.00 0.000 -1.76 ... no 0.93 0.00 0.000 -1.76 :pre :line [Restrictions:] Loading
