Loading doc/src/Section_errors.txt +6 −0 Original line number Diff line number Diff line Loading @@ -11171,6 +11171,12 @@ Self-explanatory. :dd If the fix changes the timestep, the dump dcd file will not reflect the change. :dd {Energy due to X extra global DOFs will be included in minimizer energies} :dt When using fixes like box/relax, the potential energy used by the minimizer is augmented by an additional energy provided by the fix. Thus the printed converged energy may be different from the total potential energy. :dd {Energy tally does not account for 'zero yes'} :dt The energy removed by using the 'zero yes' flag is not accounted Loading doc/src/Section_tools.txt +6 −3 Original line number Diff line number Diff line Loading @@ -369,15 +369,18 @@ supports it. It has its own WWW page at msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS input data files from BIOVIA's Materias Studio files (formerly Accelrys' The msi2lmp sub-directory contains a tool for creating LAMMPS template input and data files from BIOVIA's Materias Studio files (formerly Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS. See the README file for more information. This tool has several known limitations and is no longer under active development, so there are no changes except for the occasional bugfix. See the README file in the tools/msi2lmp folder for more information. :line Loading doc/src/bonds.txt +0 −1 Original line number Diff line number Diff line Loading @@ -16,7 +16,6 @@ Bond Styles :h1 bond_none bond_nonlinear bond_oxdna bond_oxdna2 bond_quartic bond_table bond_zero Loading doc/src/fix_gle.txt +5 −4 Original line number Diff line number Diff line Loading @@ -67,9 +67,10 @@ target value as the {Tstart} and {Tstop} arguments, so that the diffusion matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that can be used for instance to model inexpensively zero-point energy effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. Please note, that the covariance matrix is expected to be given in [temperature units]. Since integrating GLE dynamics can be costly when used together with simple potentials, one can use the {every} optional keyword to Loading Loading @@ -148,7 +149,7 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html 1170-80 (2010) :link(GLE4MD) [(GLE4MD)] "http://epfl-cosmo.github.io/gle4md/"_http://epfl-cosmo.github.io/gle4md/ [(GLE4MD)] "http://gle4md.org/"_http://gle4md.org/ :link(Ceriotti2) [(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, Loading doc/src/improper_cossq.txt +1 −4 Original line number Diff line number Diff line Loading @@ -45,12 +45,9 @@ above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: K (energy/radian^2) K (energy) X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are Loading Loading
doc/src/Section_errors.txt +6 −0 Original line number Diff line number Diff line Loading @@ -11171,6 +11171,12 @@ Self-explanatory. :dd If the fix changes the timestep, the dump dcd file will not reflect the change. :dd {Energy due to X extra global DOFs will be included in minimizer energies} :dt When using fixes like box/relax, the potential energy used by the minimizer is augmented by an additional energy provided by the fix. Thus the printed converged energy may be different from the total potential energy. :dd {Energy tally does not account for 'zero yes'} :dt The energy removed by using the 'zero yes' flag is not accounted Loading
doc/src/Section_tools.txt +6 −3 Original line number Diff line number Diff line Loading @@ -369,15 +369,18 @@ supports it. It has its own WWW page at msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS input data files from BIOVIA's Materias Studio files (formerly Accelrys' The msi2lmp sub-directory contains a tool for creating LAMMPS template input and data files from BIOVIA's Materias Studio files (formerly Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS. See the README file for more information. This tool has several known limitations and is no longer under active development, so there are no changes except for the occasional bugfix. See the README file in the tools/msi2lmp folder for more information. :line Loading
doc/src/bonds.txt +0 −1 Original line number Diff line number Diff line Loading @@ -16,7 +16,6 @@ Bond Styles :h1 bond_none bond_nonlinear bond_oxdna bond_oxdna2 bond_quartic bond_table bond_zero Loading
doc/src/fix_gle.txt +5 −4 Original line number Diff line number Diff line Loading @@ -67,9 +67,10 @@ target value as the {Tstart} and {Tstop} arguments, so that the diffusion matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that can be used for instance to model inexpensively zero-point energy effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. Please note, that the covariance matrix is expected to be given in [temperature units]. Since integrating GLE dynamics can be costly when used together with simple potentials, one can use the {every} optional keyword to Loading Loading @@ -148,7 +149,7 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html 1170-80 (2010) :link(GLE4MD) [(GLE4MD)] "http://epfl-cosmo.github.io/gle4md/"_http://epfl-cosmo.github.io/gle4md/ [(GLE4MD)] "http://gle4md.org/"_http://gle4md.org/ :link(Ceriotti2) [(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, Loading
doc/src/improper_cossq.txt +1 −4 Original line number Diff line number Diff line Loading @@ -45,12 +45,9 @@ above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: K (energy/radian^2) K (energy) X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are Loading
