Loading doc/src/fix_spring_chunk.rst +10 −1 Original line number Diff line number Diff line Loading @@ -50,7 +50,16 @@ atom. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. This fix writes the locations of the initial per-chunk center of mass coordinates to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. Since this fix depends on an instance of :doc:`compute chunk/atom <compute_chunk_atom>` it will check when reading the restart if the chunk still exists and will define the same number of chunks. The restart data is only applied when the number of chunks matches. Otherwise the center of mass coordinates are recomputed. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the energy stored in all the springs to the system's potential Loading doc/src/fix_spring_rg.rst +14 −3 Original line number Diff line number Diff line Loading @@ -59,9 +59,20 @@ the time the fix is specified, and that value is used as the target. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. This fix writes the currently used reference RG (:math:`R_{G0}`) to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. This fix computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar is the reference radius of gyration :math:`R_{G0}` used by the fix. energy change due to this fix. The scalar value calculated by this fix is "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. Loading doc/src/fix_temp_rescale.rst +7 −2 Original line number Diff line number Diff line Loading @@ -126,7 +126,11 @@ thermal degrees of freedom, and the bias is added back in. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. This fix writes the cumulative global energy change to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. The :doc:`fix_modify <fix_modify>` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute <compute>` Loading @@ -136,7 +140,8 @@ this fix and by the compute should be the same. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This fix computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar is the cumulative Loading src/fix_spring_chunk.cpp +54 −0 Original line number Diff line number Diff line Loading @@ -15,6 +15,7 @@ #include <cmath> #include <cstring> #include "atom.h" #include "comm.h" #include "update.h" #include "force.h" #include "respa.h" Loading @@ -37,6 +38,7 @@ FixSpringChunk::FixSpringChunk(LAMMPS *lmp, int narg, char **arg) : { if (narg != 6) error->all(FLERR,"Illegal fix spring/chunk command"); restart_global = 1; scalar_flag = 1; global_freq = 1; extscalar = 1; Loading Loading @@ -241,6 +243,58 @@ void FixSpringChunk::min_post_force(int vflag) post_force(vflag); } /* ---------------------------------------------------------------------- writ number of chunks and position of original COM into restart ------------------------------------------------------------------------- */ void FixSpringChunk::write_restart(FILE *fp) { double n = nchunk; if (comm->me == 0) { int size = (3*n+1) * sizeof(double); fwrite(&size,sizeof(int),1,fp); fwrite(&n,sizeof(double),1,fp); fwrite(&com0[0][0],3*sizeof(double),nchunk,fp); } } /* ---------------------------------------------------------------------- use state info from restart file to restart the Fix ------------------------------------------------------------------------- */ void FixSpringChunk::restart(char *buf) { double *list = (double *) buf; int n = list[0]; memory->destroy(com0); memory->destroy(fcom); int icompute = modify->find_compute(idchunk); if (icompute < 0) error->all(FLERR,"Chunk/atom compute does not exist for fix spring/chunk"); cchunk = (ComputeChunkAtom *) modify->compute[icompute]; if (strcmp(cchunk->style,"chunk/atom") != 0) error->all(FLERR,"Fix spring/chunk does not use chunk/atom compute"); nchunk = cchunk->setup_chunks(); cchunk->compute_ichunk(); memory->create(com0,nchunk,3,"spring/chunk:com0"); memory->create(fcom,nchunk,3,"spring/chunk:fcom"); printf("restart chunks:%d computed chunks: %d\n",n,nchunk); if (n != nchunk) { if (comm->me == 0) error->warning(FLERR,"Number of chunks has changed. Cannot use restart"); memory->destroy(com0); memory->destroy(fcom); nchunk = 1; } else { cchunk->lock(this,update->ntimestep,-1); memcpy(&com0[0][0],list+1,3*n*sizeof(double)); } } /* ---------------------------------------------------------------------- energy of stretched spring ------------------------------------------------------------------------- */ Loading src/fix_spring_chunk.h +2 −0 Original line number Diff line number Diff line Loading @@ -35,6 +35,8 @@ class FixSpringChunk : public Fix { void post_force(int); void post_force_respa(int, int, int); void min_post_force(int); void write_restart(FILE *); void restart(char *); double compute_scalar(); private: Loading Loading
doc/src/fix_spring_chunk.rst +10 −1 Original line number Diff line number Diff line Loading @@ -50,7 +50,16 @@ atom. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. This fix writes the locations of the initial per-chunk center of mass coordinates to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. Since this fix depends on an instance of :doc:`compute chunk/atom <compute_chunk_atom>` it will check when reading the restart if the chunk still exists and will define the same number of chunks. The restart data is only applied when the number of chunks matches. Otherwise the center of mass coordinates are recomputed. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the energy stored in all the springs to the system's potential Loading
doc/src/fix_spring_rg.rst +14 −3 Original line number Diff line number Diff line Loading @@ -59,9 +59,20 @@ the time the fix is specified, and that value is used as the target. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. This fix writes the currently used reference RG (:math:`R_{G0}`) to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. This fix computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar is the reference radius of gyration :math:`R_{G0}` used by the fix. energy change due to this fix. The scalar value calculated by this fix is "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. Loading
doc/src/fix_temp_rescale.rst +7 −2 Original line number Diff line number Diff line Loading @@ -126,7 +126,11 @@ thermal degrees of freedom, and the bias is added back in. **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files <restart>`. This fix writes the cumulative global energy change to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion. The :doc:`fix_modify <fix_modify>` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute <compute>` Loading @@ -136,7 +140,8 @@ this fix and by the compute should be the same. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This fix computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar is the cumulative Loading
src/fix_spring_chunk.cpp +54 −0 Original line number Diff line number Diff line Loading @@ -15,6 +15,7 @@ #include <cmath> #include <cstring> #include "atom.h" #include "comm.h" #include "update.h" #include "force.h" #include "respa.h" Loading @@ -37,6 +38,7 @@ FixSpringChunk::FixSpringChunk(LAMMPS *lmp, int narg, char **arg) : { if (narg != 6) error->all(FLERR,"Illegal fix spring/chunk command"); restart_global = 1; scalar_flag = 1; global_freq = 1; extscalar = 1; Loading Loading @@ -241,6 +243,58 @@ void FixSpringChunk::min_post_force(int vflag) post_force(vflag); } /* ---------------------------------------------------------------------- writ number of chunks and position of original COM into restart ------------------------------------------------------------------------- */ void FixSpringChunk::write_restart(FILE *fp) { double n = nchunk; if (comm->me == 0) { int size = (3*n+1) * sizeof(double); fwrite(&size,sizeof(int),1,fp); fwrite(&n,sizeof(double),1,fp); fwrite(&com0[0][0],3*sizeof(double),nchunk,fp); } } /* ---------------------------------------------------------------------- use state info from restart file to restart the Fix ------------------------------------------------------------------------- */ void FixSpringChunk::restart(char *buf) { double *list = (double *) buf; int n = list[0]; memory->destroy(com0); memory->destroy(fcom); int icompute = modify->find_compute(idchunk); if (icompute < 0) error->all(FLERR,"Chunk/atom compute does not exist for fix spring/chunk"); cchunk = (ComputeChunkAtom *) modify->compute[icompute]; if (strcmp(cchunk->style,"chunk/atom") != 0) error->all(FLERR,"Fix spring/chunk does not use chunk/atom compute"); nchunk = cchunk->setup_chunks(); cchunk->compute_ichunk(); memory->create(com0,nchunk,3,"spring/chunk:com0"); memory->create(fcom,nchunk,3,"spring/chunk:fcom"); printf("restart chunks:%d computed chunks: %d\n",n,nchunk); if (n != nchunk) { if (comm->me == 0) error->warning(FLERR,"Number of chunks has changed. Cannot use restart"); memory->destroy(com0); memory->destroy(fcom); nchunk = 1; } else { cchunk->lock(this,update->ntimestep,-1); memcpy(&com0[0][0],list+1,3*n*sizeof(double)); } } /* ---------------------------------------------------------------------- energy of stretched spring ------------------------------------------------------------------------- */ Loading
src/fix_spring_chunk.h +2 −0 Original line number Diff line number Diff line Loading @@ -35,6 +35,8 @@ class FixSpringChunk : public Fix { void post_force(int); void post_force_respa(int, int, int); void min_post_force(int); void write_restart(FILE *); void restart(char *); double compute_scalar(); private: Loading
