From 5f580b66d71f91d2b4a398bae75eb1d34e46c8ac Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Feb 2012 15:18:58 +0000 Subject: [PATCH 01/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7701 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/finish.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/finish.cpp b/src/finish.cpp index 482aa95abc..61a7e13096 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -53,7 +53,7 @@ void Finish::end(int flag) // recompute natoms in case atoms have been lost bigint nblocal = atom->nlocal; - MPI_Allreduce(&nblocal,&atom->nlocal,1,MPI_LMP_BIGINT,MPI_SUM,world); + MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); // choose flavors of statistical output // flag determines caller From c81b8c5d042d4556096da5c76c6596c2698402eb Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Feb 2012 16:58:46 +0000 Subject: [PATCH 02/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7702 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/change_box.cpp | 441 ++++++++++++++++++++++++++++++++++++++++--- src/change_box.h | 61 +++++- src/displace_box.cpp | 418 ---------------------------------------- src/displace_box.h | 105 ----------- src/domain.cpp | 31 ++- src/domain.h | 3 +- src/input.cpp | 2 +- src/pair_hybrid.cpp | 2 +- src/read_restart.cpp | 6 +- 9 files changed, 503 insertions(+), 566 deletions(-) delete mode 100644 src/displace_box.cpp delete mode 100644 src/displace_box.h diff --git a/src/change_box.cpp b/src/change_box.cpp index 34f2f67b0b..be83182742 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -11,17 +11,28 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" +#include "mpi.h" +#include "math.h" +#include "stdlib.h" #include "string.h" #include "change_box.h" -#include "domain.h" +#include "atom.h" #include "modify.h" #include "fix.h" +#include "domain.h" +#include "lattice.h" +#include "comm.h" +#include "irregular.h" #include "output.h" +#include "group.h" #include "error.h" using namespace LAMMPS_NS; -enum{ORTHO,TRICLINIC}; +enum{XYZ,TILT,BOUNDARY,ORTHO,TRICLINIC,SET,REMAP}; +enum{FINAL,DELTA,SCALE}; +enum{X,Y,Z,YZ,XZ,XY}; /* ---------------------------------------------------------------------- */ @@ -31,34 +42,414 @@ ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {} void ChangeBox::command(int narg, char **arg) { + int i; + if (domain->box_exist == 0) error->all(FLERR,"Change_box command before simulation box is defined"); - if (narg != 1) error->all(FLERR,"Illegal change_box command"); + if (narg < 2) error->all(FLERR,"Illegal change_box command"); + if (modify->nfix_restart_peratom) + error->all(FLERR,"Cannot change_box after " + "reading restart file with per-atom info"); - int style; - if (strcmp(arg[0],"ortho") == 0) style = ORTHO; - else if (strcmp(arg[0],"triclinic") == 0) style = TRICLINIC; - else error->all(FLERR,"Illegal change_box command"); + if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n"); - if (style == ORTHO && domain->triclinic == 0) - error->all(FLERR,"Change_box operation is invalid"); - if (style == TRICLINIC && domain->triclinic == 1) - error->all(FLERR,"Change_box operation is invalid"); - if (style == ORTHO && - (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0)) - error->all(FLERR,"Cannot change box to orthogonal when tilt is non-zero"); + // group - if (output->ndump) - error->all(FLERR,"Cannot change box with dumps defined"); - for (int i = 0; i < modify->nfix; i++) - if (modify->fix[i]->no_change_box) - error->all(FLERR,"Cannot change box with certain fixes defined"); + int igroup = group->find(arg[0]); + if (igroup == -1) error->all(FLERR,"Could not find change_box group ID"); + int groupbit = group->bitmask[igroup]; - if (style == ORTHO) domain->triclinic = 0; - else domain->triclinic = 1; - domain->xy = domain->yz = domain->xz = 0.0; + // parse operation arguments + // allocate ops to max possible length + // volume option does not increment nops - domain->set_global_box(); - if (style == TRICLINIC) domain->set_lamda_box(); - domain->set_local_box(); + int dimension = domain->dimension; + + ops = new Operation[narg-1]; + nops = 0; + + int index; + int iarg = 1; + while (iarg < narg) { + if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 || + strcmp(arg[iarg],"z") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = XYZ; + if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X; + else if (strcmp(arg[iarg],"y") == 0) ops[nops].dim = Y; + else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z; + + if (dimension == 2 && ops[nops].dim == Z) + error->all(FLERR,"Cannot change_box in z dimension for 2d simulation"); + + if (strcmp(arg[iarg+1],"final") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].flavor = FINAL; + ops[nops].flo = atof(arg[iarg+2]); + ops[nops].fhi = atof(arg[iarg+3]); + ops[nops].vdim1 = ops[nops].vdim2 = -1; + nops++; + iarg += 4; + } else if (strcmp(arg[iarg+1],"delta") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].flavor = DELTA; + ops[nops].dlo = atof(arg[iarg+2]); + ops[nops].dhi = atof(arg[iarg+3]); + ops[nops].vdim1 = ops[nops].vdim2 = -1; + nops++; + iarg += 4; + } else if (strcmp(arg[iarg+1],"scale") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].flavor = SCALE; + ops[nops].scale = atof(arg[iarg+2]); + ops[nops].vdim1 = ops[nops].vdim2 = -1; + nops++; + iarg += 3; + } else if (strcmp(arg[iarg+1],"volume") == 0) { + if (nops == 0 || ops[nops-1].style != XYZ || + ops[nops].dim == ops[nops-1].dim) + error->all(FLERR,"Change_box volume used incorrectly"); + if (ops[nops-1].vdim2 >= 0) + error->all(FLERR,"Change_box volume used incorrectly"); + else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim; + else ops[nops-1].vdim1 = ops[nops].dim; + iarg += 2; + + } else error->all(FLERR,"Illegal change_box command"); + + } else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 || + strcmp(arg[iarg],"yz") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = TILT; + if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY; + else if (strcmp(arg[iarg],"xz") == 0) ops[nops].dim = XZ; + else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ; + + if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ)) + error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation"); + + if (strcmp(arg[iarg+1],"final") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].flavor = FINAL; + ops[nops].ftilt = atof(arg[iarg+2]); + nops++; + iarg += 3; + } else if (strcmp(arg[iarg+1],"delta") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].flavor = DELTA; + ops[nops].dtilt = atof(arg[iarg+2]); + nops++; + iarg += 3; + } else error->all(FLERR,"Illegal change_box command"); + + } else if (strcmp(arg[iarg],"boundary") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = BOUNDARY; + ops[nops].boundindex = iarg+1; + nops++; + iarg += 4; + + } else if (strcmp(arg[iarg],"ortho") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = ORTHO; + nops++; + iarg += 1; + + } else if (strcmp(arg[iarg],"triclinic") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = TRICLINIC; + nops++; + iarg += 1; + + } else if (strcmp(arg[iarg],"set") == 0) { + if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = SET; + nops++; + iarg += 1; + + } else if (strcmp(arg[iarg],"remap") == 0) { + if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command"); + ops[nops].style = REMAP; + nops++; + iarg += 1; + + } else break; + } + + if (nops == 0) error->all(FLERR,"Illegal change_box command"); + + // read options from end of input line + + options(narg-iarg,&arg[iarg]); + + // compute scale factors if FINAL,DELTA used since they have distance units + + int flag = 0; + for (int i = 0; i < nops; i++) + if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1; + + if (flag && scaleflag && domain->lattice == NULL) + error->all(FLERR,"Use of change_box with undefined lattice"); + + if (flag && scaleflag) { + scale[0] = domain->lattice->xlattice; + scale[1] = domain->lattice->ylattice; + scale[2] = domain->lattice->zlattice; + } + else scale[0] = scale[1] = scale[2] = 1.0; + + // perform sequence of operations + // first insure atoms are in current box & update box via shrink-wrap + // then save current box state so can remap atoms from it + + domain->pbc(); + domain->reset_box(); + save_box_state(); + + for (int i = 0; i < nops; i++) { + if (ops[i].style == XYZ) { + double volume; + if (domain->dimension == 2) volume = domain->xprd * domain->yprd; + else volume = domain->xprd * domain->yprd * domain->zprd; + + if (ops[i].flavor == FINAL) { + domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo; + domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi; + if (ops[i].vdim1) + volume_preserve(ops[i].vdim1,ops[i].vdim2,volume); + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + + } else if (ops[i].flavor == DELTA) { + domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo; + domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi; + if (ops[i].vdim1) + volume_preserve(ops[i].vdim1,ops[i].vdim2,volume); + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + + } else if (ops[i].flavor == SCALE) { + double mid = 0.5 * + (domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]); + double delta = domain->boxlo[ops[i].dim] - mid; + domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta; + delta = domain->boxhi[ops[i].dim] - mid; + domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta; + if (ops[i].vdim1) + volume_preserve(ops[i].vdim1,ops[i].vdim2,volume); + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + } + + } else if (ops[i].style == TILT) { + if (domain->triclinic == 0) + error->all(FLERR,"Cannot change box tilt factors for orthogonal box"); + + if (ops[i].flavor == FINAL) { + if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt; + else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt; + else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt; + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + + } else if (ops[i].flavor == DELTA) { + if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt; + else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt; + else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt; + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + } + + } else if (ops[i].style == BOUNDARY) { + domain->set_boundary(3,&arg[ops[i].boundindex],1); + if (domain->dimension == 2 && domain->zperiodic == 0) + error->all(FLERR, + "Cannot run 2d simulation with nonperiodic Z dimension"); + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + + } else if (ops[i].style == ORTHO) { + if (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0) + error->all(FLERR, + "Cannot change box to orthogonal when tilt is non-zero"); + if (output->ndump) + error->all(FLERR, + "Cannot change box ortho/triclinic with dumps defined"); + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->no_change_box) + error->all(FLERR, + "Cannot change box ortho/triclinic with " + "certain fixes defined"); + domain->triclinic = 0; + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + + } else if (ops[i].style == TRICLINIC) { + if (output->ndump) + error->all(FLERR, + "Cannot change box ortho/triclinic with dumps defined"); + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->no_change_box) + error->all(FLERR, + "Cannot change box ortho/triclinic with " + "certain fixes defined"); + domain->triclinic = 1; + domain->set_lamda_box(); + domain->set_initial_box(); + domain->set_global_box(); + domain->set_local_box(); + domain->print_box(" "); + + } else if (ops[i].style == SET) { + save_box_state(); + + } else if (ops[i].style == REMAP) { + + // convert atoms to lamda coords, using last box state + // convert atoms back to box coords, using current box state + // save current box state + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + domain->x2lamda(x[i],x[i],boxlo,h_inv); + + for (i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + domain->lamda2x(x[i],x[i]); + + save_box_state(); + } + } + + // clean up + + delete [] ops; + + // apply shrink-wrap boundary conditions + + if (domain->nonperiodic == 2) domain->reset_box(); + + // move atoms back inside simulation box and to new processors + // use remap() instead of pbc() + // in case box moved a long distance relative to atoms + // use irregular() in case box moved a long distance relative to atoms + + double **x = atom->x; + int *image = atom->image; + int nlocal = atom->nlocal; + for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); + + if (domain->triclinic) domain->x2lamda(atom->nlocal); + domain->reset_box(); + Irregular *irregular = new Irregular(lmp); + irregular->migrate_atoms(); + delete irregular; + if (domain->triclinic) domain->lamda2x(atom->nlocal); + + // check if any atoms were lost + + domain->print_box(" "); + + bigint natoms; + bigint nblocal = atom->nlocal; + MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); + if (natoms != atom->natoms) { + char str[128]; + sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT + " current " BIGINT_FORMAT,atom->natoms,natoms); + error->warning(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- + parse optional parameters +------------------------------------------------------------------------- */ + +void ChangeBox::options(int narg, char **arg) +{ + if (narg < 0) error->all(FLERR,"Illegal change_box command"); + + scaleflag = 1; + + int iarg = 0; + while (iarg < narg) { + if (strcmp(arg[iarg],"units") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command"); + if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; + else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; + else error->all(FLERR,"Illegal change_box command"); + iarg += 2; + } else error->all(FLERR,"Illegal change_box command"); + } +} + +/* ---------------------------------------------------------------------- + save current box state for converting atoms to lamda coords +------------------------------------------------------------------------- */ + +void ChangeBox::save_box_state() +{ + boxlo[0] = domain->boxlo[0]; + boxlo[1] = domain->boxlo[1]; + boxlo[2] = domain->boxlo[2]; + + for (int i = 0; i < 6; i++) + h_inv[i] = domain->h_inv[i]; +} + +/* ---------------------------------------------------------------------- + reset box lengths of dim1/2 to preserve old volume + which changed due to change in 3rd dim +------------------------------------------------------------------------- */ + +void ChangeBox::volume_preserve(int dim1, int dim2, double oldvol) +{ + double newvol; + if (domain->dimension == 2) newvol = domain->xprd * domain->yprd; + else newvol = domain->xprd * domain->yprd * domain->zprd; + + double scale = oldvol/newvol; + double mid,delta; + + // change dim1 only + + if (dim2 < 0) { + mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]); + delta = domain->boxlo[dim1] - mid; + domain->boxlo[dim1] = mid + scale*delta; + delta = domain->boxhi[dim1] - mid; + domain->boxhi[dim1] = mid + scale*delta; + + // change dim1 and dim2, keeping their relative aspect constant + // means both are scaled by sqrt(scale) + + } else { + mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]); + delta = domain->boxlo[dim1] - mid; + domain->boxlo[dim1] = mid + sqrt(scale)*delta; + delta = domain->boxhi[dim1] - mid; + domain->boxhi[dim1] = mid + sqrt(scale)*delta; + mid = 0.5 * (domain->boxlo[dim2] + domain->boxhi[dim2]); + delta = domain->boxlo[dim2] - mid; + domain->boxlo[dim2] = mid + sqrt(scale)*delta; + delta = domain->boxhi[dim2] - mid; + domain->boxhi[dim2] = mid + sqrt(scale)*delta; + } } diff --git a/src/change_box.h b/src/change_box.h index 9399dcad8e..9b2eac97ae 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -28,6 +28,28 @@ class ChangeBox : protected Pointers { public: ChangeBox(class LAMMPS *); void command(int, char **); + + private: + int scaleflag; + double scale[3]; + + struct Operation { + int style,flavor; + int dim,boundindex; + int vdim1,vdim2; + double flo,fhi,ftilt; + double dlo,dhi,dtilt; + double scale; + }; + + Operation *ops; + int nops; + + double boxlo[3],h_inv[6]; + + void options(int, char **); + void save_box_state(); + void volume_preserve(int, int, double); }; } @@ -37,7 +59,7 @@ class ChangeBox : protected Pointers { /* ERROR/WARNING messages: -E: Change_box command before simulation box is defined +E: Displace_box command before simulation box is defined Self-explanatory. @@ -47,22 +69,41 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. -E: Change_box operation is invalid +E: Cannot displace_box after reading restart file with per-atom info -Cannot change orthogonal box to orthogonal or a triclinic box to -triclinic. +This is because the restart file info cannot be migrated with the +atoms. You can get around this by performing a 0-timestep run which +will assign the restart file info to actual atoms. -E: Cannot change box to orthogonal when tilt is non-zero +E: Could not find displace_box group ID -Self-explanatory +Group ID used in the displace_box command does not exist. -E: Cannot change box with dumps defined +E: Displace_box tilt factors require triclinic box + +Cannot use tilt factors unless the simulation box is +non-orthogonal. + +E: Cannot displace_box on a non-periodic boundary Self-explanatory. -E: Cannot change box with certain fixes defined +E: Use of displace_box with undefined lattice -The change_box command cannot be used when fix ave/spatial or -fix/deform are defined . +Must use lattice command with displace_box command if units option is +set to lattice. + +E: Fix deform volume setting is invalid + +Cannot use volume style unless other dimensions are being controlled. + +E: Induced tilt by displace_box is too large + +The final tilt value must be between -1/2 and 1/2 of the perpendicular +box length. + +E: Lost atoms via displace_box: original %ld current %ld + +UNDOCUMENTED */ diff --git a/src/displace_box.cpp b/src/displace_box.cpp deleted file mode 100644 index 79f8865788..0000000000 --- a/src/displace_box.cpp +++ /dev/null @@ -1,418 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "lmptype.h" -#include "mpi.h" -#include "math.h" -#include "stdlib.h" -#include "string.h" -#include "displace_box.h" -#include "atom.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "comm.h" -#include "irregular.h" -#include "group.h" -#include "error.h" - -using namespace LAMMPS_NS; - -enum{NONE,FINAL,DELTA,SCALE,VOLUME}; -enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE}; -enum{NO_REMAP,X_REMAP}; - -/* ---------------------------------------------------------------------- */ - -DisplaceBox::DisplaceBox(LAMMPS *lmp) : Pointers(lmp) {} - -/* ---------------------------------------------------------------------- */ - -void DisplaceBox::command(int narg, char **arg) -{ - int i; - - if (domain->box_exist == 0) - error->all(FLERR,"Displace_box command before simulation box is defined"); - if (narg < 2) error->all(FLERR,"Illegal displace_box command"); - if (modify->nfix_restart_peratom) - error->all(FLERR,"Cannot displace_box after " - "reading restart file with per-atom info"); - - if (comm->me == 0 && screen) fprintf(screen,"Displacing box ...\n"); - - // group - - int igroup = group->find(arg[0]); - if (igroup == -1) error->all(FLERR,"Could not find displace_box group ID"); - int groupbit = group->bitmask[igroup]; - - // set defaults - - set = new Set[6]; - set[0].style = set[1].style = set[2].style = - set[3].style = set[4].style = set[5].style = NONE; - - // parse arguments - - int triclinic = domain->triclinic; - - int index; - int iarg = 1; - while (iarg < narg) { - if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 || - strcmp(arg[iarg],"z") == 0) { - if (strcmp(arg[iarg],"x") == 0) index = 0; - else if (strcmp(arg[iarg],"y") == 0) index = 1; - else if (strcmp(arg[iarg],"z") == 0) index = 2; - - if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command"); - if (strcmp(arg[iarg+1],"final") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal displace_box command"); - set[index].style = FINAL; - set[index].flo = atof(arg[iarg+2]); - set[index].fhi = atof(arg[iarg+3]); - iarg += 4; - } else if (strcmp(arg[iarg+1],"delta") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal displace_box command"); - set[index].style = DELTA; - set[index].dlo = atof(arg[iarg+2]); - set[index].dhi = atof(arg[iarg+3]); - iarg += 4; - } else if (strcmp(arg[iarg+1],"scale") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command"); - set[index].style = SCALE; - set[index].scale = atof(arg[iarg+2]); - iarg += 3; - } else if (strcmp(arg[iarg+1],"volume") == 0) { - set[index].style = VOLUME; - iarg += 2; - } else error->all(FLERR,"Illegal displace_box command"); - - } else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 || - strcmp(arg[iarg],"yz") == 0) { - if (triclinic == 0) - error->all(FLERR,"Displace_box tilt factors require triclinic box"); - if (strcmp(arg[iarg],"xy") == 0) index = 5; - else if (strcmp(arg[iarg],"xz") == 0) index = 4; - else if (strcmp(arg[iarg],"yz") == 0) index = 3; - if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command"); - if (strcmp(arg[iarg+1],"final") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command"); - set[index].style = FINAL; - set[index].ftilt = atof(arg[iarg+2]); - iarg += 3; - } else if (strcmp(arg[iarg+1],"delta") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command"); - set[index].style = DELTA; - set[index].dtilt = atof(arg[iarg+2]); - iarg += 3; - } else error->all(FLERR,"Illegal displace_box command"); - - } else break; - } - - // read options from end of input line - - options(narg-iarg,&arg[iarg]); - - // check periodicity - - if ((set[0].style && domain->xperiodic == 0) || - (set[1].style && domain->yperiodic == 0) || - (set[2].style && domain->zperiodic == 0)) - error->all(FLERR,"Cannot displace_box on a non-periodic boundary"); - - if (set[3].style && (domain->yperiodic == 0 || domain->zperiodic == 0)) - error->all(FLERR,"Cannot displace_box on a non-periodic boundary"); - if (set[4].style && (domain->xperiodic == 0 || domain->zperiodic == 0)) - error->all(FLERR,"Cannot displace_box on a non-periodic boundary"); - if (set[5].style && (domain->xperiodic == 0 || domain->yperiodic == 0)) - error->all(FLERR,"Cannot displace_box on a non-periodic boundary"); - - // apply scaling to FINAL,DELTA since they have distance units - - int flag = 0; - for (int i = 0; i < 6; i++) - if (set[i].style == FINAL || set[i].style == DELTA) flag = 1; - - if (flag && scaleflag && domain->lattice == NULL) - error->all(FLERR,"Use of displace_box with undefined lattice"); - - double xscale,yscale,zscale; - if (flag && scaleflag) { - xscale = domain->lattice->xlattice; - yscale = domain->lattice->ylattice; - zscale = domain->lattice->zlattice; - } - else xscale = yscale = zscale = 1.0; - - // for 3,4,5 scaling is in 1st dimension, e.g. x for xz - - double map[6]; - map[0] = xscale; map[1] = yscale; map[2] = zscale; - map[3] = yscale; map[4] = xscale; map[5] = xscale; - - for (int i = 0; i < 3; i++) { - if (set[i].style == FINAL) { - set[i].flo *= map[i]; - set[i].fhi *= map[i]; - } else if (set[i].style == DELTA) { - set[i].dlo *= map[i]; - set[i].dhi *= map[i]; - } - } - - for (int i = 3; i < 6; i++) { - if (set[i].style == FINAL) set[i].ftilt *= map[i]; - else if (set[i].style == DELTA) set[i].dtilt *= map[i]; - } - - // set initial/final values for box size and shape - // final = initial if no setting - - for (int i = 0; i < 3; i++) { - set[i].lo_stop = set[i].lo_start = domain->boxlo[i]; - set[i].hi_stop = set[i].hi_start = domain->boxhi[i]; - - if (set[i].style == FINAL) { - set[i].lo_stop = set[i].flo; - set[i].hi_stop = set[i].fhi; - } else if (set[i].style == DELTA) { - set[i].lo_stop = set[i].lo_start + set[i].dlo; - set[i].hi_stop = set[i].hi_start + set[i].dhi; - } else if (set[i].style == SCALE) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start); - } - } - - for (int i = 3; i < 6; i++) { - if (i == 5) set[i].tilt_start = domain->xy; - else if (i == 4) set[i].tilt_start = domain->xz; - else if (i == 3) set[i].tilt_start = domain->yz; - set[i].tilt_stop = set[i].tilt_start; - - if (set[i].style == FINAL) { - set[i].tilt_stop = set[i].ftilt; - } else if (set[i].style == DELTA) { - set[i].tilt_stop = set[i].tilt_start + set[i].dtilt; - } - } - - // for VOLUME, setup links to other dims - // fixed, dynamic1,2, vol_start - - for (int i = 0; i < 3; i++) { - set[i].vol_start = domain->xprd * domain->yprd * domain->zprd; - - if (set[i].style != VOLUME) continue; - int other1 = (i+1) % 3; - int other2 = (i+2) % 3; - - if (set[other1].style == NONE) { - if (set[other2].style == NONE || set[other2].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); - set[i].substyle = ONE_FROM_ONE; - set[i].fixed = other1; - set[i].dynamic1 = other2; - } else if (set[other2].style == NONE) { - if (set[other1].style == NONE || set[other1].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); - set[i].substyle = ONE_FROM_ONE; - set[i].fixed = other2; - set[i].dynamic1 = other1; - } else if (set[other1].style == VOLUME) { - if (set[other2].style == NONE || set[other2].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); - set[i].substyle = TWO_FROM_ONE; - set[i].fixed = other1; - set[i].dynamic1 = other2; - } else if (set[other2].style == VOLUME) { - if (set[other1].style == NONE || set[other1].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); - set[i].substyle = TWO_FROM_ONE; - set[i].fixed = other2; - set[i].dynamic1 = other1; - } else { - set[i].substyle = ONE_FROM_TWO; - set[i].dynamic2 = other1; - set[i].dynamic2 = other2; - } - } - - // set new box size for VOLUME dims that are linked to other dims - - for (int i = 0; i < 3; i++) { - if (set[i].style != VOLUME) continue; - - if (set[i].substyle == ONE_FROM_ONE) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); - - } else if (set[i].substyle == ONE_FROM_TWO) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].dynamic2].hi_stop - - set[set[i].dynamic2].lo_stop)); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].dynamic2].hi_stop - - set[set[i].dynamic2].lo_stop)); - - } else if (set[i].substyle == TWO_FROM_ONE) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*sqrt(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].fixed].hi_start - - set[set[i].fixed].lo_start) * - (set[i].hi_start - set[i].lo_start)); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*sqrt(set[i].vol_start / - (set[set[i].dynamic1].hi_stop - - set[set[i].dynamic1].lo_stop) / - (set[set[i].fixed].hi_start - - set[set[i].fixed].lo_start) * - (set[i].hi_start - set[i].lo_start)); - } - } - - // check that final tilt is not illegal value - - double xprd_stop = set[0].hi_stop - set[0].lo_stop; - double yprd_stop = set[0].hi_stop - set[0].lo_stop; - - if (set[3].tilt_stop < -0.5*yprd_stop || set[3].tilt_stop > 0.5*yprd_stop || - set[4].tilt_stop < -0.5*xprd_stop || set[4].tilt_stop > 0.5*xprd_stop || - set[5].tilt_stop < -0.5*xprd_stop || set[5].tilt_stop > 0.5*xprd_stop) - error->all(FLERR,"Induced tilt by displace_box is too large"); - - // convert atoms to lamda coords - - if (remapflag == X_REMAP) { - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - domain->x2lamda(x[i],x[i]); - } - - // reset global and local box to new size/shape - - domain->boxlo[0] = set[0].lo_stop; - domain->boxlo[1] = set[1].lo_stop; - domain->boxlo[2] = set[2].lo_stop; - domain->boxhi[0] = set[0].hi_stop; - domain->boxhi[1] = set[1].hi_stop; - domain->boxhi[2] = set[2].hi_stop; - - if (triclinic) { - domain->yz = set[3].tilt_stop; - domain->xz = set[4].tilt_stop; - domain->xy = set[5].tilt_stop; - } - - domain->set_global_box(); - domain->set_local_box(); - - // convert atoms back to box coords - - if (remapflag == X_REMAP) { - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - domain->lamda2x(x[i],x[i]); - } - - // move atoms back inside simulation box and to new processors - // use remap() instead of pbc() - // in case box moved a long distance relative to atoms - // use irregular() in case box moved a long distance relative to atoms - - double **x = atom->x; - int *image = atom->image; - int nlocal = atom->nlocal; - for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); - - if (domain->triclinic) domain->x2lamda(atom->nlocal); - domain->reset_box(); - Irregular *irregular = new Irregular(lmp); - irregular->migrate_atoms(); - delete irregular; - if (domain->triclinic) domain->lamda2x(atom->nlocal); - - // clean up - - delete [] set; - - // check if any atoms were lost - - bigint natoms; - bigint nblocal = atom->nlocal; - MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); - if (natoms != atom->natoms) { - char str[128]; - sprintf(str,"Lost atoms via displace_box: original " BIGINT_FORMAT - " current " BIGINT_FORMAT,atom->natoms,natoms); - error->all(FLERR,str); - } -} - -/* ---------------------------------------------------------------------- - parse optional parameters at end of displace_box input line -------------------------------------------------------------------------- */ - -void DisplaceBox::options(int narg, char **arg) -{ - if (narg < 0) error->all(FLERR,"Illegal displace_box command"); - - remapflag = X_REMAP; - scaleflag = 1; - - int iarg = 0; - while (iarg < narg) { - if (strcmp(arg[iarg],"remap") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command"); - if (strcmp(arg[iarg+1],"x") == 0) remapflag = X_REMAP; - else if (strcmp(arg[iarg+1],"none") == 0) remapflag = NO_REMAP; - else error->all(FLERR,"Illegal displace_box command"); - iarg += 2; - } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command"); - if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; - else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; - else error->all(FLERR,"Illegal displace_box command"); - iarg += 2; - } else error->all(FLERR,"Illegal displace_box command"); - } -} diff --git a/src/displace_box.h b/src/displace_box.h deleted file mode 100644 index 44df201c36..0000000000 --- a/src/displace_box.h +++ /dev/null @@ -1,105 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef COMMAND_CLASS - -CommandStyle(displace_box,DisplaceBox) - -#else - -#ifndef LMP_DISPLACE_BOX_H -#define LMP_DISPLACE_BOX_H - -#include "pointers.h" - -namespace LAMMPS_NS { - -class DisplaceBox : protected Pointers { - public: - DisplaceBox(class LAMMPS *); - void command(int, char **); - - private: - int remapflag,scaleflag; - - struct Set { - int style,substyle; - double flo,fhi,ftilt; - double dlo,dhi,dtilt; - double scale; - double lo_start,hi_start; - double lo_stop,hi_stop; - double tilt_start,tilt_stop; - double vol_start; - int fixed,dynamic1,dynamic2; - }; - Set *set; - - void options(int, char **); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Displace_box command before simulation box is defined - -Self-explanatory. - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Cannot displace_box after reading restart file with per-atom info - -This is because the restart file info cannot be migrated with the -atoms. You can get around this by performing a 0-timestep run which -will assign the restart file info to actual atoms. - -E: Could not find displace_box group ID - -Group ID used in the displace_box command does not exist. - -E: Displace_box tilt factors require triclinic box - -Cannot use tilt factors unless the simulation box is -non-orthogonal. - -E: Cannot displace_box on a non-periodic boundary - -Self-explanatory. - -E: Use of displace_box with undefined lattice - -Must use lattice command with displace_box command if units option is -set to lattice. - -E: Fix deform volume setting is invalid - -Cannot use volume style unless other dimensions are being controlled. - -E: Induced tilt by displace_box is too large - -The final tilt value must be between -1/2 and 1/2 of the perpendicular -box length. - -E: Lost atoms via displace_box: original %ld current %ld - -UNDOCUMENTED - -*/ diff --git a/src/domain.cpp b/src/domain.cpp index c729ac16bb..a83f958f6a 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1109,10 +1109,12 @@ int Domain::find_region(char *name) } /* ---------------------------------------------------------------------- - boundary settings from the input script + (re)set boundary settings + flag = 0, called from the input script + flag = 1, called from change box command ------------------------------------------------------------------------- */ -void Domain::set_boundary(int narg, char **arg) +void Domain::set_boundary(int narg, char **arg, int flag) { if (narg != 3) error->all(FLERR,"Illegal boundary command"); @@ -1127,7 +1129,10 @@ void Domain::set_boundary(int narg, char **arg) else if (c == 'f') boundary[idim][iside] = 1; else if (c == 's') boundary[idim][iside] = 2; else if (c == 'm') boundary[idim][iside] = 3; - else error->all(FLERR,"Illegal boundary command"); + else { + if (flag == 0) error->all(FLERR,"Illegal boundary command"); + if (flag == 1) error->all(FLERR,"Illegal change_box command"); + } } for (int idim = 0; idim < 3; idim++) @@ -1257,6 +1262,26 @@ void Domain::x2lamda(double *x, double *lamda) lamda[2] = h_inv[2]*delta[2]; } +/* ---------------------------------------------------------------------- + convert box coords to triclinic 0-1 lamda coords for one atom + use my_boxlo & my_h_inv stored by caller for previous state of box + lamda = H^-1 (x - x0) + x and lamda can point to same 3-vector +------------------------------------------------------------------------- */ + +void Domain::x2lamda(double *x, double *lamda, + double *my_boxlo, double *my_h_inv) +{ + double delta[3]; + delta[0] = x[0] - my_boxlo[0]; + delta[1] = x[1] - my_boxlo[1]; + delta[2] = x[2] - my_boxlo[2]; + + lamda[0] = my_h_inv[0]*delta[0] + my_h_inv[5]*delta[1] + my_h_inv[4]*delta[2]; + lamda[1] = my_h_inv[1]*delta[1] + my_h_inv[3]*delta[2]; + lamda[2] = my_h_inv[2]*delta[2]; +} + /* ---------------------------------------------------------------------- convert 8 lamda corner pts of lo/hi box to box coords return bboxlo/hi = bounding box around 8 corner pts in box coords diff --git a/src/domain.h b/src/domain.h index 0496783c1f..d21119cffb 100644 --- a/src/domain.h +++ b/src/domain.h @@ -107,13 +107,14 @@ class Domain : protected Pointers { void add_region(int, char **); void delete_region(int, char **); int find_region(char *); - void set_boundary(int, char **); + void set_boundary(int, char **, int); void print_box(const char *); virtual void lamda2x(int); virtual void x2lamda(int); void lamda2x(double *, double *); void x2lamda(double *, double *); + void x2lamda(double *, double *, double *, double *); void bbox(double *, double *, double *, double *); void box_corners(); diff --git a/src/input.cpp b/src/input.cpp index 865975c68c..9c1905168e 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -930,7 +930,7 @@ void Input::boundary() { if (domain->box_exist) error->all(FLERR,"Boundary command after simulation box is defined"); - domain->set_boundary(narg,arg); + domain->set_boundary(narg,arg,0); } /* ---------------------------------------------------------------------- */ diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 2ffd9c096e..73dd0709d5 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -16,6 +16,7 @@ #include "string.h" #include "ctype.h" #include "pair_hybrid.h" +#include "style_pair.h" #include "atom.h" #include "force.h" #include "pair.h" @@ -763,4 +764,3 @@ double PairHybrid::memory_usage() for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage(); return bytes; } - diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 02e313a8d0..c015449ff4 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -464,7 +464,8 @@ void ReadRestart::header() if (flag == VERSION) { char *version = read_char(); if (strcmp(version,universe->version) != 0 && me == 0) { - error->warning(FLERR,"Restart file version does not match LAMMPS version"); + error->warning(FLERR, + "Restart file version does not match LAMMPS version"); if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n", version,universe->version); } @@ -581,7 +582,8 @@ void ReadRestart::header() boundary[2][0] != domain->boundary[2][0] || boundary[2][1] != domain->boundary[2][1]) { if (me == 0) - error->warning(FLERR,"Restart file used different boundary settings, " + error->warning(FLERR, + "Restart file used different boundary settings, " "using restart file values"); } } From a3c28800f4657db0c78232cd1766e7d4187d8744 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 6 Feb 2012 16:58:56 +0000 Subject: [PATCH 03/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7703 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 24 +-- doc/Section_commands.txt | 3 +- doc/Section_howto.html | 4 +- doc/Section_howto.txt | 4 +- doc/boundary.html | 5 +- doc/boundary.txt | 5 +- doc/change_box.html | 297 ++++++++++++++++++++++++++++++++++---- doc/change_box.txt | 293 +++++++++++++++++++++++++++++++++---- doc/displace_atoms.html | 36 ++--- doc/displace_atoms.txt | 36 ++--- doc/displace_box.html | 191 ------------------------ doc/displace_box.txt | 181 ----------------------- doc/fix_deform.html | 2 +- doc/fix_deform.txt | 2 +- 14 files changed, 597 insertions(+), 486 deletions(-) delete mode 100644 doc/displace_box.html delete mode 100644 doc/displace_box.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 2fa418e8ca..7c1a07a6e7 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -290,7 +290,7 @@ in the command's documentation.

delete_atoms, delete_bonds, displace_atoms, -displace_box, minimize, +change_box, minimize, neb prd, run, temper

Miscellaneous: @@ -317,17 +317,17 @@ in the command's documentation. angle_coeffangle_styleatom_modifyatom_stylebond_coeffbond_style boundarychange_boxclearcommunicatecomputecompute_modify create_atomscreate_boxdelete_atomsdelete_bondsdielectricdihedral_coeff -dihedral_styledimensiondisplace_atomsdisplace_boxdumpdump image -dump_modifyechofixfix_modifygroupif -improper_coeffimproper_styleincludejumpkspace_modifykspace_style -labellatticelogmassminimizemin_modify -min_stylenebneigh_modifyneighbornewtonnext -packagepair_coeffpair_modifypair_stylepair_writepartition -prdprintprocessorsquitread_dataread_restart -regionreplicatereset_timesteprestartrunrun_style -setshellspecial_bondssuffixtadtemper -thermothermo_modifythermo_styletimestepuncomputeundump -unfixunitsvariablevelocitywrite_restart +dihedral_styledimensiondisplace_atomsdumpdump imagedump_modify +echofixfix_modifygroupifimproper_coeff +improper_styleincludejumpkspace_modifykspace_stylelabel +latticelogmassminimizemin_modifymin_style +nebneigh_modifyneighbornewtonnextpackage +pair_coeffpair_modifypair_stylepair_writepartitionprd +printprocessorsquitread_dataread_restartregion +replicatereset_timesteprestartrunrun_styleset +shellspecial_bondssuffixtadtemperthermo +thermo_modifythermo_styletimestepuncomputeundumpunfix +unitsvariablevelocitywrite_restart

diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 773a5ed031..08d67735b0 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -286,7 +286,7 @@ Actions: "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, -"displace_box"_displace_box.html, "minimize"_minimize.html, +"change_box"_change_box.html, "minimize"_minimize.html, "neb"_neb.html "prd"_prd.html, "run"_run.html, "temper"_temper.html Miscellaneous: @@ -330,7 +330,6 @@ in the command's documentation. "dihedral_style"_dihedral_style.html, "dimension"_dimension.html, "displace_atoms"_displace_atoms.html, -"displace_box"_displace_box.html, "dump"_dump.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 221685fea3..041124e229 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1660,8 +1660,8 @@ derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at most 7*6/2 = 21 distinct elements.

At zero temperature, it is easy to estimate these derivatives by -deforming the cell in one of the six directions using the command -displace_box and measuring the change in the +deforming the simulation box in one of the six directions using the +change_box command and measuring the change in the stress tensor. A general-purpose script that does this is given in the examples/elastic directory described in this section. diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index b19befe7f2..1f14a0a51b 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1647,8 +1647,8 @@ derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at most 7*6/2 = 21 distinct elements. At zero temperature, it is easy to estimate these derivatives by -deforming the cell in one of the six directions using the command -"displace_box"_displace_box.html and measuring the change in the +deforming the simulation box in one of the six directions using the +"change_box"_change_box.html command and measuring the change in the stress tensor. A general-purpose script that does this is given in the examples/elastic directory described in "this section"_Section_example.html. diff --git a/doc/boundary.html b/doc/boundary.html index 38544ed2d8..602a3d4f0d 100644 --- a/doc/boundary.html +++ b/doc/boundary.html @@ -77,7 +77,10 @@ triclinic representations.

Restrictions:

This command cannot be used after the simulation box is defined by a -read_data or create_box command. +read_data or create_box command or +read_restart command. See the +change_box command for how to change the simulation +box boundaries after it has been defined.

For 2d simulations, the z dimension must be periodic.

diff --git a/doc/boundary.txt b/doc/boundary.txt index cfdb43ce21..ec559d7f2f 100644 --- a/doc/boundary.txt +++ b/doc/boundary.txt @@ -72,7 +72,10 @@ triclinic representations. [Restrictions:] This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. +"read_data"_read_data.html or "create_box"_create_box.html command or +"read_restart"_read_restart.html command. See the +"change_box"_change_box.html command for how to change the simulation +box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. diff --git a/doc/change_box.html b/doc/change_box.html index e258ec2337..b504671ee9 100644 --- a/doc/change_box.html +++ b/doc/change_box.html @@ -13,51 +13,292 @@

Syntax:

-
change_box style 
+
change_box group-ID parameter args ... keyword args ... 
 

-
  • style = ortho or triclinic 
+
    • group-ID = ID of group of atoms to (optionally) displace 
 
-
        ortho = convert simulation box from non-orthogonal (triclinic) to orthogonal
-  triclinic = convert simulation box from orthogonal to non-orthogonal (triclinic) 
+
    • one or more parameter/arg pairs may be appended 
+
+
      parameter = x or y or z or xy or xz or yz or boundary or ortho or triclinic or set or remap
+  x, y, z args = style value(s)
+    style = final or delta or scale or volume
+      final values = lo hi
+        lo hi = box boundaries after displacement (distance units)
+      delta values = dlo dhi
+        dlo dhi = change in box boundaries after displacement (distance units)
+      scale values = factor
+        factor = multiplicative factor for change in box length after displacement
+      volume value = none = adjust this dim to preserve volume of system
+  xy, xz, yz args = style value
+    style = final or delta
+      final value = tilt
+        tilt = tilt factor after displacement (distance units)
+      delta value = dtilt
+        dtilt = change in tilt factor after displacement (distance units)
+  boundary args = x y z
+    x,y,z = p or s or f or m, one or two letters
+    p is periodic
+    f is non-periodic and fixed
+    s is non-periodic and shrink-wrapped
+    m is non-periodic and shrink-wrapped with a minimum value
+  ortho args = none = change box to orthogonal
+  (triclinic args = none = change box to triclinic
+  set args = none = store state of current box
+  remap args = none = remap atom coords from last saved state to current box 
 
      
+
    • zero or more keyword/value pairs may be appended 
+
+
    • keyword = units 
+
+
        units value = lattice or box
+    lattice = distances are defined in lattice units
+    box = distances are defined in simulation box units 
+
      
+
+
    
 
    Examples:
 
    
-
    change_box ortho
-change_box triclinic 
+
    change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap 
 
    
 
    Description:
 
    
-
    By default LAMMPS runs a simulation in an orthogonal, axis-aligned
-simulation box.  LAMMPS can also run simulations in non-orthogonal
-(triclinic) simulation boxes.  A box is
-defined as either orthogonal or non-orthogonal when it is created via
-the create_box, read_data, or
-read_restart commands.
+
    Change the volume and/or shape and/or boundary conditions for the
+simulation box.  Orthogonal simulation boxes have 3 adjustable size
+parameters (x,y,z).  Triclinic (non-orthogonal) simulation boxes have
+6 adjustable size/shape parameters (x,y,z,xy,xz,yz).  Any or all of
+them can be adjusted independently by this command.  Thus it can be
+used to expand or contract a box, or to apply a shear strain to a
+non-orthogonal box.  It can also be used to change the boundary
+conditions for the simulation box, similar to the
+boundary command.
 
    
-
    This command allows you to toggle the existing simulation box from
-orthogonal to non-orthogonal and vice versa.  For example, an initial
+
    The size and shape of the initial simulation box are specified by the
+create_box or read_data or
+read_restart command used to setup the simulation.
+The size and shape may be altered by subsequent runs, e.g. by use of
+the fix npt or fix deform commands.
+The create_box, read data, and
+read_restart commands also determine whether the
+simulation box is orthogonal or triclinic and their doc pages explain
+the meaning of the xy,xz,yz tilt factors.
+
    
+
    See Section_howto 12 of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+
    
+
    The keywords used in this command are applied sequentially to the
+simulation box and the atoms in it, in the order specified.
+
    
+
    Before the sequence of keywords are invoked, the current box
+size/shape are stored, in case a remap keyword is used to map the
+atom coordinates from the previous box size/shape to the current one.
+
    
+
    After all the keywords have been processed, any shrink-wrap boundary
+conditions are invoked (see the boundary command)
+which may change simulation box boundaries, and atoms are migrated to
+new owning processors.
+
    
+
    IMPORTANT NOTE: It is possible to lose atoms with this command.
+E.g. by changing the box without remapping the atoms, and having atoms
+end up outside of non-periodic boundaries.  It is also possible when
+remapping atoms to put them (nearly) on top of each other which will
+lead to bad dynamics.  E.g. by converting a boundary from non-periodic
+to periodic.
+
    
+
    IMPORTANT NOTE: The simulation box size/shape can be changed by
+arbitrarily large amounts by this command.  This is not a problem,
+except that the mapping of processors to the simulation box is not
+changed from its initial 3d configuration; see the
+processors command.  Thus, if the box size/shape
+changes dramatically, the mapping of processors to the simulation box
+may not end up as optimal as the initial mapping attempted to be.
+
    
+
    
+
+
    For the x, y, and z parameters, this is the meaning of their
+styles and values.
+
    
+
    For style final, the final lo and hi box boundaries of a dimension
+are specified.  The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+
    
+
    For style delta, plus or minus changes in the lo/hi box boundaries
+of a dimension are specified.  The values can be in lattice or box
+distance units.  See the discussion of the units keyword below.
+
    
+
    For style scale, a multiplicative factor to apply to the box length
+of a dimension is specified.  For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11.  A
+factor less than 1.0 means compression.
+
    
+
    The volume style changes the specified dimension in such a way that
+the overall box volume remains constant with respect to the operation
+performed by the preceding keyword.  The volume style can only be
+used following a keyword that changed the volume, which is any of the
+x, y, z keywords.  If the preceding keyword "key" had a volume
+style, then both it and the current keyword apply to the keyword
+preceding "key".  I.e. this sequence of keywords is allowed:
+
    
+
    change_box all x scale 1.1 y volume z volume 
+
    
+
    The volume style changes the associated dimension so that the
+overall box volume is unchanged relative to its value before the
+preceding keyword was invoked. 
+
    
+
    If "x scale 1.1 z volume" is used, then the z box length will
+shrink by the same 1.1 factor the x box length was increased by.
+
    
+
    If "x scale 1.1 y volume z volume" is used, then the y,z box lengths
+will each shrink by sqrt(1.1) to keep the volume constant.  In this
+case, the y,z box lengths shrink so as to keep their relative aspect
+ratio constant.
+
    
+
    If "x scale 1.1 z volume y scale 1.1 z volume" is used, then
+the final box will be a factor of 10% larger in x and y, and a
+factor of 21% smaller in z, so as to keep the volume constant.
+
    
+
    IMPORTANT NOTE: For solids or liquids, when one dimension of the box
+is expanded, it may be physically undesirable to hold the other 2 box
+lengths constant since that implies a density change.  For solids,
+adjusting the other dimensions via the volume style may make
+physical sense (just as for a liquid), but may not be correct for
+materials and potentials whose Poisson ratio is not 0.5.
+
    
+
    For the scale and volume styles, the box length is expanded or
+compressed around its mid point.
+
    
+
    
+
+
    For the xy, xz, and yz parameters, this is the meaning of their
+styles and values.  Note that changing the tilt factors of a triclinic
+box does not change its volume.
+
    
+
    For style final, the final tilt factor is specified.  The value
+can be in lattice or box distance units.  See the discussion of the
+units keyword below.
+
    
+
    For style delta, a plus or minus change in the tilt factor is
+specified.  The value can be in lattice or box distance units.  See
+the discussion of the units keyword below.
+
    
+
    All of these styles change the xy, xz, yz tilt factors.  In LAMMPS,
+tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
+than half the distance of the parallel box length.  For example, if
+xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
+factor must be between -5 and 5.  Similarly, both xz and yz must be
+between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a
+limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent.  Any tilt factor specified by this command
+must be within these limits.
+
    
+
    
+
+
    The boundary keyword takes arguments that have exactly the same
+meaning as they do for the boundary command.  In each
+dimension, a single letter assigns the same style to both the lower
+and upper face of the box.  Two letters assigns the first style to the
+lower face and the second style to the upper face.
+
    
+
    The style p means the box is periodic; the other styles mean
+non-periodic. For style f, the position of the face is fixed.  For
+style s, the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move.  For style m, shrink-wrapping occurs, but is bounded by the
+current box edge in that dimension, so that the box will become no
+smaller.  See the boundary command for more
+explanation of these style options.
+
    
+
    Note that the "boundary" command itself can only be used before the
+simulation box is defined via a read_data or
+create_box or read_restart
+command.  This command allows the boundary conditions to be changed
+later in your input script.  Also note that the
+read_restart will change boundary conditions to
+match what is stored in the restart file.  So if you wish to change
+them, you should use the change_box command after the read_restart
+command.
+
    
+
    
+
+
    The ortho and triclinic keywords convert the simulation box to be
+orthogonal or triclinic (non-orthongonal).  See this
+section for a discussion of how non-orthongal
+boxes are represented in LAMMPS.
+
    
+
    The simulation box is defined as either orthogonal or triclinic when
+it is created via the create_box,
+read_data, or read_restart
+commands.
+
    
+
    These keywords allow you to toggle the existing simulation box from
+orthogonal to triclinic and vice versa.  For example, an initial
 equilibration simulation can be run in an orthogonal box, the box can
-be toggled to non-orthogonal, and then a non-equilibrium MD (NEMD)
+be toggled to triclinic, and then a non-equilibrium MD (NEMD)
 simulation can be run with deformation
 via the fix deform command.
 
    
-
    Note that if the simulation box is currently non-orthogonal and has
-non-zero tilt in xy, yz, or xz, then it cannot be converted to an
-orthogonal box.
+
    If the simulation box is currently triclinic and has non-zero tilt in
+xy, yz, or xz, then it cannot be converted to an orthogonal box.
 
    
+
    
+
+
    The set keyword saves the current box size/shape.  This can be
+useful if you wish to use the remap keyword more than once or if you
+wish it to be applied to an intermediate box size/shape in a sequence
+of keyword operations.  Note that the box size/shape is saved before
+any of the keywords are processed, i.e. the box size/shape at the time
+the create_box command is encountered in the input script.
+
    
+
    The remap keyword remaps atom coordinates from the last saved box
+size/shape to the current box state.  For example, if you stretch the
+box in the x dimension or tilt it in the xy plane via the x and xy
+keywords, then the remap commmand will dilate or tilt the atoms to
+conform to the new box size/shape, as if the atoms moved with the box
+as it deformed.
+
    
+
    Note that this operation is performed without regard to periodic
+boundaries.  Any shrink-wrapping of non-periodic boundaries (see the
+boundary command occurs after all keywords, including
+this one, have been processed.
+
    
+
    Only atoms in the specified group are remapped.
+
    
+
    IMPORTANT NOTE: If you do not explicitly specify the remap keyword,
+atom coordinates will not be changed even though the box size/shape
+changes.  This may be the behavior you desire, but can also cause
+atoms to be lost.
+
    
+
    
+
+
    The units keyword determines the meaning of the distance units used
+to define various arguments.  A box value selects standard distance
+units as defined by the units command, e.g. Angstroms for
+units = real or metal.  A lattice value means the distance units are
+in lattice spacings.  The lattice command must have
+been previously used to define the lattice spacing.
+
    
+
    
+
 
    Restrictions:
 
    
-
    At the point in the input script when this command is issued, no
-dumps can be active, nor can a fix
-ave/spatial or fix deform be
-active.  This is because these commands test whether the simulation
-box is orthogonal when they are first issued.  Note that these
-commands can appear in your script before a change_box command is
-issued, so long as an undump or unfix
-command is also used to turn them off.
+
    If you use the ortho or triclinic keywords, then at the point in
+the input script when this command is issued, no dumps can
+be active, nor can a fix ave/spatial or fix
+deform be active.  This is because these commands
+test whether the simulation box is orthogonal when they are first
+issued.  Note that these commands can be used in your script before a
+change_box command is issued, so long as an undump or
+unfix command is also used to turn them off.
 
    
-
    Related commands: none
+
    Related commands:
 
    
-
    Default: none
+
    fix deform, boundary
+
    
+
    Default:
+
    
+
    The option default is units = lattice.
 
    
 
diff --git a/doc/change_box.txt b/doc/change_box.txt
index 78c2c757d9..1b16b42dce 100644
--- a/doc/change_box.txt
+++ b/doc/change_box.txt
@@ -10,48 +10,285 @@ change_box command :h3
 
 [Syntax:]
 
-change_box style :pre
+change_box group-ID parameter args ... keyword args ... :pre
 
-style = {ortho} or {triclinic} :l
-  {ortho} = convert simulation box from non-orthogonal (triclinic) to orthogonal
-  {triclinic} = convert simulation box from orthogonal to non-orthogonal (triclinic) :pre
+group-ID = ID of group of atoms to (optionally) displace :ulb,l
+one or more parameter/arg pairs may be appended :l
+parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} or {boundary} or {ortho} or {triclinic} or {set} or {remap}
+  {x}, {y}, {z} args = style value(s)
+    style = {final} or {delta} or {scale} or {volume}
+      {final} values = lo hi
+        lo hi = box boundaries after displacement (distance units)
+      {delta} values = dlo dhi
+        dlo dhi = change in box boundaries after displacement (distance units)
+      {scale} values = factor
+        factor = multiplicative factor for change in box length after displacement
+      {volume} value = none = adjust this dim to preserve volume of system
+  {xy}, {xz}, {yz} args = style value
+    style = {final} or {delta}
+      {final} value = tilt
+        tilt = tilt factor after displacement (distance units)
+      {delta} value = dtilt
+        dtilt = change in tilt factor after displacement (distance units)
+  {boundary} args = x y z
+    x,y,z = {p} or {s} or {f} or {m}, one or two letters
+    {p} is periodic
+    {f} is non-periodic and fixed
+    {s} is non-periodic and shrink-wrapped
+    {m} is non-periodic and shrink-wrapped with a minimum value
+  {ortho} args = none = change box to orthogonal
+  (triclinic} args = none = change box to triclinic
+  {set} args = none = store state of current box
+  {remap} args = none = remap atom coords from last saved state to current box :pre
+
+zero or more keyword/value pairs may be appended :l
+keyword = {units} :l
+  {units} value = {lattice} or {box}
+    lattice = distances are defined in lattice units
+    box = distances are defined in simulation box units :pre
+:ule
 
 [Examples:]
 
-change_box ortho
-change_box triclinic :pre
+change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap :pre
 
 [Description:]
 
-By default LAMMPS runs a simulation in an orthogonal, axis-aligned
-simulation box.  LAMMPS can also run simulations in "non-orthogonal
-(triclinic) simulation boxes"_Section_howto.html#howto_12.  A box is
-defined as either orthogonal or non-orthogonal when it is created via
-the "create_box"_create_box.html, "read_data"_read_data.html, or
-"read_restart"_read_restart.html commands.
+Change the volume and/or shape and/or boundary conditions for the
+simulation box.  Orthogonal simulation boxes have 3 adjustable size
+parameters (x,y,z).  Triclinic (non-orthogonal) simulation boxes have
+6 adjustable size/shape parameters (x,y,z,xy,xz,yz).  Any or all of
+them can be adjusted independently by this command.  Thus it can be
+used to expand or contract a box, or to apply a shear strain to a
+non-orthogonal box.  It can also be used to change the boundary
+conditions for the simulation box, similar to the
+"boundary"_boundary.html command.
 
-This command allows you to toggle the existing simulation box from
-orthogonal to non-orthogonal and vice versa.  For example, an initial
+The size and shape of the initial simulation box are specified by the
+"create_box"_create_box.html or "read_data"_read_data.html or
+"read_restart"_read_restart.html command used to setup the simulation.
+The size and shape may be altered by subsequent runs, e.g. by use of
+the "fix npt"_fix_nh.html or "fix deform"_fix_deform.html commands.
+The "create_box"_create_box.html, "read data"_read_data.html, and
+"read_restart"_read_restart.html commands also determine whether the
+simulation box is orthogonal or triclinic and their doc pages explain
+the meaning of the xy,xz,yz tilt factors.
+
+See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+
+The keywords used in this command are applied sequentially to the
+simulation box and the atoms in it, in the order specified.
+
+Before the sequence of keywords are invoked, the current box
+size/shape are stored, in case a {remap} keyword is used to map the
+atom coordinates from the previous box size/shape to the current one.
+
+After all the keywords have been processed, any shrink-wrap boundary
+conditions are invoked (see the "boundary"_boundary.html command)
+which may change simulation box boundaries, and atoms are migrated to
+new owning processors.
+
+IMPORTANT NOTE: It is possible to lose atoms with this command.
+E.g. by changing the box without remapping the atoms, and having atoms
+end up outside of non-periodic boundaries.  It is also possible when
+remapping atoms to put them (nearly) on top of each other which will
+lead to bad dynamics.  E.g. by converting a boundary from non-periodic
+to periodic.
+
+IMPORTANT NOTE: The simulation box size/shape can be changed by
+arbitrarily large amounts by this command.  This is not a problem,
+except that the mapping of processors to the simulation box is not
+changed from its initial 3d configuration; see the
+"processors"_processors.html command.  Thus, if the box size/shape
+changes dramatically, the mapping of processors to the simulation box
+may not end up as optimal as the initial mapping attempted to be.
+
+:line
+
+For the {x}, {y}, and {z} parameters, this is the meaning of their
+styles and values.
+
+For style {final}, the final lo and hi box boundaries of a dimension
+are specified.  The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+
+For style {delta}, plus or minus changes in the lo/hi box boundaries
+of a dimension are specified.  The values can be in lattice or box
+distance units.  See the discussion of the units keyword below.
+
+For style {scale}, a multiplicative factor to apply to the box length
+of a dimension is specified.  For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11.  A
+factor less than 1.0 means compression.
+
+The {volume} style changes the specified dimension in such a way that
+the overall box volume remains constant with respect to the operation
+performed by the preceding keyword.  The {volume} style can only be
+used following a keyword that changed the volume, which is any of the
+{x}, {y}, {z} keywords.  If the preceding keyword "key" had a {volume}
+style, then both it and the current keyword apply to the keyword
+preceding "key".  I.e. this sequence of keywords is allowed:
+
+change_box all x scale 1.1 y volume z volume :pre
+
+The {volume} style changes the associated dimension so that the
+overall box volume is unchanged relative to its value before the
+preceding keyword was invoked. 
+
+If "x scale 1.1 z volume" is used, then the z box length will
+shrink by the same 1.1 factor the x box length was increased by.
+
+If "x scale 1.1 y volume z volume" is used, then the y,z box lengths
+will each shrink by sqrt(1.1) to keep the volume constant.  In this
+case, the y,z box lengths shrink so as to keep their relative aspect
+ratio constant.
+
+If "x scale 1.1 z volume y scale 1.1 z volume" is used, then
+the final box will be a factor of 10% larger in x and y, and a
+factor of 21% smaller in z, so as to keep the volume constant.
+
+IMPORTANT NOTE: For solids or liquids, when one dimension of the box
+is expanded, it may be physically undesirable to hold the other 2 box
+lengths constant since that implies a density change.  For solids,
+adjusting the other dimensions via the {volume} style may make
+physical sense (just as for a liquid), but may not be correct for
+materials and potentials whose Poisson ratio is not 0.5.
+
+For the {scale} and {volume} styles, the box length is expanded or
+compressed around its mid point.
+
+:line
+
+For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
+styles and values.  Note that changing the tilt factors of a triclinic
+box does not change its volume.
+
+For style {final}, the final tilt factor is specified.  The value
+can be in lattice or box distance units.  See the discussion of the
+units keyword below.
+
+For style {delta}, a plus or minus change in the tilt factor is
+specified.  The value can be in lattice or box distance units.  See
+the discussion of the units keyword below.
+
+All of these styles change the xy, xz, yz tilt factors.  In LAMMPS,
+tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
+than half the distance of the parallel box length.  For example, if
+xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
+factor must be between -5 and 5.  Similarly, both xz and yz must be
+between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a
+limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent.  Any tilt factor specified by this command
+must be within these limits.
+
+:line
+
+The {boundary} keyword takes arguments that have exactly the same
+meaning as they do for the "boundary"_boundary.html command.  In each
+dimension, a single letter assigns the same style to both the lower
+and upper face of the box.  Two letters assigns the first style to the
+lower face and the second style to the upper face.
+
+The style {p} means the box is periodic; the other styles mean
+non-periodic. For style {f}, the position of the face is fixed.  For
+style {s}, the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move.  For style {m}, shrink-wrapping occurs, but is bounded by the
+current box edge in that dimension, so that the box will become no
+smaller.  See the "boundary"_boundary.html command for more
+explanation of these style options.
+
+Note that the "boundary" command itself can only be used before the
+simulation box is defined via a "read_data"_read_data.html or
+"create_box"_create_box.html or "read_restart"_read_restart.html
+command.  This command allows the boundary conditions to be changed
+later in your input script.  Also note that the
+"read_restart"_read_restart.html will change boundary conditions to
+match what is stored in the restart file.  So if you wish to change
+them, you should use the change_box command after the read_restart
+command.
+
+:line
+
+The {ortho} and {triclinic} keywords convert the simulation box to be
+orthogonal or triclinic (non-orthongonal).  See "this
+section"_Section_howto#howto_13 for a discussion of how non-orthongal
+boxes are represented in LAMMPS.
+
+The simulation box is defined as either orthogonal or triclinic when
+it is created via the "create_box"_create_box.html,
+"read_data"_read_data.html, or "read_restart"_read_restart.html
+commands.
+
+These keywords allow you to toggle the existing simulation box from
+orthogonal to triclinic and vice versa.  For example, an initial
 equilibration simulation can be run in an orthogonal box, the box can
-be toggled to non-orthogonal, and then a "non-equilibrium MD (NEMD)
+be toggled to triclinic, and then a "non-equilibrium MD (NEMD)
 simulation"_Section_howto.html#howto_13 can be run with deformation
 via the "fix deform"_fix_deform.html command.
 
-Note that if the simulation box is currently non-orthogonal and has
-non-zero tilt in xy, yz, or xz, then it cannot be converted to an
-orthogonal box.
+If the simulation box is currently triclinic and has non-zero tilt in
+xy, yz, or xz, then it cannot be converted to an orthogonal box.
+
+:line
+
+The {set} keyword saves the current box size/shape.  This can be
+useful if you wish to use the {remap} keyword more than once or if you
+wish it to be applied to an intermediate box size/shape in a sequence
+of keyword operations.  Note that the box size/shape is saved before
+any of the keywords are processed, i.e. the box size/shape at the time
+the create_box command is encountered in the input script.
+
+The {remap} keyword remaps atom coordinates from the last saved box
+size/shape to the current box state.  For example, if you stretch the
+box in the x dimension or tilt it in the xy plane via the {x} and {xy}
+keywords, then the {remap} commmand will dilate or tilt the atoms to
+conform to the new box size/shape, as if the atoms moved with the box
+as it deformed.
+
+Note that this operation is performed without regard to periodic
+boundaries.  Any shrink-wrapping of non-periodic boundaries (see the
+"boundary"_boundary.html command occurs after all keywords, including
+this one, have been processed.
+
+Only atoms in the specified group are remapped.
+
+IMPORTANT NOTE: If you do not explicitly specify the {remap} keyword,
+atom coordinates will not be changed even though the box size/shape
+changes.  This may be the behavior you desire, but can also cause
+atoms to be lost.
+
+:line
+
+The {units} keyword determines the meaning of the distance units used
+to define various arguments.  A {box} value selects standard distance
+units as defined by the "units"_units.html command, e.g. Angstroms for
+units = real or metal.  A {lattice} value means the distance units are
+in lattice spacings.  The "lattice"_lattice.html command must have
+been previously used to define the lattice spacing.
+
+:line
 
 [Restrictions:]
 
-At the point in the input script when this command is issued, no
-"dumps"_dump.html can be active, nor can a "fix
-ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be
-active.  This is because these commands test whether the simulation
-box is orthogonal when they are first issued.  Note that these
-commands can appear in your script before a change_box command is
-issued, so long as an "undump"_undump.html or "unfix"_unfix.html
-command is also used to turn them off.
+If you use the {ortho} or {triclinic} keywords, then at the point in
+the input script when this command is issued, no "dumps"_dump.html can
+be active, nor can a "fix ave/spatial"_fix_ave_spatial.html or "fix
+deform"_fix_deform.html be active.  This is because these commands
+test whether the simulation box is orthogonal when they are first
+issued.  Note that these commands can be used in your script before a
+change_box command is issued, so long as an "undump"_undump.html or
+"unfix"_unfix.html command is also used to turn them off.
 
-[Related commands:] none
+[Related commands:]
 
-[Default:] none
+"fix deform"_fix_deform.html, "boundary"_boundary.html
+
+[Default:]
+
+The option default is units = lattice.
diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html
index 3c433bc2c3..9f46e08d97 100644
--- a/doc/displace_atoms.html
+++ b/doc/displace_atoms.html
@@ -76,29 +76,29 @@ define the lattice spacing.
 
    
 
    
 
-
    Care should be taken not to move atoms on top of other atoms.  After
-the move, atoms are remapped into the periodic simulation box if
-needed.
+
    IMPORTANT NOTE: Care should be taken not to move atoms on top of other
+atoms.  After the move, atoms are remapped into the periodic
+simulation box if needed, and any shrink-wrap boundary conditions (see
+the boundary command) are enforced which may change
+the box size.  Other than this effect, this command does not change
+the size or shape of the simulation box.  See the
+change_box command if that effect is desired.
 
    
-
    Atoms can be moved arbitrarily long distances by this command.  If the
-simulation box is non-periodic, this can change its size or shape.
-This is not a problem, except that the mapping of processors to the
-simulation box is not changed by this command from its initial 3d
-configuration; see the processors command.  Thus, if
-the box size or shape changes dramatically, the simulation may not be
-as well load-balanced (atoms per processor) as the initial mapping
-tried to achieve.
+
    IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
+command.  If the simulation box is non-periodic and shrink-wrapped
+(see the boundary command), this can change its size
+or shape.  This is not a problem, except that the mapping of
+processors to the simulation box is not changed by this command from
+its initial 3d configuration; see the processors
+command.  Thus, if the box size/shape changes dramatically, the
+mapping of processors to the simulation box may not end up as optimal
+as the initial mapping attempted to be.
 
    
-
    Restrictions:
-
    
-
    This command requires inter-processor communication to migrate atoms
-once they have been displaced.  This means that your system must be
-ready to perform a simulation before using this command (force fields
-are setup, atom masses are set, etc).
+
    Restrictions: none
 
    
 
    Related commands:
 
    
-
    lattice
+
    lattice, change_box
 
    
 
    Default:
 
    
diff --git a/doc/displace_atoms.txt b/doc/displace_atoms.txt
index d26f58e258..53585c059c 100644
--- a/doc/displace_atoms.txt
+++ b/doc/displace_atoms.txt
@@ -68,29 +68,29 @@ define the lattice spacing.
 
 :line
 
-Care should be taken not to move atoms on top of other atoms.  After
-the move, atoms are remapped into the periodic simulation box if
-needed.
+IMPORTANT NOTE: Care should be taken not to move atoms on top of other
+atoms.  After the move, atoms are remapped into the periodic
+simulation box if needed, and any shrink-wrap boundary conditions (see
+the "boundary"_boundary.html command) are enforced which may change
+the box size.  Other than this effect, this command does not change
+the size or shape of the simulation box.  See the
+"change_box"_change_box.html command if that effect is desired.
 
-Atoms can be moved arbitrarily long distances by this command.  If the
-simulation box is non-periodic, this can change its size or shape.
-This is not a problem, except that the mapping of processors to the
-simulation box is not changed by this command from its initial 3d
-configuration; see the "processors"_processors.html command.  Thus, if
-the box size or shape changes dramatically, the simulation may not be
-as well load-balanced (atoms per processor) as the initial mapping
-tried to achieve.
+IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
+command.  If the simulation box is non-periodic and shrink-wrapped
+(see the "boundary"_boundary.html command), this can change its size
+or shape.  This is not a problem, except that the mapping of
+processors to the simulation box is not changed by this command from
+its initial 3d configuration; see the "processors"_processors.html
+command.  Thus, if the box size/shape changes dramatically, the
+mapping of processors to the simulation box may not end up as optimal
+as the initial mapping attempted to be.
 
-[Restrictions:]
-
-This command requires inter-processor communication to migrate atoms
-once they have been displaced.  This means that your system must be
-ready to perform a simulation before using this command (force fields
-are setup, atom masses are set, etc).
+[Restrictions:] none
 
 [Related commands:]
 
-"lattice"_lattice.html
+"lattice"_lattice.html, "change_box"_change_box.html
 
 [Default:]
 
diff --git a/doc/displace_box.html b/doc/displace_box.html
deleted file mode 100644
index d589e686c1..0000000000
--- a/doc/displace_box.html
+++ /dev/null
@@ -1,191 +0,0 @@
-
-
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
-
    
-
-
-
-
-
-
-
    
-
-
    displace_box command 
-
    
-
    Syntax:
-
    
-
    displace_box group-ID parameter args ... keyword value ... 
-
    
-
    • group-ID = ID of group of atoms to displace 
-
-
    • one or more parameter/arg pairs may be appended 
-
-
      parameter = x or y or z or xy or xz or yz
-  x, y, z args = style value(s)
-    style = final or delta or scale or volume
-      final values = lo hi
-        lo hi = box boundaries at end of run (distance units)
-      delta values = dlo dhi
-        dlo dhi = change in box boundaries at end of run (distance units)
-      scale values = factor
-        factor = multiplicative factor for change in box length at end of run
-      volume value = none = adjust this dim to preserve volume of system
-  xy, xz, yz args = style value
-    style = final or delta
-      final value = tilt
-        tilt = tilt factor at end of run (distance units)
-      delta value = dtilt
-        dtilt = change in tilt factor at end of run (distance units) 
-
      
-
    • zero or more keyword/value pairs may be appended 
-
-
    • keyword = remap or units 
-
-
        remap value = x or none
-    x = remap coords of atoms in group into deforming box
-    none = no remapping of coords
-  units value = lattice or box
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units 
-
      
-
-
    
-
    Examples:
-
    
-
    displace_box all xy final -2.0 z final 0.0 5.0 units box
-displace_box all x scale 1.1 y volume z volume 
-
    
-
    Description:
-
    
-
    Change the volume and/or shape of the simulation box.  Orthogonal
-simulation boxes have 3 adjustable parameters (x,y,z).  Triclinic
-(non-orthogonal) simulation boxes have 6 adjustable parameters
-(x,y,z,xy,xz,yz).  Any or all of them can be adjusted independently
-and simultaneously by this command.  This fix can be used to expand or
-contract a box, or to apply a shear strain to a non-orthogonal box.
-
    
-
    Any parameter varied by this command must refer to a periodic
-dimension - see the boundary command.  For parameters
-"xy", "xz", and "yz" this means both affected dimensions must be
-periodic, e.g. x and y for "xy".  Dimensions not varied by this
-command can be periodic or non-periodic.
-
    
-
    The size and shape of the initial simulation box are specified by the
-create_box or read_data or
-read_restart command used to setup the simulation,
-or they are the values from the end of the previous run.  The
-create_box, read data, and
-read_restart commands also determine whether the
-simulation box is orthogonal or triclinic and their doc pages explain
-the meaning of the xy,xz,yz tilt factors.  If the displace_box command
-changes the xy,xz,yz tilt factors, then the simulation box must be
-triclinic, even if its initial tilt factors are 0.0.
-
    
-
    
-
-
    For the x, y, and z parameters, this is the meaning of their
-styles and values.
-
    
-
    For style final, the final lo and hi box boundaries of a dimension
-are specified.  The values can be in lattice or box distance units.
-See the discussion of the units keyword below.
-
    
-
    For style delta, plus or minus changes in the lo/hi box boundaries
-of a dimension are specified.  The values can be in lattice or box
-distance units.  See the discussion of the units keyword below.
-
    
-
    For style scale, a multiplicative factor to apply to the box length
-of a dimension is specified.  For example, if the initial box length
-is 10, and the factor is 1.1, then the final box length will be 11.  A
-factor less than 1.0 means compression.
-
    
-
    The volume style changes the specified dimension in such a way that
-the box volume remains constant while other box dimensions are changed
-explicitly via the styles discussed above.  For example, "x scale 1.1
-y scale 1.1 z volume" will shrink the z box length as the x,y box
-lengths increase, to keep the volume constant (product of x,y,z
-lengths).  If "x scale 1.1 z volume" is specified and parameter y is
-unspecified, then the z box length will shrink as x increases to keep
-the product of x,z lengths constant.  If "x scale 1.1 y volume z
-volume" is specified, then both the y,z box lengths will shrink as x
-increases to keep the volume constant (product of x,y,z lengths).  In
-this case, the y,z box lengths shrink so as to keep their relative
-aspect ratio constant.
-
    
-
    For solids or liquids, note that when one dimension of the box is
-expanded by this command, it may be physically undesirable to hold the
-other 2 box lengths constant (unspecified by this command) since that
-implies a density change.  Using the volume style for those 2
-dimensions to keep the box volume constant may make more physical
-sense, but may also not be correct for materials and potentials whose
-Poisson ratio is not 0.5.
-
    
-
    For the scale and volume styles, the box length is expanded or
-compressed around its mid point.
-
    
-
    
-
-
    For the xy, xz, and yz parameters, this is the meaning of their
-styles and values.  Note that changing the tilt factors of a triclinic
-box does not change its volume.
-
    
-
    For style final, the final tilt factor is specified.  The value
-can be in lattice or box distance units.  See the discussion of the
-units keyword below.
-
    
-
    For style delta, a plus or minus change in the tilt factor is
-specified.  The value can be in lattice or box distance units.  See
-the discussion of the units keyword below.
-
    
-
    All of these styles change the xy, xz, yz tilt factors.  In LAMMPS,
-tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
-the distance of the parallel box length.  For example, if xlo = 2 and
-xhi = 12, then the x box length is 10 and the xy tilt factor must be
-between -5 and 5.  Similarly, both xz and yz must be between
--(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
-since if the maximum tilt factor is 5 (as in this example), then
-configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
-equivalent.  Any tilt factor specified by this command must be within
-these limits.
-
    
-
    
-
-
    The remap keyword determines whether atom positions are re-mapped to
-the new box.  If remap is set to x (the default), atoms in the fix
-group are re-mapped; otherwise they are not.  If remap is set to
-none, then this remapping does not take place.
-
    
-
    The units keyword determines the meaning of the distance units used
-to define various arguments.  A box value selects standard distance
-units as defined by the units command, e.g. Angstroms for
-units = real or metal.  A lattice value means the distance units are
-in lattice spacings.  The lattice command must have
-been previously used to define the lattice spacing.
-
    
-
    
-
-
    The simulation box size or shape can be changed by arbitrarily large
-amounts by this command.  This is not a problem, except that the
-mapping of processors to the simulation box is not changed by this
-command from its initial 3d configuration; see the
-processors command.  Thus, if the box size or shape
-changes dramatically, the simulation may not be as well load-balanced
-(atoms per processor) as the initial mapping tried to achieve.
-
    
-
    Restrictions:
-
    
-
    Any box dimension varied by this fix must be periodic.
-
    
-
    This command requires inter-processor communication to migrate atoms
-once they have moved.  This means that your system must be ready to
-perform a simulation before using this command (force fields are
-setup, atom masses are set, etc).
-
    
-
    Related commands:
-
    
-
    fix deform
-
    
-
    Default:
-
    
-
    The option defaults are remap = x and units = lattice.
-
    
-
diff --git a/doc/displace_box.txt b/doc/displace_box.txt
deleted file mode 100644
index 263c53d0ae..0000000000
--- a/doc/displace_box.txt
+++ /dev/null
@@ -1,181 +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
-
-displace_box command :h3
-
-[Syntax:]
-
-displace_box group-ID parameter args ... keyword value ... :pre
-
-group-ID = ID of group of atoms to displace :ulb,l
-one or more parameter/arg pairs may be appended :l
-parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
-  {x}, {y}, {z} args = style value(s)
-    style = {final} or {delta} or {scale} or {volume}
-      {final} values = lo hi
-        lo hi = box boundaries at end of run (distance units)
-      {delta} values = dlo dhi
-        dlo dhi = change in box boundaries at end of run (distance units)
-      {scale} values = factor
-        factor = multiplicative factor for change in box length at end of run
-      {volume} value = none = adjust this dim to preserve volume of system
-  {xy}, {xz}, {yz} args = style value
-    style = {final} or {delta}
-      {final} value = tilt
-        tilt = tilt factor at end of run (distance units)
-      {delta} value = dtilt
-        dtilt = change in tilt factor at end of run (distance units) :pre
-
-zero or more keyword/value pairs may be appended :l
-keyword = {remap} or {units} :l
-  {remap} value = {x} or {none}
-    x = remap coords of atoms in group into deforming box
-    none = no remapping of coords
-  {units} value = {lattice} or {box}
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units :pre
-:ule
-
-[Examples:]
-
-displace_box all xy final -2.0 z final 0.0 5.0 units box
-displace_box all x scale 1.1 y volume z volume :pre
-
-[Description:]
-
-Change the volume and/or shape of the simulation box.  Orthogonal
-simulation boxes have 3 adjustable parameters (x,y,z).  Triclinic
-(non-orthogonal) simulation boxes have 6 adjustable parameters
-(x,y,z,xy,xz,yz).  Any or all of them can be adjusted independently
-and simultaneously by this command.  This fix can be used to expand or
-contract a box, or to apply a shear strain to a non-orthogonal box.
-
-Any parameter varied by this command must refer to a periodic
-dimension - see the "boundary"_boundary.html command.  For parameters
-"xy", "xz", and "yz" this means both affected dimensions must be
-periodic, e.g. x and y for "xy".  Dimensions not varied by this
-command can be periodic or non-periodic.
-
-The size and shape of the initial simulation box are specified by the
-"create_box"_create_box.html or "read_data"_read_data.html or
-"read_restart"_read_restart.html command used to setup the simulation,
-or they are the values from the end of the previous run.  The
-"create_box"_create_box.html, "read data"_read_data.html, and
-"read_restart"_read_restart.html commands also determine whether the
-simulation box is orthogonal or triclinic and their doc pages explain
-the meaning of the xy,xz,yz tilt factors.  If the displace_box command
-changes the xy,xz,yz tilt factors, then the simulation box must be
-triclinic, even if its initial tilt factors are 0.0.
-
-:line
-
-For the {x}, {y}, and {z} parameters, this is the meaning of their
-styles and values.
-
-For style {final}, the final lo and hi box boundaries of a dimension
-are specified.  The values can be in lattice or box distance units.
-See the discussion of the units keyword below.
-
-For style {delta}, plus or minus changes in the lo/hi box boundaries
-of a dimension are specified.  The values can be in lattice or box
-distance units.  See the discussion of the units keyword below.
-
-For style {scale}, a multiplicative factor to apply to the box length
-of a dimension is specified.  For example, if the initial box length
-is 10, and the factor is 1.1, then the final box length will be 11.  A
-factor less than 1.0 means compression.
-
-The {volume} style changes the specified dimension in such a way that
-the box volume remains constant while other box dimensions are changed
-explicitly via the styles discussed above.  For example, "x scale 1.1
-y scale 1.1 z volume" will shrink the z box length as the x,y box
-lengths increase, to keep the volume constant (product of x,y,z
-lengths).  If "x scale 1.1 z volume" is specified and parameter {y} is
-unspecified, then the z box length will shrink as x increases to keep
-the product of x,z lengths constant.  If "x scale 1.1 y volume z
-volume" is specified, then both the y,z box lengths will shrink as x
-increases to keep the volume constant (product of x,y,z lengths).  In
-this case, the y,z box lengths shrink so as to keep their relative
-aspect ratio constant.
-
-For solids or liquids, note that when one dimension of the box is
-expanded by this command, it may be physically undesirable to hold the
-other 2 box lengths constant (unspecified by this command) since that
-implies a density change.  Using the {volume} style for those 2
-dimensions to keep the box volume constant may make more physical
-sense, but may also not be correct for materials and potentials whose
-Poisson ratio is not 0.5.
-
-For the {scale} and {volume} styles, the box length is expanded or
-compressed around its mid point.
-
-:line
-
-For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
-styles and values.  Note that changing the tilt factors of a triclinic
-box does not change its volume.
-
-For style {final}, the final tilt factor is specified.  The value
-can be in lattice or box distance units.  See the discussion of the
-units keyword below.
-
-For style {delta}, a plus or minus change in the tilt factor is
-specified.  The value can be in lattice or box distance units.  See
-the discussion of the units keyword below.
-
-All of these styles change the xy, xz, yz tilt factors.  In LAMMPS,
-tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
-the distance of the parallel box length.  For example, if xlo = 2 and
-xhi = 12, then the x box length is 10 and the xy tilt factor must be
-between -5 and 5.  Similarly, both xz and yz must be between
--(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
-since if the maximum tilt factor is 5 (as in this example), then
-configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
-equivalent.  Any tilt factor specified by this command must be within
-these limits.
-
-:line
-
-The {remap} keyword determines whether atom positions are re-mapped to
-the new box.  If {remap} is set to {x} (the default), atoms in the fix
-group are re-mapped; otherwise they are not.  If {remap} is set to
-{none}, then this remapping does not take place.
-
-The {units} keyword determines the meaning of the distance units used
-to define various arguments.  A {box} value selects standard distance
-units as defined by the "units"_units.html command, e.g. Angstroms for
-units = real or metal.  A {lattice} value means the distance units are
-in lattice spacings.  The "lattice"_lattice.html command must have
-been previously used to define the lattice spacing.
-
-:line
-
-The simulation box size or shape can be changed by arbitrarily large
-amounts by this command.  This is not a problem, except that the
-mapping of processors to the simulation box is not changed by this
-command from its initial 3d configuration; see the
-"processors"_processors.html command.  Thus, if the box size or shape
-changes dramatically, the simulation may not be as well load-balanced
-(atoms per processor) as the initial mapping tried to achieve.
-
-[Restrictions:]
-
-Any box dimension varied by this fix must be periodic.
-
-This command requires inter-processor communication to migrate atoms
-once they have moved.  This means that your system must be ready to
-perform a simulation before using this command (force fields are
-setup, atom masses are set, etc).
-
-[Related commands:]
-
-"fix deform"_fix_deform.html
-
-[Default:]
-
-The option defaults are remap = x and units = lattice.
diff --git a/doc/fix_deform.html b/doc/fix_deform.html
index 76b723d59c..6be57e95ca 100644
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@@ -533,7 +533,7 @@ xy) that is shrink-wrapped via the boundary comamn
 
    
 
    Related commands:
 
    
-
    displace_box
+
    change_box
 
    
 
    Default:
 
    
diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt
index 51baaea5a9..5a3a2ae584 100644
--- a/doc/fix_deform.txt
+++ b/doc/fix_deform.txt
@@ -523,7 +523,7 @@ xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
 
 [Related commands:]
 
-"displace_box"_displace_box.html
+"change_box"_change_box.html
 
 [Default:]
 

From 6b52c82ee32c5e83b40797a2a8fb8b19acfffd79 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 17:01:34 +0000
Subject: [PATCH 04/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7704
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/change_box.html | 24 +++++++++++++++---------
 doc/change_box.txt  | 24 +++++++++++++++---------
 2 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/doc/change_box.html b/doc/change_box.html
index b504671ee9..ba1a8eab6e 100644
--- a/doc/change_box.html
+++ b/doc/change_box.html
@@ -147,18 +147,24 @@ preceding "key".  I.e. this sequence of keywords is allowed:
 overall box volume is unchanged relative to its value before the
 preceding keyword was invoked. 
 
    
-
    If "x scale 1.1 z volume" is used, then the z box length will
-shrink by the same 1.1 factor the x box length was increased by.
+
    If the following command is used, then the z box length will shrink by
+the same 1.1 factor the x box length was increased by:
 
    
-
    If "x scale 1.1 y volume z volume" is used, then the y,z box lengths
-will each shrink by sqrt(1.1) to keep the volume constant.  In this
-case, the y,z box lengths shrink so as to keep their relative aspect
-ratio constant.
+
    change_box all x scale 1.1 z volume 
+
    
+
    If the following command is used, then the y,z box lengths will each
+shrink by sqrt(1.1) to keep the volume constant.  In this case, the
+y,z box lengths shrink so as to keep their relative aspect ratio
+constant:
 
    
-
    If "x scale 1.1 z volume y scale 1.1 z volume" is used, then
-the final box will be a factor of 10% larger in x and y, and a
-factor of 21% smaller in z, so as to keep the volume constant.
+
    change_box all"x scale 1.1 y volume z volume 
+
    
+
    If the following command is used, then the final box will be a factor
+of 10% larger in x and y, and a factor of 21% smaller in z, so as to
+keep the volume constant:
 
    
+
    change_box all x scale 1.1 z volume y scale 1.1 z volume 
+
    
 
    IMPORTANT NOTE: For solids or liquids, when one dimension of the box
 is expanded, it may be physically undesirable to hold the other 2 box
 lengths constant since that implies a density change.  For solids,
diff --git a/doc/change_box.txt b/doc/change_box.txt
index 1b16b42dce..af0f8010c1 100644
--- a/doc/change_box.txt
+++ b/doc/change_box.txt
@@ -139,17 +139,23 @@ The {volume} style changes the associated dimension so that the
 overall box volume is unchanged relative to its value before the
 preceding keyword was invoked. 
 
-If "x scale 1.1 z volume" is used, then the z box length will
-shrink by the same 1.1 factor the x box length was increased by.
+If the following command is used, then the z box length will shrink by
+the same 1.1 factor the x box length was increased by:
 
-If "x scale 1.1 y volume z volume" is used, then the y,z box lengths
-will each shrink by sqrt(1.1) to keep the volume constant.  In this
-case, the y,z box lengths shrink so as to keep their relative aspect
-ratio constant.
+change_box all x scale 1.1 z volume :pre
 
-If "x scale 1.1 z volume y scale 1.1 z volume" is used, then
-the final box will be a factor of 10% larger in x and y, and a
-factor of 21% smaller in z, so as to keep the volume constant.
+If the following command is used, then the y,z box lengths will each
+shrink by sqrt(1.1) to keep the volume constant.  In this case, the
+y,z box lengths shrink so as to keep their relative aspect ratio
+constant:
+
+change_box all"x scale 1.1 y volume z volume :pre
+
+If the following command is used, then the final box will be a factor
+of 10% larger in x and y, and a factor of 21% smaller in z, so as to
+keep the volume constant:
+
+change_box all x scale 1.1 z volume y scale 1.1 z volume :pre
 
 IMPORTANT NOTE: For solids or liquids, when one dimension of the box
 is expanded, it may be physically undesirable to hold the other 2 box

From 7a536019cbd77949dad25960efc74e12bd552e7d Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 17:03:33 +0000
Subject: [PATCH 05/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7705
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/version.h b/src/version.h
index fcffba6c6f..527d6254ea 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "8 Feb 2012"
+#define LAMMPS_VERSION "9 Feb 2012"

From 37596a506079d2bd78a300229d1d8b60d5ca0e16 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 17:45:32 +0000
Subject: [PATCH 06/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7707
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/USER-CUDA/pair_eam_cuda.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/USER-CUDA/pair_eam_cuda.cpp b/src/USER-CUDA/pair_eam_cuda.cpp
index 1c9c710a9f..ee9a701b25 100644
--- a/src/USER-CUDA/pair_eam_cuda.cpp
+++ b/src/USER-CUDA/pair_eam_cuda.cpp
@@ -195,9 +195,9 @@ void PairEAMCuda::array2spline()
   memory->destroy(rhor_spline);
   memory->destroy(z2r_spline);
 
-  memory->create(frho_spline,nfrho,nrho+1,7,"pair:frho");
-  memory->create(rhor_spline,nrhor,nr+1,7,"pair:rhor");
-  memory->create(z2r_spline,nz2r,nr+1,7,"pair:z2r");
+  memory->create(frho_spline,nfrho,nrho+1,8,"pair:frho");
+  memory->create(rhor_spline,nrhor,nr+1,8,"pair:rhor");
+  memory->create(z2r_spline,nz2r,nr+1,8,"pair:z2r");
 
   for (int i = 0; i < nfrho; i++){
     interpolate(nrho,drho,frho[i],frho_spline[i]);

From ee4ad64c5308336328ce63aad014f657103c5bf4 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 17:47:51 +0000
Subject: [PATCH 07/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7708
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/version.h b/src/version.h
index 527d6254ea..cf7a4f7edb 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "9 Feb 2012"
+#define LAMMPS_VERSION "10 Feb 2012"

From 4c98b2d1a9359b70e9682f32bbaf29ea0f2d03ec Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 18:19:20 +0000
Subject: [PATCH 08/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7710
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 python/lammps.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index 23abd7f772..4b40721a03 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -33,8 +33,8 @@ class lammps:
     except:
       try:
         self.lib = CDLL("_lammps_serial.so")
-      #except:
-      #  raise OSError,"Could not load LAMMPS dynamic library"
+      except:
+        raise OSError,"Could not load LAMMPS dynamic library"
 
     # create an instance of LAMMPS
     # don't know how to pass an MPI communicator from PyPar

From 8972482fd9bf4cf9116636a75415e3432787ec22 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 18:43:49 +0000
Subject: [PATCH 09/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7711
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/MC/fix_bond_create.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 52f3ab045d..577d5a7f8e 100755
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -111,7 +111,8 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
   if (iatomtype == jatomtype && 
       ((imaxbond != jmaxbond) || (inewtype != jnewtype)))
-    error->all(FLERR,"Inconsistent iparam/jparam values in fix bond/create command");
+    error->all(FLERR,
+	       "Inconsistent iparam/jparam values in fix bond/create command");
 
   // initialize Marsaglia RNG with processor-unique seed
 
@@ -249,7 +250,8 @@ void FixBondCreate::setup(int vflag)
 	if (newton_bond) {
 	  m = atom->map(bond_atom[i][j]);
 	  if (m < 0)
-	    error->one(FLERR,"Could not count initial bonds in fix bond/create");
+	    error->one(FLERR,
+		       "Could not count initial bonds in fix bond/create");
 	  bondcount[m]++;
 	}
       }
@@ -422,7 +424,8 @@ void FixBondCreate::post_integrate()
     n1 = nspecial[i][0];
     n3 = nspecial[i][2];
     if (n3 == atom->maxspecial)
-      error->one(FLERR,"New bond exceeded special list size in fix bond/create");
+      error->one(FLERR,
+		 "New bond exceeded special list size in fix bond/create");
     for (m = n3; m > n1; m--) slist[m+1] = slist[m];
     slist[n1] = tag[j];
     nspecial[i][0]++;

From 75990ce095fe775caff49e81968b2c9266d86852 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 6 Feb 2012 18:44:03 +0000
Subject: [PATCH 10/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7712
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/change_box.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/change_box.cpp b/src/change_box.cpp
index be83182742..3be6926389 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -365,8 +365,6 @@ void ChangeBox::command(int narg, char **arg)
 
   // check if any atoms were lost
 
-  domain->print_box("  ");
-
   bigint natoms;
   bigint nblocal = atom->nlocal;
   MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);

From 3844c08c56cb54ad8de00ec036b683ade9f00b3f Mon Sep 17 00:00:00 2001
From: pscrozi 
Date: Mon, 6 Feb 2012 19:18:46 +0000
Subject: [PATCH 11/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7713
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/KSPACE/pppm.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 46e9ada2a9..0e1ec2422b 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -874,7 +874,7 @@ void PPPM::set_grid()
   acons[7][5] = 1755948832039.0 / 36229939200000.0;
   acons[7][6] = 4887769399.0 / 37838389248.0;
 
-  double q2 = qsqsum / force->dielectric;
+  double q2 = qsqsum * force->qqrd2e / force->dielectric;
   bigint natoms = atom->natoms;
 
   // use xprd,yprd,zprd even if triclinic so grid size is the same

From 5da2efed0daba7484ba7f0fbca74e0ca6ba41e52 Mon Sep 17 00:00:00 2001
From: pscrozi 
Date: Mon, 6 Feb 2012 21:12:20 +0000
Subject: [PATCH 12/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@7714
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/pair_table.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index b2c34d98bc..77af72f917 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -622,8 +622,8 @@ void PairTable::compute_table(Table *tb)
 
     // ep0,epn = dE/dr at inner and at cut
 
-    double ep0 = - tb->f[0];
-    double epn = - tb->f[tlm1];
+    double ep0 = - tb->f[0] / (2.0 * sqrt(tb->innersq));
+    double epn = - tb->f[tlm1] / (2.0 * tb->cut);
     spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2);
 
     // fp0,fpn = dh/dg at inner and at cut