git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7702 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -11,17 +11,28 @@
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See the README file in the top-level LAMMPS directory.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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------------------------------------------------------------------------- */
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#include "lmptype.h"
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#include "mpi.h"
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "string.h"
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#include "change_box.h"
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#include "change_box.h"
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#include "domain.h"
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#include "atom.h"
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#include "modify.h"
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#include "modify.h"
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#include "fix.h"
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#include "fix.h"
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#include "domain.h"
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#include "lattice.h"
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#include "comm.h"
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#include "irregular.h"
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#include "output.h"
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#include "output.h"
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#include "group.h"
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#include "error.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace LAMMPS_NS;
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enum{ORTHO,TRICLINIC};
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enum{XYZ,TILT,BOUNDARY,ORTHO,TRICLINIC,SET,REMAP};
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enum{FINAL,DELTA,SCALE};
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enum{X,Y,Z,YZ,XZ,XY};
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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@ -31,34 +42,414 @@ ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {}
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void ChangeBox::command(int narg, char **arg)
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void ChangeBox::command(int narg, char **arg)
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{
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{
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int i;
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"Change_box command before simulation box is defined");
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error->all(FLERR,"Change_box command before simulation box is defined");
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if (narg != 1) error->all(FLERR,"Illegal change_box command");
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if (narg < 2) error->all(FLERR,"Illegal change_box command");
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if (modify->nfix_restart_peratom)
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error->all(FLERR,"Cannot change_box after "
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"reading restart file with per-atom info");
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int style;
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if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
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if (strcmp(arg[0],"ortho") == 0) style = ORTHO;
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else if (strcmp(arg[0],"triclinic") == 0) style = TRICLINIC;
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else error->all(FLERR,"Illegal change_box command");
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if (style == ORTHO && domain->triclinic == 0)
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// group
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error->all(FLERR,"Change_box operation is invalid");
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if (style == TRICLINIC && domain->triclinic == 1)
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error->all(FLERR,"Change_box operation is invalid");
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if (style == ORTHO &&
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(domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0))
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error->all(FLERR,"Cannot change box to orthogonal when tilt is non-zero");
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if (output->ndump)
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int igroup = group->find(arg[0]);
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error->all(FLERR,"Cannot change box with dumps defined");
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if (igroup == -1) error->all(FLERR,"Could not find change_box group ID");
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for (int i = 0; i < modify->nfix; i++)
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int groupbit = group->bitmask[igroup];
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if (modify->fix[i]->no_change_box)
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error->all(FLERR,"Cannot change box with certain fixes defined");
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if (style == ORTHO) domain->triclinic = 0;
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// parse operation arguments
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else domain->triclinic = 1;
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// allocate ops to max possible length
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domain->xy = domain->yz = domain->xz = 0.0;
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// volume option does not increment nops
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domain->set_global_box();
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int dimension = domain->dimension;
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if (style == TRICLINIC) domain->set_lamda_box();
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domain->set_local_box();
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ops = new Operation[narg-1];
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nops = 0;
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int index;
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
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strcmp(arg[iarg],"z") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = XYZ;
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if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X;
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else if (strcmp(arg[iarg],"y") == 0) ops[nops].dim = Y;
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else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z;
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if (dimension == 2 && ops[nops].dim == Z)
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error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
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if (strcmp(arg[iarg+1],"final") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].flavor = FINAL;
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ops[nops].flo = atof(arg[iarg+2]);
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ops[nops].fhi = atof(arg[iarg+3]);
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ops[nops].vdim1 = ops[nops].vdim2 = -1;
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nops++;
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iarg += 4;
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} else if (strcmp(arg[iarg+1],"delta") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].flavor = DELTA;
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ops[nops].dlo = atof(arg[iarg+2]);
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ops[nops].dhi = atof(arg[iarg+3]);
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ops[nops].vdim1 = ops[nops].vdim2 = -1;
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nops++;
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iarg += 4;
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} else if (strcmp(arg[iarg+1],"scale") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].flavor = SCALE;
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ops[nops].scale = atof(arg[iarg+2]);
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ops[nops].vdim1 = ops[nops].vdim2 = -1;
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nops++;
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iarg += 3;
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} else if (strcmp(arg[iarg+1],"volume") == 0) {
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if (nops == 0 || ops[nops-1].style != XYZ ||
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ops[nops].dim == ops[nops-1].dim)
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error->all(FLERR,"Change_box volume used incorrectly");
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if (ops[nops-1].vdim2 >= 0)
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error->all(FLERR,"Change_box volume used incorrectly");
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else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
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else ops[nops-1].vdim1 = ops[nops].dim;
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iarg += 2;
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} else error->all(FLERR,"Illegal change_box command");
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} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
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strcmp(arg[iarg],"yz") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = TILT;
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if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY;
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else if (strcmp(arg[iarg],"xz") == 0) ops[nops].dim = XZ;
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else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ;
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if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ))
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error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
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if (strcmp(arg[iarg+1],"final") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].flavor = FINAL;
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ops[nops].ftilt = atof(arg[iarg+2]);
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nops++;
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iarg += 3;
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} else if (strcmp(arg[iarg+1],"delta") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].flavor = DELTA;
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ops[nops].dtilt = atof(arg[iarg+2]);
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nops++;
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iarg += 3;
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} else error->all(FLERR,"Illegal change_box command");
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} else if (strcmp(arg[iarg],"boundary") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = BOUNDARY;
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ops[nops].boundindex = iarg+1;
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nops++;
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iarg += 4;
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} else if (strcmp(arg[iarg],"ortho") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = ORTHO;
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nops++;
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iarg += 1;
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} else if (strcmp(arg[iarg],"triclinic") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = TRICLINIC;
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nops++;
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iarg += 1;
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} else if (strcmp(arg[iarg],"set") == 0) {
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if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = SET;
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nops++;
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iarg += 1;
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} else if (strcmp(arg[iarg],"remap") == 0) {
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if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command");
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ops[nops].style = REMAP;
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nops++;
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iarg += 1;
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} else break;
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}
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if (nops == 0) error->all(FLERR,"Illegal change_box command");
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// read options from end of input line
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options(narg-iarg,&arg[iarg]);
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// compute scale factors if FINAL,DELTA used since they have distance units
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int flag = 0;
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for (int i = 0; i < nops; i++)
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if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1;
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if (flag && scaleflag && domain->lattice == NULL)
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error->all(FLERR,"Use of change_box with undefined lattice");
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if (flag && scaleflag) {
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scale[0] = domain->lattice->xlattice;
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scale[1] = domain->lattice->ylattice;
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scale[2] = domain->lattice->zlattice;
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}
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else scale[0] = scale[1] = scale[2] = 1.0;
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// perform sequence of operations
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// first insure atoms are in current box & update box via shrink-wrap
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// then save current box state so can remap atoms from it
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domain->pbc();
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domain->reset_box();
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save_box_state();
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for (int i = 0; i < nops; i++) {
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if (ops[i].style == XYZ) {
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double volume;
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if (domain->dimension == 2) volume = domain->xprd * domain->yprd;
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else volume = domain->xprd * domain->yprd * domain->zprd;
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if (ops[i].flavor == FINAL) {
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domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
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domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
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if (ops[i].vdim1)
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volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
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domain->set_initial_box();
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domain->set_global_box();
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domain->set_local_box();
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domain->print_box(" ");
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} else if (ops[i].flavor == DELTA) {
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domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
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domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
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if (ops[i].vdim1)
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volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
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domain->set_initial_box();
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domain->set_global_box();
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domain->set_local_box();
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domain->print_box(" ");
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} else if (ops[i].flavor == SCALE) {
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double mid = 0.5 *
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(domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
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double delta = domain->boxlo[ops[i].dim] - mid;
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domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
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delta = domain->boxhi[ops[i].dim] - mid;
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domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
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if (ops[i].vdim1)
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volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
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domain->set_initial_box();
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domain->set_global_box();
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domain->set_local_box();
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domain->print_box(" ");
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}
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} else if (ops[i].style == TILT) {
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if (domain->triclinic == 0)
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error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
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if (ops[i].flavor == FINAL) {
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if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
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else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
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else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
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domain->set_initial_box();
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domain->set_global_box();
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domain->set_local_box();
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domain->print_box(" ");
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|
} else if (ops[i].flavor == DELTA) {
|
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if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
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else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
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else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
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|
domain->set_initial_box();
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|
domain->set_global_box();
|
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domain->set_local_box();
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|
domain->print_box(" ");
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|
}
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||||||
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|
||||||
|
} else if (ops[i].style == BOUNDARY) {
|
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|
domain->set_boundary(3,&arg[ops[i].boundindex],1);
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||||||
|
if (domain->dimension == 2 && domain->zperiodic == 0)
|
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|
error->all(FLERR,
|
||||||
|
"Cannot run 2d simulation with nonperiodic Z dimension");
|
||||||
|
domain->set_initial_box();
|
||||||
|
domain->set_global_box();
|
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|
domain->set_local_box();
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||||||
|
|
||||||
|
} 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++)
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||||||
|
if (modify->fix[i]->no_change_box)
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||||||
|
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;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -28,6 +28,28 @@ class ChangeBox : protected Pointers {
|
|||||||
public:
|
public:
|
||||||
ChangeBox(class LAMMPS *);
|
ChangeBox(class LAMMPS *);
|
||||||
void command(int, char **);
|
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:
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
E: Change_box command before simulation box is defined
|
E: Displace_box command before simulation box is defined
|
||||||
|
|
||||||
Self-explanatory.
|
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
|
documentation for the command. You can use -echo screen as a
|
||||||
command-line option when running LAMMPS to see the offending line.
|
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
|
This is because the restart file info cannot be migrated with the
|
||||||
triclinic.
|
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.
|
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
|
Must use lattice command with displace_box command if units option is
|
||||||
fix/deform are defined .
|
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
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
@ -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");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
@ -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
|
|
||||||
|
|
||||||
*/
|
|
||||||
@ -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");
|
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 == 'f') boundary[idim][iside] = 1;
|
||||||
else if (c == 's') boundary[idim][iside] = 2;
|
else if (c == 's') boundary[idim][iside] = 2;
|
||||||
else if (c == 'm') boundary[idim][iside] = 3;
|
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++)
|
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];
|
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
|
convert 8 lamda corner pts of lo/hi box to box coords
|
||||||
return bboxlo/hi = bounding box around 8 corner pts in box coords
|
return bboxlo/hi = bounding box around 8 corner pts in box coords
|
||||||
|
|||||||
@ -107,13 +107,14 @@ class Domain : protected Pointers {
|
|||||||
void add_region(int, char **);
|
void add_region(int, char **);
|
||||||
void delete_region(int, char **);
|
void delete_region(int, char **);
|
||||||
int find_region(char *);
|
int find_region(char *);
|
||||||
void set_boundary(int, char **);
|
void set_boundary(int, char **, int);
|
||||||
void print_box(const char *);
|
void print_box(const char *);
|
||||||
|
|
||||||
virtual void lamda2x(int);
|
virtual void lamda2x(int);
|
||||||
virtual void x2lamda(int);
|
virtual void x2lamda(int);
|
||||||
void lamda2x(double *, double *);
|
void lamda2x(double *, double *);
|
||||||
void x2lamda(double *, double *);
|
void x2lamda(double *, double *);
|
||||||
|
void x2lamda(double *, double *, double *, double *);
|
||||||
void bbox(double *, double *, double *, double *);
|
void bbox(double *, double *, double *, double *);
|
||||||
void box_corners();
|
void box_corners();
|
||||||
|
|
||||||
|
|||||||
@ -930,7 +930,7 @@ void Input::boundary()
|
|||||||
{
|
{
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Boundary command after simulation box is defined");
|
error->all(FLERR,"Boundary command after simulation box is defined");
|
||||||
domain->set_boundary(narg,arg);
|
domain->set_boundary(narg,arg,0);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -16,6 +16,7 @@
|
|||||||
#include "string.h"
|
#include "string.h"
|
||||||
#include "ctype.h"
|
#include "ctype.h"
|
||||||
#include "pair_hybrid.h"
|
#include "pair_hybrid.h"
|
||||||
|
#include "style_pair.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "force.h"
|
#include "force.h"
|
||||||
#include "pair.h"
|
#include "pair.h"
|
||||||
@ -763,4 +764,3 @@ double PairHybrid::memory_usage()
|
|||||||
for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
|
for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
|
||||||
return bytes;
|
return bytes;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -464,7 +464,8 @@ void ReadRestart::header()
|
|||||||
if (flag == VERSION) {
|
if (flag == VERSION) {
|
||||||
char *version = read_char();
|
char *version = read_char();
|
||||||
if (strcmp(version,universe->version) != 0 && me == 0) {
|
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",
|
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
|
||||||
version,universe->version);
|
version,universe->version);
|
||||||
}
|
}
|
||||||
@ -581,7 +582,8 @@ void ReadRestart::header()
|
|||||||
boundary[2][0] != domain->boundary[2][0] ||
|
boundary[2][0] != domain->boundary[2][0] ||
|
||||||
boundary[2][1] != domain->boundary[2][1]) {
|
boundary[2][1] != domain->boundary[2][1]) {
|
||||||
if (me == 0)
|
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");
|
"using restart file values");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user