void Ridge::UpdateMapping()
{
for (int i = 0; i < atom->nlocal; i++) domain->remap(atom->x[i],atom->image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
return;
}
void ReadRestart::command(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal read_restart command");
if (domain->box_exist)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// if filename contains "*", search dir for latest restart file
char *file = new char[strlen(arg[0]) + 16];
if (strchr(arg[0],'*')) {
int n;
if (me == 0) {
file_search(arg[0],file);
n = strlen(file) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(file,n,MPI_CHAR,0,world);
} else strcpy(file,arg[0]);
// check for multiproc files and an MPI-IO filename
if (strchr(arg[0],'%')) multiproc = 1;
else multiproc = 0;
if (strstr(arg[0],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiioflag)
error->all(FLERR,
"Read restart MPI-IO output not allowed with '%' in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
if (!mpiio->mpiio_exists)
error->all(FLERR,"Reading from MPI-IO filename when "
"MPIIO package is not installed");
}
// open single restart file or base file for multiproc case
if (me == 0) {
if (screen) fprintf(screen,"Reading restart file ...\n");
char *hfile;
if (multiproc) {
hfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(hfile,"%s%s%s",file,"base",ptr+1);
*ptr = '%';
} else hfile = file;
fp = fopen(hfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
if (multiproc) delete [] hfile;
}
// read magic string, endian flag, numeric version
magic_string();
endian();
int incompatible = version_numeric();
// read header info which creates simulation box
header(incompatible);
domain->box_exist = 1;
// problem setup using info from header
int n;
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
// read groups, ntype-length arrays, force field, fix info from file
// nextra = max # of extra quantities stored with each atom
group->read_restart(fp);
type_arrays();
force_fields();
int nextra = modify->read_restart(fp);
atom->nextra_store = nextra;
memory->create(atom->extra,n,nextra,"atom:extra");
// read file layout info
file_layout();
// close header file if in multiproc mode
if (multiproc && me == 0) fclose(fp);
// read per-proc info
AtomVec *avec = atom->avec;
int maxbuf = 0;
double *buf = NULL;
int m,flag;
// MPI-IO input from single file
if (mpiioflag) {
// add calls to RestartMPIIO class
// reopen header file
// perform reads
// allow for different # of procs reading than wrote the file
// mpiio->open(file);
// mpiio->read();
// mpiio->close();
// then process atom info as
//m = 0;
//while (m < n) m += avec->unpack_restart(&buf[m]);
}
// input of single native file
// nprocs_file = # of chunks in file
// proc 0 reads a chunk and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
else if (multiproc == 0) {
int triclinic = domain->triclinic;
double *x,lamda[3];
double *coord,*sublo,*subhi;
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
if (read_int() != PERPROC)
error->all(FLERR,"Invalid flag in peratom section of restart file");
n = read_int();
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
read_double_vec(n,buf);
m = 0;
while (m < n) {
x = &buf[m+1];
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
}
else m += static_cast<int> (buf[m]);
}
}
if (me == 0) fclose(fp);
}
// input of multiple native files with procs <= files
// # of files = multiproc_file
// each proc reads a subset of files, striding by nprocs
// each proc keeps all atoms in all perproc chunks in its files
else if (nprocs <= multiproc_file) {
char *procfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
for (int iproc = me; iproc < multiproc_file; iproc += nprocs) {
*ptr = '\0';
sprintf(procfile,"%s%d%s",file,iproc,ptr+1);
*ptr = '%';
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
int procsperfile;
fread(&procsperfile,sizeof(int),1,fp);
for (int i = 0; i < procsperfile; i++) {
fread(&flag,sizeof(int),1,fp);
if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
fread(buf,sizeof(double),n,fp);
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
}
fclose(fp);
}
delete [] procfile;
}
// input of multiple native files with procs > files
// # of files = multiproc_file
// cluster procs based on # of files
// 1st proc in each cluster reads per-proc chunks from file
// sends chunks round-robin to other procs in its cluster
// each proc keeps all atoms in its perproc chunks in file
else {
// nclusterprocs = # of procs in my cluster that read from one file
// filewriter = 1 if this proc reads file, else 0
// fileproc = ID of proc in my cluster who reads from file
// clustercomm = MPI communicator within my cluster of procs
int nfile = multiproc_file;
int icluster = static_cast<int> ((bigint) me * nfile/nprocs);
int fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
int nclusterprocs = fileprocnext - fileproc;
int filereader = 0;
if (me == fileproc) filereader = 1;
MPI_Comm clustercomm;
MPI_Comm_split(world,icluster,0,&clustercomm);
if (filereader) {
char *procfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(procfile,"%s%d%s",file,icluster,ptr+1);
*ptr = '%';
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
delete [] procfile;
}
int flag,procsperfile;
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&procsperfile,sizeof(int),1,fp);
}
MPI_Bcast(&procsperfile,1,MPI_INT,0,clustercomm);
int tmp,iproc;
MPI_Status status;
MPI_Request request;
for (int i = 0; i < procsperfile; i++) {
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
fread(buf,sizeof(double),n,fp);
if (i % nclusterprocs) {
iproc = me + (i % nclusterprocs);
MPI_Send(&n,1,MPI_INT,iproc,0,world);
MPI_Recv(&tmp,0,MPI_INT,iproc,0,world,&status);
MPI_Rsend(buf,n,MPI_DOUBLE,iproc,0,world);
}
} else if (i % nclusterprocs == me - fileproc) {
MPI_Recv(&n,1,MPI_INT,fileproc,0,world,&status);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
MPI_Irecv(buf,n,MPI_DOUBLE,fileproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,fileproc,0,world);
MPI_Wait(&request,&status);
}
if (i % nclusterprocs == me - fileproc) {
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
}
}
if (filereader) fclose(fp);
MPI_Comm_free(&clustercomm);
}
// clean-up memory
delete [] file;
memory->destroy(buf);
// for multiproc or MPI-IO files:
// perform irregular comm to migrate atoms to correct procs
if (multiproc || mpiioflag) {
// create a temporary fix to hold and migrate extra atom info
// necessary b/c irregular will migrate atoms
if (nextra) {
char cextra[8],fixextra[8];
sprintf(cextra,"%d",nextra);
sprintf(fixextra,"%d",modify->nfix_restart_peratom);
char **newarg = new char*[5];
newarg[0] = (char *) "_read_restart";
newarg[1] = (char *) "all";
newarg[2] = (char *) "READ_RESTART";
newarg[3] = cextra;
newarg[4] = fixextra;
modify->add_fix(5,newarg);
delete [] newarg;
}
// move atoms to new processors via irregular()
// in case read by different proc than wrote restart file
// first do map_init() since irregular->migrate_atoms() will do map_clear()
if (atom->map_style) atom->map_init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// put extra atom info held by fix back into atom->extra
// destroy temporary fix
if (nextra) {
memory->destroy(atom->extra);
memory->create(atom->extra,atom->nmax,nextra,"atom:extra");
int ifix = modify->find_fix("_read_restart");
FixReadRestart *fix = (FixReadRestart *) modify->fix[ifix];
int *count = fix->count;
double **extra = fix->extra;
double **atom_extra = atom->extra;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < count[i]; j++)
atom_extra[i][j] = extra[i][j];
modify->delete_fix("_read_restart");
}
}
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
}
}
// check if tags are being used
// create global mapping and bond topology now that system is defined
flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] > 0) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all == 0) atom->tag_enable = 0;
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
Special special(lmp);
special.build();
}
}
void ReadRestart::command(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal read_restart command");
if (domain->box_exist)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// if filename contains "*", search dir for latest restart file
char *file = new char[strlen(arg[0]) + 16];
if (strchr(arg[0],'*')) {
int n;
if (me == 0) {
file_search(arg[0],file);
n = strlen(file) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(file,n,MPI_CHAR,0,world);
} else strcpy(file,arg[0]);
// check if filename contains "%"
int multiproc;
if (strchr(file,'%')) multiproc = 1;
else multiproc = 0;
// open single restart file or base file for multiproc case
// auto-detect whether byte swapping needs to be done as file is read
if (me == 0) {
if (screen) fprintf(screen,"Reading restart file ...\n");
char *hfile;
if (multiproc) {
hfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(hfile,"%s%s%s",file,"base",ptr+1);
*ptr = '%';
} else hfile = file;
fp = fopen(hfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
swapflag = autodetect(&fp,hfile);
if (multiproc) delete [] hfile;
}
MPI_Bcast(&swapflag,1,MPI_INT,0,world);
// read header info and create atom style and simulation box
header();
domain->box_exist = 1;
// problem setup using info from header
int n;
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
// read groups, ntype-length arrays, force field, fix info from file
// nextra = max # of extra quantities stored with each atom
group->read_restart(fp);
type_arrays();
force_fields();
int nextra = modify->read_restart(fp);
atom->nextra_store = nextra;
memory->create(atom->extra,n,nextra,"atom:extra");
// single file:
// nprocs_file = # of chunks in file
// proc 0 reads chunks one at a time and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
// close restart file when done
AtomVec *avec = atom->avec;
int maxbuf = 0;
double *buf = NULL;
int m;
if (multiproc == 0) {
int triclinic = domain->triclinic;
double *x,lamda[3];
double *coord,*sublo,*subhi;
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
n = read_int();
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
if (n > 0) {
if (me == 0) nread_double(buf,n,fp);
MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
}
m = 0;
while (m < n) {
x = &buf[m+1];
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
}
else m += static_cast<int> (buf[m]);
}
}
if (me == 0) fclose(fp);
// one file per proc:
// nprocs_file = # of files
// each proc reads 1/P fraction of files, keeping all atoms in the files
// perform irregular comm to migrate atoms to correct procs
// close restart file when done
} else {
if (me == 0) fclose(fp);
char *perproc = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
for (int iproc = me; iproc < nprocs_file; iproc += nprocs) {
*ptr = '\0';
sprintf(perproc,"%s%d%s",file,iproc,ptr+1);
*ptr = '%';
fp = fopen(perproc,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",perproc);
error->one(FLERR,str);
}
nread_int(&n,1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
if (n > 0) nread_double(buf,n,fp);
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
fclose(fp);
}
delete [] perproc;
// create a temporary fix to hold and migrate extra atom info
// necessary b/c irregular will migrate atoms
if (nextra) {
char cextra[8],fixextra[8];
sprintf(cextra,"%d",nextra);
sprintf(fixextra,"%d",modify->nfix_restart_peratom);
char **newarg = new char*[5];
newarg[0] = (char *) "_read_restart";
newarg[1] = (char *) "all";
newarg[2] = (char *) "READ_RESTART";
newarg[3] = cextra;
newarg[4] = fixextra;
modify->add_fix(5,newarg);
delete [] newarg;
}
// move atoms to new processors via irregular()
// in case read by different proc than wrote restart file
// first do map_init() since irregular->migrate_atoms() will do map_clear()
if (atom->map_style) atom->map_init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// put extra atom info held by fix back into atom->extra
// destroy temporary fix
if (nextra) {
memory->destroy(atom->extra);
memory->create(atom->extra,atom->nmax,nextra,"atom:extra");
int ifix = modify->find_fix("_read_restart");
FixReadRestart *fix = (FixReadRestart *) modify->fix[ifix];
int *count = fix->count;
double **extra = fix->extra;
double **atom_extra = atom->extra;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < count[i]; j++)
atom_extra[i][j] = extra[i][j];
modify->delete_fix("_read_restart");
}
}
// clean-up memory
delete [] file;
memory->destroy(buf);
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
}
}
// check if tags are being used
// create global mapping and bond topology now that system is defined
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] > 0) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (atom->natoms > 0 && flag_all == 0) atom->tag_enable = 0;
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
Special special(lmp);
special.build();
}
}
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 < 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");
if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
// group
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find change_box group ID");
int groupbit = group->bitmask[igroup];
// parse operation arguments
// allocate ops to max possible length
// volume option does not increment nops
int dimension = domain->dimension;
ops = new Operation[narg-1];
memset(ops,0,(narg-1)*sizeof(Operation));
nops = 0;
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 = force->numeric(FLERR,arg[iarg+2]);
ops[nops].fhi = force->numeric(FLERR,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 = force->numeric(FLERR,arg[iarg+2]);
ops[nops].dhi = force->numeric(FLERR,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 = force->numeric(FLERR,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 = force->numeric(FLERR,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 = force->numeric(FLERR,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) {
ops[nops].style = ORTHO;
nops++;
iarg += 1;
} else if (strcmp(arg[iarg],"triclinic") == 0) {
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) {
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) {
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
// no exchange() since doesn't matter if atoms are assigned to correct procs
// save current box state so can remap atoms from it, if requested
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
save_box_state();
for (int m = 0; m < nops; m++) {
if (ops[m].style == XYZ) {
double volume;
if (domain->dimension == 2) volume = domain->xprd * domain->yprd;
else volume = domain->xprd * domain->yprd * domain->zprd;
if (ops[m].flavor == FINAL) {
domain->boxlo[ops[m].dim] = scale[ops[m].dim]*ops[m].flo;
domain->boxhi[ops[m].dim] = scale[ops[m].dim]*ops[m].fhi;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == DELTA) {
domain->boxlo[ops[m].dim] += scale[ops[m].dim]*ops[m].dlo;
domain->boxhi[ops[m].dim] += scale[ops[m].dim]*ops[m].dhi;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == SCALE) {
double mid = 0.5 *
(domain->boxlo[ops[m].dim] + domain->boxhi[ops[m].dim]);
double delta = domain->boxlo[ops[m].dim] - mid;
domain->boxlo[ops[m].dim] = mid + ops[m].scale*delta;
delta = domain->boxhi[ops[m].dim] - mid;
domain->boxhi[ops[m].dim] = mid + ops[m].scale*delta;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[m].style == TILT) {
if (domain->triclinic == 0)
error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
if (ops[m].flavor == FINAL) {
if (ops[m].dim == XY) domain->xy = scale[X]*ops[m].ftilt;
else if (ops[m].dim == XZ) domain->xz = scale[X]*ops[m].ftilt;
else if (ops[m].dim == YZ) domain->yz = scale[Y]*ops[m].ftilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == DELTA) {
if (ops[m].dim == XY) domain->xy += scale[X]*ops[m].dtilt;
else if (ops[m].dim == XZ) domain->xz += scale[X]*ops[m].dtilt;
else if (ops[m].dim == YZ) domain->yz += scale[Y]*ops[m].dtilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[m].style == BOUNDARY) {
domain->set_boundary(3,&arg[ops[m].boundindex],1);
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,
"Cannot change box z boundary to "
"nonperiodic for a 2d simulation");
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
} else if (ops[m].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[m].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[m].style == SET) {
save_box_state();
} else if (ops[m].style == REMAP) {
if (modify->check_rigid_group_overlap(groupbit))
error->warning(FLERR,"Attempting to remap atoms in rigid bodies");
// 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) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// 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;
imageint *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(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// 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 && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
int style;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of displace_atoms with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
if (style == MOVE) {
double delx = xscale*atof(arg[2]);
double dely = yscale*atof(arg[3]);
double delz = zscale*atof(arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*atof(arg[3]);
d_hi = xscale*atof(arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*atof(arg[3]);
d_hi = yscale*atof(arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*atof(arg[3]);
d_hi = zscale*atof(arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[6]);
coord_hi = xscale*atof(arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[6]);
coord_hi = yscale*atof(arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[6]);
coord_hi = zscale*atof(arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*atof(arg[2]);
double dy = yscale*atof(arg[3]);
double dz = zscale*atof(arg[4]);
int seed = atoi(arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
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
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_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(FLERR,str);
}
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
groupbit = group->bitmask[igroup];
int style = -1;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else if (strcmp(arg[1],"rotate") == 0) style = ROTATE;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
else if (style == ROTATE) options(narg-9,&arg[9]);
// setup scaling
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector or specified variable(s)
if (style == MOVE) {
move(0,arg[2],xscale);
move(1,arg[3],yscale);
move(2,arg[4],zscale);
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*force->numeric(FLERR,arg[3]);
d_hi = xscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*force->numeric(FLERR,arg[3]);
d_hi = yscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*force->numeric(FLERR,arg[3]);
d_hi = zscale*force->numeric(FLERR,arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*force->numeric(FLERR,arg[6]);
coord_hi = xscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*force->numeric(FLERR,arg[6]);
coord_hi = yscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*force->numeric(FLERR,arg[6]);
coord_hi = zscale*force->numeric(FLERR,arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*force->numeric(FLERR,arg[2]);
double dy = yscale*force->numeric(FLERR,arg[3]);
double dz = zscale*force->numeric(FLERR,arg[4]);
int seed = force->inumeric(FLERR,arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if (style == ROTATE) {
double theta_new;
double axis[3],point[3],qrotate[4],qnew[4];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
double *quat;
int dim = domain->dimension;
point[0] = xscale*force->numeric(FLERR,arg[2]);
point[1] = yscale*force->numeric(FLERR,arg[3]);
point[2] = zscale*force->numeric(FLERR,arg[4]);
axis[0] = force->numeric(FLERR,arg[5]);
axis[1] = force->numeric(FLERR,arg[6]);
axis[2] = force->numeric(FLERR,arg[7]);
double theta = force->numeric(FLERR,arg[8]);
if (dim == 2 && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Invalid displace_atoms rotate axis for 2d");
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Zero length rotation vector with displace_atoms");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
double angle = MY_PI*theta/180.0;
double sine = sin(angle);
double cosine = cos(angle);
double ddotr;
// flags for additional orientation info stored by some atom styles
int ellipsoid_flag = atom->ellipsoid_flag;
int line_flag = atom->line_flag;
int tri_flag = atom->tri_flag;
int body_flag = atom->body_flag;
int theta_flag = 0;
int quat_flag = 0;
if (line_flag) theta_flag = 1;
if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1;
// AtomVec pointers to retrieve per-atom storage of extra quantities
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
double **x = atom->x;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
d[0] = x[i][0] - point[0];
d[1] = x[i][1] - point[1];
d[2] = x[i][2] - point[2];
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x[i][0] = point[0] + c[0] + disp[0];
x[i][1] = point[1] + c[1] + disp[1];
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
// theta for lines
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(avec_line->bonus[line[i]].theta+angle,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
// quats for ellipsoids, tris, and bodies
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
if (quat) {
qrotate[0] = cosine;
qrotate[1] = runit[0]*sine;
qrotate[2] = runit[1]*sine;
qrotate[3] = runit[2]*sine;
MathExtra::quatquat(qrotate,quat,qnew);
quat[0] = qnew[0];
quat[1] = qnew[1];
quat[2] = qnew[2];
quat[3] = qnew[3];
}
}
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
imageint *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(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// 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 && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
void CreateAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Create_atoms command before simulation box is defined");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot create_atoms after "
"reading restart file with per-atom info");
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");
ntype = force->inumeric(FLERR,arg[0]);
int iarg;
if (strcmp(arg[1],"box") == 0) {
style = BOX;
iarg = 2;
nregion = -1;
} else if (strcmp(arg[1],"region") == 0) {
style = REGION;
if (narg < 3) error->all(FLERR,"Illegal create_atoms command");
nregion = domain->find_region(arg[2]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
domain->regions[nregion]->prematch();
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
xone[0] = force->numeric(FLERR,arg[2]);
xone[1] = force->numeric(FLERR,arg[3]);
xone[2] = force->numeric(FLERR,arg[4]);
iarg = 5;
} else if (strcmp(arg[1],"random") == 0) {
style = RANDOM;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
nrandom = force->inumeric(FLERR,arg[2]);
seed = force->inumeric(FLERR,arg[3]);
if (strcmp(arg[4],"NULL") == 0) nregion = -1;
else {
nregion = domain->find_region(arg[4]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
domain->regions[nregion]->prematch();
}
iarg = 5;
} else error->all(FLERR,"Illegal create_atoms command");
// process optional keywords
int scaleflag = 1;
remapflag = 0;
mode = ATOM;
int molseed;
varflag = 0;
vstr = xstr = ystr = zstr = NULL;
quatone[0] = quatone[1] = quatone[2] = 0.0;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int ibasis = force->inumeric(FLERR,arg[iarg+1]);
int itype = force->inumeric(FLERR,arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid basis setting in create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"yes") == 0) remapflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1) error->all(FLERR,"Molecule template ID for "
"create_atoms does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"create_atoms has multiple molecules");
mode = MOLECULE;
onemol = atom->molecules[imol];
molseed = force->inumeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms 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 create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"var") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
delete [] vstr;
int n = strlen(arg[iarg+1]) + 1;
vstr = new char[n];
strcpy(vstr,arg[iarg+1]);
varflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"set") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"x") == 0) {
delete [] xstr;
int n = strlen(arg[iarg+2]) + 1;
xstr = new char[n];
strcpy(xstr,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"y") == 0) {
delete [] ystr;
int n = strlen(arg[iarg+2]) + 1;
ystr = new char[n];
strcpy(ystr,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"z") == 0) {
delete [] zstr;
int n = strlen(arg[iarg+2]) + 1;
zstr = new char[n];
strcpy(zstr,arg[iarg+2]);
} else error->all(FLERR,"Illegal create_atoms command");
iarg += 3;
} else if (strcmp(arg[iarg],"rotate") == 0) {
if (style != SINGLE)
error->all(FLERR,"Cannot use create_atoms rotate unless single style");
if (iarg+5 > narg) error->all(FLERR,"Illegal create_atoms command");
double thetaone;
double axisone[3];
thetaone = force->numeric(FLERR,arg[iarg+1]);
axisone[0] = force->numeric(FLERR,arg[iarg+2]);
axisone[1] = force->numeric(FLERR,arg[iarg+3]);
axisone[2] = force->numeric(FLERR,arg[iarg+4]);
if (axisone[0] == 0.0 && axisone[1] == 0.0 && axisone[2] == 0.0)
error->all(FLERR,"Illegal create_atoms command");
if (domain->dimension == 2 && (axisone[0] != 0.0 || axisone[1] != 0.0))
error->all(FLERR,"Invalid create_atoms rotation vector for 2d model");
MathExtra::norm3(axisone);
MathExtra::axisangle_to_quat(axisone,thetaone,quatone);
iarg += 5;
} else error->all(FLERR,"Illegal create_atoms command");
}
// error checks
if (mode == ATOM && (ntype <= 0 || ntype > atom->ntypes))
error->all(FLERR,"Invalid atom type in create_atoms command");
if (style == RANDOM) {
if (nrandom < 0) error->all(FLERR,"Illegal create_atoms command");
if (seed <= 0) error->all(FLERR,"Illegal create_atoms command");
}
// error check and further setup for mode = MOLECULE
ranmol = NULL;
if (mode == MOLECULE) {
if (onemol->xflag == 0)
error->all(FLERR,"Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Create_atoms molecule must have atom types");
if (ntype+onemol->ntypes <= 0 || ntype+onemol->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms mol command");
if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR,
"Create_atoms molecule has atom IDs, but system does not");
onemol->check_attributes(0);
// create_atoms uses geoemetric center of molecule for insertion
onemol->compute_center();
// molecule random number generator, different for each proc
ranmol = new RanMars(lmp,molseed+comm->me);
}
// error check and further setup for variable test
if (!vstr && (xstr || ystr || zstr))
error->all(FLERR,"Incomplete use of variables in create_atoms command");
if (vstr && (!xstr && !ystr && !zstr))
error->all(FLERR,"Incomplete use of variables in create_atoms command");
if (varflag) {
vvar = input->variable->find(vstr);
if (vvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->equalstyle(vvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->internalstyle(xvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->internalstyle(yvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->internalstyle(zvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
}
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
if (style == BOX || style == REGION) {
if (nbasis == 0)
error->all(FLERR,"Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
}
// set bounds for my proc in sublo[3] & subhi[3]
// if periodic and style = BOX or REGION, i.e. using lattice:
// should create exactly 1 atom when 2 images are both "on" the boundary
// either image may be slightly inside/outside true box due to round-off
// if I am lo proc, decrement lower bound by EPSILON
// this will insure lo image is created
// if I am hi proc, decrement upper bound by 2.0*EPSILON
// this will insure hi image is not created
// thus insertion box is EPSILON smaller than true box
// and is shifted away from true boundary
// which is where atoms are likely to be generated
triclinic = domain->triclinic;
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (style == BOX || style == REGION) {
if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
}
} else {
if (domain->xperiodic) {
if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0];
if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1];
if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2];
if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2];
}
}
}
// Record wall time for atom creation
MPI_Barrier(world);
double time1 = MPI_Wtime();
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c creating atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// add atoms/molecules in one of 3 ways
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
if (style == SINGLE) add_single();
else if (style == RANDOM) add_random();
else add_lattice();
// init per-atom fix/compute/variable values for created atoms
atom->data_fix_compute_variable(nlocal_previous,atom->nlocal);
// set new total # of atoms and error check
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
error->all(FLERR,"Too many total atoms");
// add IDs for newly created atoms
// check that atom IDs are valid
if (atom->tag_enable) atom->tag_extend();
atom->tag_check();
// if global map exists, reset it
// invoke map_init() b/c atom count has grown
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
// for MOLECULE mode:
// molecule can mean just a mol ID or bonds/angles/etc or mol templates
// set molecule IDs for created atoms if atom->molecule_flag is set
// reset new molecule bond,angle,etc and special values if defined
// send atoms to new owning procs via irregular comm
// since not all atoms I created will be within my sub-domain
// perform special list build if needed
if (mode == MOLECULE) {
int molecule_flag = atom->molecule_flag;
int molecular = atom->molecular;
tagint *molecule = atom->molecule;
// molcreate = # of molecules I created
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
// increment total bonds,angles,etc
bigint nmolme = molcreate;
bigint nmoltotal;
MPI_Allreduce(&nmolme,&nmoltotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
atom->nbonds += nmoltotal * onemol->nbonds;
atom->nangles += nmoltotal * onemol->nangles;
atom->ndihedrals += nmoltotal * onemol->ndihedrals;
atom->nimpropers += nmoltotal * onemol->nimpropers;
// if atom style template
// maxmol = max molecule ID across all procs, for previous atoms
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
tagint moloffset;
if (molecule_flag) {
tagint max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
tagint maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_LMP_TAGINT,MPI_MAX,world);
MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
moloffset = moloffset - molcreate + maxmol;
}
// loop over molecules I created
// set their molecule ID
// reset their bond,angle,etc and special values
int natoms = onemol->natoms;
tagint offset = 0;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int *num_improper = atom->num_improper;
tagint **bond_atom = atom->bond_atom;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
tagint **improper_atom1 = atom->improper_atom1;
tagint **improper_atom2 = atom->improper_atom2;
tagint **improper_atom3 = atom->improper_atom3;
tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
if (tag) offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) {
if (molecule_flag) molecule[ilocal] = moloffset + i+1;
if (molecular == 2) {
atom->molindex[ilocal] = 0;
atom->molatom[ilocal] = m;
} else if (molecular) {
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
if (onemol->angleflag)
for (int j = 0; j < num_angle[ilocal]; j++) {
angle_atom1[ilocal][j] += offset;
angle_atom2[ilocal][j] += offset;
angle_atom3[ilocal][j] += offset;
}
if (onemol->dihedralflag)
for (int j = 0; j < num_dihedral[ilocal]; j++) {
dihedral_atom1[ilocal][j] += offset;
dihedral_atom2[ilocal][j] += offset;
dihedral_atom3[ilocal][j] += offset;
dihedral_atom4[ilocal][j] += offset;
}
if (onemol->improperflag)
for (int j = 0; j < num_improper[ilocal]; j++) {
improper_atom1[ilocal][j] += offset;
improper_atom2[ilocal][j] += offset;
improper_atom3[ilocal][j] += offset;
improper_atom4[ilocal][j] += offset;
}
if (onemol->specialflag)
for (int j = 0; j < nspecial[ilocal][2]; j++)
special[ilocal][j] += offset;
}
ilocal++;
}
}
// perform irregular comm to migrate atoms to new owning procs
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int 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(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// clean up
delete ranmol;
if (domain->lattice) delete [] basistype;
delete [] vstr;
delete [] xstr;
delete [] ystr;
delete [] zstr;
// for MOLECULE mode:
// create special bond lists for molecular systems,
// but not for atom style template
// only if onemol added bonds but not special info
if (mode == MOLECULE) {
if (atom->molecular == 1 && onemol->bondflag && !onemol->specialflag) {
Special special(lmp);
special.build();
}
}
// print status
MPI_Barrier(world);
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(screen," create_atoms CPU = %g secs\n",time2-time1);
}
if (logfile) {
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(logfile," create_atoms CPU = %g secs\n",time2-time1);
}
}
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
int style;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else if (strcmp(arg[1],"rotate") == 0) style = ROTATE;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
else if (style == ROTATE) options(narg-9,&arg[9]);
// setup scaling
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
if (style == MOVE) {
double delx = xscale*atof(arg[2]);
double dely = yscale*atof(arg[3]);
double delz = zscale*atof(arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*atof(arg[3]);
d_hi = xscale*atof(arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*atof(arg[3]);
d_hi = yscale*atof(arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*atof(arg[3]);
d_hi = zscale*atof(arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[6]);
coord_hi = xscale*atof(arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[6]);
coord_hi = yscale*atof(arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[6]);
coord_hi = zscale*atof(arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*atof(arg[2]);
double dy = yscale*atof(arg[3]);
double dz = zscale*atof(arg[4]);
int seed = atoi(arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if (style == ROTATE) {
double axis[3],point[3];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
int dim = domain->dimension;
point[0] = xscale*atof(arg[2]);
point[1] = yscale*atof(arg[3]);
point[2] = zscale*atof(arg[4]);
axis[0] = atof(arg[5]);
axis[1] = atof(arg[6]);
axis[2] = atof(arg[7]);
double theta = atof(arg[8]);
if (dim == 2 and (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Invalid displace_atoms rotate axis for 2d");
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Zero length rotation vector with displace_atoms");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
double sine = sin(MY_PI*theta/180.0);
double cosine = cos(MY_PI*theta/180.0);
double ddotr;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
d[0] = x[i][0] - point[0];
d[1] = x[i][1] - point[1];
d[2] = x[i][2] - point[2];
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x[i][0] = point[0] + c[0] + disp[0];
x[i][1] = point[1] + c[1] + disp[1];
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
tagint *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
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
void Balance::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Balance command before simulation box is defined");
if (me == 0 && screen) fprintf(screen,"Balancing ...\n");
// parse required arguments
if (narg < 2) error->all(FLERR,"Illegal balance command");
thresh = force->numeric(FLERR,arg[0]);
int dimension = domain->dimension;
int *procgrid = comm->procgrid;
style = -1;
xflag = yflag = zflag = NONE;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
xflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[0]-1 > narg)
error->all(FLERR,"Illegal balance command");
xflag = USER;
delete [] user_xsplit;
user_xsplit = new double[procgrid[0]+1];
user_xsplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[0]; i++)
user_xsplit[i] = force->numeric(FLERR,arg[iarg++]);
user_xsplit[procgrid[0]] = 1.0;
}
} else if (strcmp(arg[iarg],"y") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
yflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[1]-1 > narg)
error->all(FLERR,"Illegal balance command");
yflag = USER;
delete [] user_ysplit;
user_ysplit = new double[procgrid[1]+1];
user_ysplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[1]; i++)
user_ysplit[i] = force->numeric(FLERR,arg[iarg++]);
user_ysplit[procgrid[1]] = 1.0;
}
} else if (strcmp(arg[iarg],"z") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
zflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[2]-1 > narg)
error->all(FLERR,"Illegal balance command");
zflag = USER;
delete [] user_zsplit;
user_zsplit = new double[procgrid[2]+1];
user_zsplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[2]; i++)
user_zsplit[i] = force->numeric(FLERR,arg[iarg++]);
user_zsplit[procgrid[2]] = 1.0;
}
} else if (strcmp(arg[iarg],"shift") == 0) {
if (style != -1) error->all(FLERR,"Illegal balance command");
if (iarg+4 > narg) error->all(FLERR,"Illegal balance command");
style = SHIFT;
if (strlen(arg[iarg+1]) > 3) error->all(FLERR,"Illegal balance command");
strcpy(bstr,arg[iarg+1]);
nitermax = force->inumeric(FLERR,arg[iarg+2]);
if (nitermax <= 0) error->all(FLERR,"Illegal balance command");
stopthresh = force->numeric(FLERR,arg[iarg+3]);
if (stopthresh < 1.0) error->all(FLERR,"Illegal balance command");
iarg += 4;
} else if (strcmp(arg[iarg],"rcb") == 0) {
if (style != -1) error->all(FLERR,"Illegal balance command");
style = BISECTION;
iarg++;
} else break;
}
// error checks
if (style == XYZ) {
if (zflag != NONE && dimension == 2)
error->all(FLERR,"Cannot balance in z dimension for 2d simulation");
if (xflag == USER)
for (int i = 1; i <= procgrid[0]; i++)
if (user_xsplit[i-1] >= user_xsplit[i])
error->all(FLERR,"Illegal balance command");
if (yflag == USER)
for (int i = 1; i <= procgrid[1]; i++)
if (user_ysplit[i-1] >= user_ysplit[i])
error->all(FLERR,"Illegal balance command");
if (zflag == USER)
for (int i = 1; i <= procgrid[2]; i++)
if (user_zsplit[i-1] >= user_zsplit[i])
error->all(FLERR,"Illegal balance command");
}
if (style == SHIFT) {
const int blen=strlen(bstr);
for (int i = 0; i < blen; i++) {
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
error->all(FLERR,"Balance shift string is invalid");
if (bstr[i] == 'z' && dimension == 2)
error->all(FLERR,"Balance shift string is invalid");
for (int j = i+1; j < blen; j++)
if (bstr[i] == bstr[j])
error->all(FLERR,"Balance shift string is invalid");
}
}
if (style == BISECTION && comm->style == 0)
error->all(FLERR,"Balance rcb cannot be used with comm_style brick");
// process remaining optional args
options(iarg,narg,arg);
if (wtflag) weight_storage(NULL);
// insure particles are in current box & update box via shrink-wrap
// init entire system since comm->setup is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
// must reset atom map after exchange() since it clears it
MPI_Barrier(world);
double start_time = MPI_Wtime();
lmp->init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
if (atom->map_style) atom->map_set();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// imbinit = initial imbalance
double maxinit;
init_imbalance(0);
set_weights();
double imbinit = imbalance_factor(maxinit);
// no load-balance if imbalance doesn't exceed threshold
// unless switching from tiled to non tiled layout, then force rebalance
if (comm->layout == LAYOUT_TILED && style != BISECTION) {
} else if (imbinit < thresh) return;
// debug output of initial state
#ifdef BALANCE_DEBUG
if (outflag) dumpout(update->ntimestep);
#endif
int niter = 0;
// perform load-balance
// style XYZ = explicit setting of cutting planes of logical 3d grid
if (style == XYZ) {
if (comm->layout == LAYOUT_UNIFORM) {
if (xflag == USER || yflag == USER || zflag == USER)
comm->layout = LAYOUT_NONUNIFORM;
} else if (comm->layout == LAYOUT_NONUNIFORM) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
comm->layout = LAYOUT_UNIFORM;
} else if (comm->layout == LAYOUT_TILED) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
comm->layout = LAYOUT_UNIFORM;
else comm->layout = LAYOUT_NONUNIFORM;
}
if (xflag == UNIFORM) {
for (int i = 0; i < procgrid[0]; i++)
comm->xsplit[i] = i * 1.0/procgrid[0];
comm->xsplit[procgrid[0]] = 1.0;
} else if (xflag == USER)
for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i];
if (yflag == UNIFORM) {
for (int i = 0; i < procgrid[1]; i++)
comm->ysplit[i] = i * 1.0/procgrid[1];
comm->ysplit[procgrid[1]] = 1.0;
} else if (yflag == USER)
for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i];
if (zflag == UNIFORM) {
for (int i = 0; i < procgrid[2]; i++)
comm->zsplit[i] = i * 1.0/procgrid[2];
comm->zsplit[procgrid[2]] = 1.0;
} else if (zflag == USER)
for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i];
}
// style SHIFT = adjust cutting planes of logical 3d grid
if (style == SHIFT) {
comm->layout = LAYOUT_NONUNIFORM;
shift_setup_static(bstr);
niter = shift();
}
// style BISECTION = recursive coordinate bisectioning
if (style == BISECTION) {
comm->layout = LAYOUT_TILED;
bisection(1);
}
// reset proc sub-domains
// for either brick or tiled comm style
if (domain->triclinic) domain->set_lamda_box();
domain->set_local_box();
// move particles to new processors via irregular()
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
if (wtflag) fixstore->disable = 0;
if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc);
else irregular->migrate_atoms(1);
if (wtflag) fixstore->disable = 1;
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// output of final result
if (outflag) dumpout(update->ntimestep);
// check if any particles 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 balance: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(FLERR,str);
}
// imbfinal = final imbalance
double maxfinal;
double imbfinal = imbalance_factor(maxfinal);
// stats output
double stop_time = MPI_Wtime();
if (me == 0) {
if (screen) {
fprintf(screen," rebalancing time: %g seconds\n",stop_time-start_time);
fprintf(screen," iteration count = %d\n",niter);
for (int i = 0; i < nimbalance; ++i) imbalances[i]->info(screen);
fprintf(screen," initial/final max load/proc = %g %g\n",
maxinit,maxfinal);
fprintf(screen," initial/final imbalance factor = %g %g\n",
imbinit,imbfinal);
}
if (logfile) {
fprintf(logfile," rebalancing time: %g seconds\n",stop_time-start_time);
fprintf(logfile," iteration count = %d\n",niter);
for (int i = 0; i < nimbalance; ++i) imbalances[i]->info(logfile);
fprintf(logfile," initial/final max load/proc = %g %g\n",
maxinit,maxfinal);
fprintf(logfile," initial/final imbalance factor = %g %g\n",
imbinit,imbfinal);
}
}
if (style != BISECTION) {
if (me == 0) {
if (screen) {
fprintf(screen," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
fprintf(screen," %g",comm->xsplit[i]);
fprintf(screen,"\n");
fprintf(screen," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
fprintf(screen," %g",comm->ysplit[i]);
fprintf(screen,"\n");
fprintf(screen," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
fprintf(screen," %g",comm->zsplit[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
fprintf(logfile," %g",comm->xsplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
fprintf(logfile," %g",comm->ysplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
fprintf(logfile," %g",comm->zsplit[i]);
fprintf(logfile,"\n");
}
}
}
}