diff --git a/src/Makefile.package b/src/Makefile.package index 0c8aa9d85..c52fa151c 100644 --- a/src/Makefile.package +++ b/src/Makefile.package @@ -1,9 +1,9 @@ # Settings for libraries used by specific LAMMPS packages # this file is auto-edited when those packages are included/excluded -PKG_INC = -I../../lib/reax -I../../lib/poems -I../../lib/meam -PKG_PATH = -L../../lib/reax -L../../lib/poems -L../../lib/meam -PKG_LIB = -lreax -lpoems -lmeam +PKG_INC = -I../../lib/atc -I../../lib/reax -I../../lib/poems -I../../lib/meam +PKG_PATH = -L../../lib/atc -L../../lib/reax -L../../lib/poems -L../../lib/meam +PKG_LIB = -latc -lreax -lpoems -lmeam -PKG_SYSPATH = $(reax_SYSPATH) $(meam_SYSPATH) -PKG_SYSLIB = $(reax_SYSLIB) $(meam_SYSLIB) +PKG_SYSPATH = $(user-atc_SYSPATH) $(reax_SYSPATH) $(meam_SYSPATH) +PKG_SYSLIB = $(user-atc_SYSLIB) $(reax_SYSLIB) $(meam_SYSLIB) diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 04591e68d..daa783fa4 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -1,750 +1,753 @@ /* ---------------------------------------------------------------------- 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 "stdlib.h" #include "string.h" #include "atom_vec_hybrid.h" #include "atom.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; #define MIN(A,B) ((A) < (B)) ? (A) : (B) #define MAX(A,B) ((A) > (B)) ? (A) : (B) #define DELTA 10000 /* ---------------------------------------------------------------------- */ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) : AtomVec(lmp, narg, arg) { int i,k; if (narg < 1) error->all("Illegal atom_style command"); // create sub-styles nstyles = narg; styles = new AtomVec*[nstyles]; keywords = new char*[nstyles]; for (i = 0; i < narg; i++) { for (k = 0; k < i; k++) if (strcmp(arg[i],keywords[k]) == 0) error->all("Atom style hybrid cannot use same atom style twice"); if (strcmp(arg[i],"hybrid") == 0) error->all("Atom style hybrid cannot have hybrid as an argument"); styles[i] = atom->new_avec(arg[i],0,NULL); keywords[i] = new char[strlen(arg[i])+1]; strcpy(keywords[i],arg[i]); } // hybrid settings are MAX or MIN of sub-style settings // hybrid sizes are minimial values plus extra values for each sub-style + molecular = 0; + comm_x_only = comm_f_only = 1; + size_forward = 3; size_reverse = 3; size_border = 6; size_data_atom = 5; size_data_vel = 4; xcol_data = 3; for (k = 0; k < nstyles; k++) { molecular = MAX(molecular,styles[k]->molecular); bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow); angles_allow = MAX(angles_allow,styles[k]->angles_allow); dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow); impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow); mass_type = MAX(mass_type,styles[k]->mass_type); shape_type = MAX(shape_type,styles[k]->shape_type); dipole_type = MAX(dipole_type,styles[k]->dipole_type); comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only); comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only); size_forward += styles[k]->size_forward - 3; size_reverse += styles[k]->size_reverse - 3; size_border += styles[k]->size_border - 6; size_data_atom += styles[k]->size_data_atom - 5; size_data_vel += styles[k]->size_data_vel - 4; } size_velocity = 3; if (atom->omega_flag) size_velocity += 3; if (atom->angmom_flag) size_velocity += 3; } /* ---------------------------------------------------------------------- */ AtomVecHybrid::~AtomVecHybrid() { for (int k = 0; k < nstyles; k++) delete styles[k]; delete [] styles; for (int k = 0; k < nstyles; k++) delete [] keywords[k]; delete [] keywords; } /* ---------------------------------------------------------------------- grow atom arrays n = 0 grows arrays by DELTA n > 0 allocates arrays to size n ------------------------------------------------------------------------- */ void AtomVecHybrid::grow(int n) { if (n == 0) nmax += DELTA; else nmax = n; atom->nmax = nmax; int tmp = atom->nextra_grow; atom->nextra_grow = 0; for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax); atom->nextra_grow = tmp; // pointers for arrays used directly by hybrid style tag = atom->tag; type = atom->type; mask = atom->mask; image = atom->image; x = atom->x; v = atom->v; f = atom->f; omega = atom->omega; angmom = atom->angmom; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::reset_special() { for (int k = 0; k < nstyles; k++) styles[k]->reset_special(); } /* ---------------------------------------------------------------------- copy array values for all sub-styles ------------------------------------------------------------------------- */ void AtomVecHybrid::copy(int i, int j) { int tmp = atom->nextra_grow; atom->nextra_grow = 0; for (int k = 0; k < nstyles; k++) styles[k]->copy(i,j); atom->nextra_grow = tmp; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j); } /* ---------------------------------------------------------------------- */ int AtomVecHybrid::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { int i,j,k,m; double dx,dy,dz; m = 0; if (pbc_flag == 0) { for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0]; buf[m++] = x[j][1]; buf[m++] = x[j][2]; for (k = 0; k < nstyles; k++) m += styles[k]->pack_comm_one(j,&buf[m]); } } else { if (domain->triclinic == 0) { dx = pbc[0]*domain->xprd; dy = pbc[1]*domain->yprd; dz = pbc[2]*domain->zprd; } else { dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; dz = pbc[2]*domain->zprd; } for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0] + dx; buf[m++] = x[j][1] + dy; buf[m++] = x[j][2] + dz; for (k = 0; k < nstyles; k++) m += styles[k]->pack_comm_one(j,&buf[m]); } } return m; } /* ---------------------------------------------------------------------- */ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) { int i,j,k,m; double dx,dy,dz; int omega_flag = atom->omega_flag; int angmom_flag = atom->angmom_flag; m = 0; if (pbc_flag == 0) { for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0]; buf[m++] = x[j][1]; buf[m++] = x[j][2]; buf[m++] = v[j][0]; buf[m++] = v[j][1]; buf[m++] = v[j][2]; if (omega_flag) { buf[m++] = omega[j][0]; buf[m++] = omega[j][1]; buf[m++] = omega[j][2]; } if (angmom_flag) { buf[m++] = angmom[j][0]; buf[m++] = angmom[j][1]; buf[m++] = angmom[j][2]; } for (k = 0; k < nstyles; k++) m += styles[k]->pack_comm_one(j,&buf[m]); } } else { if (domain->triclinic == 0) { dx = pbc[0]*domain->xprd; dy = pbc[1]*domain->yprd; dz = pbc[2]*domain->zprd; } else { dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; dz = pbc[2]*domain->zprd; } for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0] + dx; buf[m++] = x[j][1] + dy; buf[m++] = x[j][2] + dz; buf[m++] = v[j][0]; buf[m++] = v[j][1]; buf[m++] = v[j][2]; if (omega_flag) { buf[m++] = omega[j][0]; buf[m++] = omega[j][1]; buf[m++] = omega[j][2]; } if (angmom_flag) { buf[m++] = angmom[j][0]; buf[m++] = angmom[j][1]; buf[m++] = angmom[j][2]; } for (k = 0; k < nstyles; k++) m += styles[k]->pack_comm_one(j,&buf[m]); } } return m; } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::unpack_comm(int n, int first, double *buf) { int i,k,last; int m = 0; last = first + n; for (i = first; i < last; i++) { x[i][0] = buf[m++]; x[i][1] = buf[m++]; x[i][2] = buf[m++]; for (k = 0; k < nstyles; k++) m += styles[k]->unpack_comm_one(i,&buf[m]); } } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::unpack_comm_vel(int n, int first, double *buf) { int i,k,last; int omega_flag = atom->omega_flag; int angmom_flag = atom->angmom_flag; int m = 0; last = first + n; for (i = first; i < last; i++) { x[i][0] = buf[m++]; x[i][1] = buf[m++]; x[i][2] = buf[m++]; v[i][0] = buf[m++]; v[i][1] = buf[m++]; v[i][2] = buf[m++]; if (omega_flag) { omega[i][0] = buf[m++]; omega[i][1] = buf[m++]; omega[i][2] = buf[m++]; } if (angmom_flag) { angmom[i][0] = buf[m++]; angmom[i][1] = buf[m++]; angmom[i][2] = buf[m++]; } for (k = 0; k < nstyles; k++) m += styles[k]->unpack_comm_one(i,&buf[m]); } } /* ---------------------------------------------------------------------- */ int AtomVecHybrid::pack_reverse(int n, int first, double *buf) { int i,k,last; int m = 0; last = first + n; for (i = first; i < last; i++) { buf[m++] = f[i][0]; buf[m++] = f[i][1]; buf[m++] = f[i][2]; for (k = 0; k < nstyles; k++) m += styles[k]->pack_reverse_one(i,&buf[m]); } return m; } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf) { int i,j,k,m; m = 0; for (i = 0; i < n; i++) { j = list[i]; f[j][0] += buf[m++]; f[j][1] += buf[m++]; f[j][2] += buf[m++]; for (k = 0; k < nstyles; k++) m += styles[k]->unpack_reverse_one(j,&buf[m]); } } /* ---------------------------------------------------------------------- */ int AtomVecHybrid::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) { int i,j,k,m; double dx,dy,dz; m = 0; if (pbc_flag == 0) { for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0]; buf[m++] = x[j][1]; buf[m++] = x[j][2]; buf[m++] = tag[j]; buf[m++] = type[j]; buf[m++] = mask[j]; for (k = 0; k < nstyles; k++) m += styles[k]->pack_border_one(j,&buf[m]); } } else { if (domain->triclinic == 0) { dx = pbc[0]*domain->xprd; dy = pbc[1]*domain->yprd; dz = pbc[2]*domain->zprd; } else { dx = pbc[0]; dy = pbc[1]; dz = pbc[2]; } for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0] + dx; buf[m++] = x[j][1] + dy; buf[m++] = x[j][2] + dz; buf[m++] = tag[j]; buf[m++] = type[j]; buf[m++] = mask[j]; for (k = 0; k < nstyles; k++) m += styles[k]->pack_border_one(j,&buf[m]); } } return m; } /* ---------------------------------------------------------------------- */ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) { int i,j,k,m; double dx,dy,dz; int omega_flag = atom->omega_flag; int angmom_flag = atom->angmom_flag; m = 0; if (pbc_flag == 0) { for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0]; buf[m++] = x[j][1]; buf[m++] = x[j][2]; buf[m++] = tag[j]; buf[m++] = type[j]; buf[m++] = mask[j]; buf[m++] = v[j][0]; buf[m++] = v[j][1]; buf[m++] = v[j][2]; if (omega_flag) { buf[m++] = omega[j][0]; buf[m++] = omega[j][1]; buf[m++] = omega[j][2]; } if (angmom_flag) { buf[m++] = angmom[j][0]; buf[m++] = angmom[j][1]; buf[m++] = angmom[j][2]; } for (k = 0; k < nstyles; k++) m += styles[k]->pack_border_one(j,&buf[m]); } } else { if (domain->triclinic == 0) { dx = pbc[0]*domain->xprd; dy = pbc[1]*domain->yprd; dz = pbc[2]*domain->zprd; } else { dx = pbc[0]; dy = pbc[1]; dz = pbc[2]; } for (i = 0; i < n; i++) { j = list[i]; buf[m++] = x[j][0] + dx; buf[m++] = x[j][1] + dy; buf[m++] = x[j][2] + dz; buf[m++] = tag[j]; buf[m++] = type[j]; buf[m++] = mask[j]; buf[m++] = v[j][0]; buf[m++] = v[j][1]; buf[m++] = v[j][2]; if (omega_flag) { buf[m++] = omega[j][0]; buf[m++] = omega[j][1]; buf[m++] = omega[j][2]; } if (angmom_flag) { buf[m++] = angmom[j][0]; buf[m++] = angmom[j][1]; buf[m++] = angmom[j][2]; } for (k = 0; k < nstyles; k++) m += styles[k]->pack_border_one(j,&buf[m]); } } return m; } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::unpack_border(int n, int first, double *buf) { int i,k,m,last; m = 0; last = first + n; for (i = first; i < last; i++) { if (i == nmax) grow(0); x[i][0] = buf[m++]; x[i][1] = buf[m++]; x[i][2] = buf[m++]; tag[i] = static_cast<int> (buf[m++]); type[i] = static_cast<int> (buf[m++]); mask[i] = static_cast<int> (buf[m++]); for (k = 0; k < nstyles; k++) m += styles[k]->unpack_border_one(i,&buf[m]); } } /* ---------------------------------------------------------------------- */ void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf) { int i,k,m,last; int omega_flag = atom->omega_flag; int angmom_flag = atom->angmom_flag; m = 0; last = first + n; for (i = first; i < last; i++) { if (i == nmax) grow(0); x[i][0] = buf[m++]; x[i][1] = buf[m++]; x[i][2] = buf[m++]; tag[i] = static_cast<int> (buf[m++]); type[i] = static_cast<int> (buf[m++]); mask[i] = static_cast<int> (buf[m++]); v[i][0] = buf[m++]; v[i][1] = buf[m++]; v[i][2] = buf[m++]; if (omega_flag) { omega[i][0] = buf[m++]; omega[i][1] = buf[m++]; omega[i][2] = buf[m++]; } if (angmom_flag) { angmom[i][0] = buf[m++]; angmom[i][1] = buf[m++]; angmom[i][2] = buf[m++]; } for (k = 0; k < nstyles; k++) m += styles[k]->unpack_border_one(i,&buf[m]); } } /* ---------------------------------------------------------------------- pack data for atom I for sending to another proc pack each sub-style one after the other ------------------------------------------------------------------------- */ int AtomVecHybrid::pack_exchange(int i, double *buf) { int k; int tmp = atom->nextra_grow; atom->nextra_grow = 0; int m = 0; for (k = 0; k < nstyles; k++) m += styles[k]->pack_exchange(i,&buf[m]); atom->nextra_grow = tmp; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); buf[0] = m; return m; } /* ---------------------------------------------------------------------- unpack data for single atom received from another proc unpack each sub-style one after the other grow() occurs here so arrays for all sub-styles are grown ------------------------------------------------------------------------- */ int AtomVecHybrid::unpack_exchange(double *buf) { int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); int tmp = atom->nextra_grow; atom->nextra_grow = 0; int m = 0; for (int k = 0; k < nstyles; k++) { m += styles[k]->unpack_exchange(&buf[m]); atom->nlocal--; } atom->nextra_grow = tmp; if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal,&buf[m]); atom->nlocal++; return m; } /* ---------------------------------------------------------------------- size of restart data for all atoms owned by this proc include extra data stored by fixes ------------------------------------------------------------------------- */ int AtomVecHybrid::size_restart() { int tmp = atom->nextra_restart; atom->nextra_restart = 0; int n = 0; for (int k = 0; k < nstyles; k++) n += styles[k]->size_restart(); atom->nextra_restart = tmp; int nlocal = atom->nlocal; if (atom->nextra_restart) for (int iextra = 0; iextra < atom->nextra_restart; iextra++) for (int i = 0; i < nlocal; i++) n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); return n; } /* ---------------------------------------------------------------------- pack atom I's data for restart file including extra quantities xyz must be 1st 3 values, so that read_restart can test on them pack each sub-style one after the other ------------------------------------------------------------------------- */ int AtomVecHybrid::pack_restart(int i, double *buf) { int tmp = atom->nextra_restart; atom->nextra_restart = 0; int m = 0; for (int k = 0; k < nstyles; k++) m += styles[k]->pack_restart(i,&buf[m]); atom->nextra_restart = tmp; if (atom->nextra_restart) for (int iextra = 0; iextra < atom->nextra_restart; iextra++) m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); buf[0] = m; return m; } /* ---------------------------------------------------------------------- unpack data for one atom from restart file including extra quantities unpack each sub-style one after the other grow() occurs here so arrays for all sub-styles are grown ------------------------------------------------------------------------- */ int AtomVecHybrid::unpack_restart(double *buf) { int nlocal = atom->nlocal; if (nlocal == nmax) { grow(0); if (atom->nextra_store) atom->extra = memory->grow_2d_double_array(atom->extra,nmax, atom->nextra_store, "atom:extra"); } int tmp = atom->nextra_store; atom->nextra_store = 0; int m = 0; for (int k = 0; k < nstyles; k++) { m += styles[k]->unpack_restart(&buf[m]); atom->nlocal--; } atom->nextra_store = tmp; double **extra = atom->extra; if (atom->nextra_store) { int size = static_cast<int> (buf[0]) - m; for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; } atom->nlocal++; return m; } /* ---------------------------------------------------------------------- create one atom of itype at coord create each sub-style one after the other grow() occurs here so arrays for all sub-styles are grown ------------------------------------------------------------------------- */ void AtomVecHybrid::create_atom(int itype, double *coord) { int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); for (int k = 0; k < nstyles; k++) { styles[k]->create_atom(itype,coord); atom->nlocal--; } atom->nlocal++; } /* ---------------------------------------------------------------------- unpack one line from Atoms section of data file grow() occurs here so arrays for all sub-styles are grown ------------------------------------------------------------------------- */ void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values) { int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); tag[nlocal] = atoi(values[0]); if (tag[nlocal] <= 0) error->one("Invalid atom ID in Atoms section of data file"); type[nlocal] = atoi(values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one("Invalid atom type in Atoms section of data file"); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; x[nlocal][2] = coord[2]; image[nlocal] = imagetmp; mask[nlocal] = 1; // each sub-style parses sub-style specific values int m = 5; for (int k = 0; k < nstyles; k++) m += styles[k]->data_atom_hybrid(nlocal,&values[m]); atom->nlocal++; } /* ---------------------------------------------------------------------- unpack one line from Velocities section of data file ------------------------------------------------------------------------- */ void AtomVecHybrid::data_vel(int m, char **values) { v[m][0] = atof(values[0]); v[m][1] = atof(values[1]); v[m][2] = atof(values[2]); // each sub-style parses sub-style specific values int n = 3; for (int k = 0; k < nstyles; k++) n += styles[k]->data_vel_hybrid(m,&values[n]); } /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ double AtomVecHybrid::memory_usage() { double bytes = 0.0; for (int k = 0; k < nstyles; k++) bytes += styles[k]->memory_usage(); return bytes; } diff --git a/src/style_user_ackland.h b/src/style_user_ackland.h index e69de29bb..6e7483a9f 100644 --- a/src/style_user_ackland.h +++ b/src/style_user_ackland.h @@ -0,0 +1,20 @@ +/* ---------------------------------------------------------------------- + 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 ComputeInclude +#include "compute_ackland_atom.h" +#endif + +#ifdef ComputeClass +ComputeStyle(ackland/atom,ComputeAcklandAtom) +#endif diff --git a/src/style_user_ewaldn.h b/src/style_user_ewaldn.h index e69de29bb..3eafa5074 100644 --- a/src/style_user_ewaldn.h +++ b/src/style_user_ewaldn.h @@ -0,0 +1,30 @@ +/* ---------------------------------------------------------------------- + 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 KSpaceInclude +#include "ewald_n.h" +#endif + +#ifdef KSpaceClass +KSpaceStyle(ewald/n,EwaldN) +#endif + +#ifdef PairInclude +#include "pair_buck_coul.h" +#include "pair_lj_coul.h" +#endif + +#ifdef PairClass +PairStyle(buck/coul,PairBuckCoul) +PairStyle(lj/coul,PairLJCoul) +#endif