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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3381 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-11-10 18:24:01 +00:00
parent a64de5f5d0
commit 3f3f82d909
19 changed files with 1110 additions and 1060 deletions
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2
src/MANYBODY/pair_eam.cpp
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@ -225,7 +225,7 @@ void PairEAM::compute(int eflag, int vflag)
// communicate derivative of embedding function
comm->comm_pair(this);
comm->forward_comm_pair(this);
// compute forces on each atom
// loop over neighbors of my atoms

1838
src/MEAM/pair_meam.cpp
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File diff suppressed because it is too large Load Diff

194
src/MEAM/pair_meam.h
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@ -1,97 +1,97 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef PAIR_MEAM_H
#define PAIR_MEAM_H
extern "C" {
void meam_setup_global_(int *, int *, double *, int *, double *, double *,
double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *,
double *, double *, int *);
void meam_setup_param_(int *, double *, int *, int *, int *);
void meam_setup_done_(double *);
void meam_dens_init_(int *, int *, int *, int *, int *,
double *, int *, int *, int *, int *,
double *, double *, double *, double *,
double *, double *,
double *, double *, double *, double *, double *,
int *);
void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
int *, int *, int *,
double *, double *, double *, double *,
double *, double *, double *,
double *, double *, double *, double *,
double *, double *,
double *, double *, double *, double *, int *);
void meam_force_(int *, int *, int *, int *, int *, int *,
double *, double *, int *, int *, int *,
double *, int *, int *, int *, int *, double *, double *,
double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, double *, int *);
void meam_cleanup_();
}
#include "pair.h"
namespace LAMMPS_NS {
class PairMEAM : public Pair {
public:
PairMEAM(class LAMMPS *);
~PairMEAM();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
private:
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
double *mass; // mass of each element
int *map; // mapping from atom types to elements
int *fmap; // Fortran version of map array for MEAM lib
int maxneigh;
double *scrfcn,*dscrfcn,*fcpair;
int nmax;
double *rho,*rho0,*rho1,*rho2,*rho3,*frhop;
double *gamma,*dgamma1,*dgamma2,*dgamma3,*arho2b;
double **arho1,**arho2,**arho3,**arho3b,**t_ave,**tsq_ave;
void allocate();
void read_files(char *, char *);
void neigh_f2c(int, int *, int *, int **);
void neigh_c2f(int, int *, int *, int **);
};
}
#endif
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef PAIR_MEAM_H
#define PAIR_MEAM_H
extern "C" {
void meam_setup_global_(int *, int *, double *, int *, double *, double *,
double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *,
double *, double *, int *);
void meam_setup_param_(int *, double *, int *, int *, int *);
void meam_setup_done_(double *);
void meam_dens_init_(int *, int *, int *, int *, int *,
double *, int *, int *, int *, int *,
double *, double *, double *, double *,
double *, double *,
double *, double *, double *, double *, double *,
int *);
void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
int *, int *, int *,
double *, double *, double *, double *,
double *, double *, double *,
double *, double *, double *, double *,
double *, double *,
double *, double *, double *, double *, int *);
void meam_force_(int *, int *, int *, int *, int *, int *,
double *, double *, int *, int *, int *,
double *, int *, int *, int *, int *, double *, double *,
double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, double *, int *);
void meam_cleanup_();
}
#include "pair.h"
namespace LAMMPS_NS {
class PairMEAM : public Pair {
public:
PairMEAM(class LAMMPS *);
~PairMEAM();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
private:
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
double *mass; // mass of each element
int *map; // mapping from atom types to elements
int *fmap; // Fortran version of map array for MEAM lib
int maxneigh;
double *scrfcn,*dscrfcn,*fcpair;
int nmax;
double *rho,*rho0,*rho1,*rho2,*rho3,*frhop;
double *gamma,*dgamma1,*dgamma2,*dgamma3,*arho2b;
double **arho1,**arho2,**arho3,**arho3b,**t_ave,**tsq_ave;
void allocate();
void read_files(char *, char *);
void neigh_f2c(int, int *, int *, int **);
void neigh_c2f(int, int *, int *, int **);
};
}
#endif

4
src/MOLECULE/fix_bond_break.cpp
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@ -163,7 +163,7 @@ void FixBondBreak::post_integrate()
// need updated ghost atom positions
comm->communicate();
comm->forward_comm();
// resize bond partner list and initialize it
// probability array overlays distsq array
@ -235,7 +235,7 @@ void FixBondBreak::post_integrate()
if (partner[i]) probability[i] = random->uniform();
}
comm->comm_fix(this);
comm->forward_comm_fix(this);
// break bonds
// if both atoms list each other as winning bond partner

6
src/MOLECULE/fix_bond_create.cpp
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@ -273,12 +273,12 @@ void FixBondCreate::post_integrate()
// need updated ghost atom positions
comm->communicate();
comm->forward_comm();
// forward comm of bondcount, so ghosts have it
commflag = 0;
comm->comm_fix(this);
comm->forward_comm_fix(this);
// resize bond partner list and initialize it
// probability array overlays distsq array
@ -376,7 +376,7 @@ void FixBondCreate::post_integrate()
}
commflag = 1;
comm->comm_fix(this);
comm->forward_comm_fix(this);
// create bonds for atoms I own
// if other atom is owned by another proc, it should create same bond

10
src/Makefile.package
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@ -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 -L../../lib/gpu
PKG_LIB = -latc -lreax -lpoems -lmeam -lgpu
PKG_SYSPATH = $(reax_SYSPATH) $(meam_SYSPATH)
PKG_SYSLIB = $(reax_SYSLIB) $(meam_SYSLIB)
PKG_SYSPATH = $(user-atc_SYSPATH) $(reax_SYSPATH) $(meam_SYSPATH) $(gpu_SYSPATH)
PKG_SYSLIB = $(user-atc_SYSLIB) $(reax_SYSLIB) $(meam_SYSLIB) $(gpu_SYSLIB)

2
src/OPT/pair_eam_opt.h
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@ -224,7 +224,7 @@ void PairEAMOpt::eval()
// communicate derivative of embedding function
comm->comm_pair(this);
comm->forward_comm_pair(this);
// compute forces on each atom
// loop over neighbors of my atoms

6
src/REAX/pair_reax.cpp
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@ -168,7 +168,7 @@ void PairREAX::compute(int eflag, int vflag)
// communicate local atomic bond order to ghost atomic bond order
packflag = 0;
comm->comm_pair(this);
comm->forward_comm_pair(this);
FORTRAN(molec, MOLEC)();
FORTRAN(encalc, ENCALC)();
@ -941,7 +941,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
packflag = 1;
comm->reverse_comm_pair(this);
comm->comm_pair(this);
comm->forward_comm_pair(this);
MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
w[n-1] = sumtmp;
@ -978,7 +978,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost,
}
comm->reverse_comm_pair(this);
comm->comm_pair(this);
comm->forward_comm_pair(this);
MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
w[n-1] = sumtmp;

2
src/USER-ATC/fix_atc.cpp
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@ -515,7 +515,7 @@ void FixATC::initial_integrate(int vflag)
void FixATC::final_integrate()
{
// need updated ghost atom positions
comm->comm_fix(this);
comm->forward_comm_fix(this);
try {
atcTransfer_->pre_final_integrate();

4
src/USER-CD-EAM/pair_cdeam.cpp
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@ -193,7 +193,7 @@ void PairCDEAM::compute(int eflag, int vflag)
// Communicate derivative of embedding function and densities
// and D_values (this for one-site formulation only).
communicationStage = 2;
comm->comm_pair(this);
comm->forward_comm_pair(this);
// The electron densities may not drop to zero because then the concentration would no longer be defined.
// But the concentration is not needed anyway if there is no interaction with another atom, which is the case
@ -262,7 +262,7 @@ void PairCDEAM::compute(int eflag, int vflag)
comm->reverse_comm_pair(this);
}
communicationStage = 4;
comm->comm_pair(this);
comm->forward_comm_pair(this);
}
// Stage III

12
src/comm.cpp
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@ -403,11 +403,11 @@ void Comm::setup()
}
/* ----------------------------------------------------------------------
communication of atom coords every timestep
forward communication of atom coords every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void Comm::communicate()
void Comm::forward_comm()
{
int n;
MPI_Request request;
@ -473,7 +473,7 @@ void Comm::communicate()
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void Comm::reverse_communicate()
void Comm::reverse_comm()
{
int n;
MPI_Request request;
@ -808,7 +808,7 @@ void Comm::borders()
forward communication invoked by a Pair
------------------------------------------------------------------------- */
void Comm::comm_pair(Pair *pair)
void Comm::forward_comm_pair(Pair *pair)
{
int iswap,n;
double *buf;
@ -877,7 +877,7 @@ void Comm::reverse_comm_pair(Pair *pair)
forward communication invoked by a Fix
------------------------------------------------------------------------- */
void Comm::comm_fix(Fix *fix)
void Comm::forward_comm_fix(Fix *fix)
{
int iswap,n;
double *buf;
@ -946,7 +946,7 @@ void Comm::reverse_comm_fix(Fix *fix)
forward communication invoked by a Compute
------------------------------------------------------------------------- */
void Comm::comm_compute(Compute *compute)
void Comm::forward_comm_compute(Compute *compute)
{
int iswap,n;
double *buf;

10
src/comm.h
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@ -43,16 +43,16 @@ class Comm : protected Pointers {
void init();
void set_procs(); // setup 3d grid of procs
void setup(); // setup 3d communication pattern
void communicate(); // communication of atom coords
void reverse_communicate(); // reverse communication of forces
void forward_comm(); // forward communication of atom coords
void reverse_comm(); // reverse communication of forces
void exchange(); // move atoms to new procs
void borders(); // setup list of atoms to communicate
void comm_pair(class Pair *); // forward comm from a Pair
void forward_comm_pair(class Pair *); // forward comm from a Pair
void reverse_comm_pair(class Pair *); // reverse comm from a Pair
void comm_fix(class Fix *); // forward comm from a Fix
void forward_comm_fix(class Fix *); // forward comm from a Fix
void reverse_comm_fix(class Fix *); // reverse comm from a Fix
void comm_compute(class Compute *); // forward comm from a Compute
void forward_comm_compute(class Compute *); // forward comm from a Compute
void reverse_comm_compute(class Compute *); // reverse comm from a Compute
void irregular(); // irregular communication across all procs

2
src/fix_orient_fcc.cpp
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@ -335,7 +335,7 @@ void FixOrientFCC::post_force(int vflag)
// communicate to acquire nbr data for ghost atoms
comm->comm_fix(this);
comm->forward_comm_fix(this);
// compute grain boundary force on each owned atom
// skip atoms not in group

4
src/fix_shake.cpp
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@ -503,7 +503,7 @@ void FixShake::post_force(int vflag)
// communicate results if necessary
if (nprocs > 1) comm->comm_fix(this);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup
@ -2331,7 +2331,7 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
// communicate results if necessary
if (nprocs > 1) comm->comm_fix(this);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup

8
src/min.cpp
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@ -233,7 +233,7 @@ void Min::setup()
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup(1);
@ -287,7 +287,7 @@ void Min::setup_minimal(int flag)
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
@ -394,7 +394,7 @@ double Min::energy_force(int resetflag)
if (nflag == 0) {
timer->stamp();
comm->communicate();
comm->forward_comm();
timer->stamp(TIME_COMM);
} else {
if (modify->n_min_pre_exchange) modify->min_pre_exchange();
@ -438,7 +438,7 @@ double Min::energy_force(int resetflag)
}
if (force->newton) {
comm->reverse_communicate();
comm->reverse_comm();
timer->stamp(TIME_COMM);
}

8
src/respa.cpp
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@ -353,7 +353,7 @@ void Respa::setup()
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_communicate();
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
@ -413,7 +413,7 @@ void Respa::setup_minimal(int flag)
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_communicate();
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
@ -513,7 +513,7 @@ void Respa::recurse(int ilevel)
} else if (ilevel == 0) {
timer->stamp();
comm->communicate();
comm->forward_comm();
timer->stamp(TIME_COMM);
}
@ -560,7 +560,7 @@ void Respa::recurse(int ilevel)
}
if (newton[ilevel]) {
comm->reverse_communicate();
comm->reverse_comm();
timer->stamp(TIME_COMM);
}

20
src/style_user_ackland.h
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@ -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

30
src/style_user_ewaldn.h
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@ -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

8
src/verlet.cpp
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@ -115,7 +115,7 @@ void Verlet::setup()
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup(1);
@ -165,7 +165,7 @@ void Verlet::setup_minimal(int flag)
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
}
@ -201,7 +201,7 @@ void Verlet::run(int n)
if (nflag == 0) {
timer->stamp();
comm->communicate();
comm->forward_comm();
timer->stamp(TIME_COMM);
} else {
if (n_pre_exchange) modify->pre_exchange();
@ -250,7 +250,7 @@ void Verlet::run(int n)
// reverse communication of forces
if (force->newton) {
comm->reverse_communicate();
comm->reverse_comm();
timer->stamp(TIME_COMM);
}