jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11393 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-30 18:30:18 +00:00
parent d22a9eab28
commit 1ba04dabf6
33 changed files with 102 additions and 193 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
src/MANYBODY/pair_tersoff_mod.cpp
View File

@ -57,7 +57,7 @@ void PairTersoffMOD::read_file(char *file)
FILE *fp;
if (comm->me == 0) {
fp = fopen(file,"r");
fp = open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open Tersoff potential file %s",file);

4
src/MEAM/pair_meam.cpp
View File

@ -460,7 +460,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
FILE *fp;
if (comm->me == 0) {
fp = fopen(globalfile,"r");
fp = open_potential(globalfile);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open MEAM potential file %s",globalfile);
@ -641,7 +641,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
// open user param file on proc 0
if (comm->me == 0) {
fp = fopen(userfile,"r");
fp = open_potential(userfile);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open MEAM potential file %s",userfile);

2
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
View File

@ -105,10 +105,10 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jtype = type[j];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];

12
src/MPIIO/dump_atom_mpiio.cpp
View File

@ -546,7 +546,7 @@ int DumpAtomMPIIO::convert_string_omp(int n, double *mybuf)
int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
{
MPI_Status mpiStatus;
double *localbuf = mybuf;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -581,7 +581,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none)
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
{
int tid = omp_get_thread_num();
int m=0;
@ -593,7 +593,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4],static_cast<int> (mybuf[bufOffset[tid]+m+5]),static_cast<int> (mybuf[bufOffset[tid]+m+6]),static_cast<int> (mybuf[bufOffset[tid]+m+7]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (localbuf[bufOffset[tid]+m]),static_cast<int> (localbuf[bufOffset[tid]+m+1]),localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4],static_cast<int> (localbuf[bufOffset[tid]+m+5]),static_cast<int> (localbuf[bufOffset[tid]+m+6]),static_cast<int> (localbuf[bufOffset[tid]+m+7]));
m += size_one;
}
}
@ -637,7 +637,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
{
MPI_Status mpiStatus;
double *localbuf = mybuf;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -672,7 +672,7 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none)
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
{
int tid = omp_get_thread_num();
int m=0;
@ -684,7 +684,7 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (localbuf[bufOffset[tid]+m]),static_cast<int> (localbuf[bufOffset[tid]+m+1]),localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4]);
m += size_one;
}
}

10
src/MPIIO/dump_custom_mpiio.cpp
View File

@ -566,7 +566,7 @@ void DumpCustomMPIIO::write_string(int n, double *mybuf)
int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
{
MPI_Status mpiStatus;
double *localbuf = mybuf;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -601,7 +601,7 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none)
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
{
int tid = omp_get_thread_num();
int m=0;
@ -615,11 +615,11 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
for (int j = 0; j < size_one; j++) {
if (vtype[j] == INT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (localbuf[bufOffset[tid]+m]));
else if (vtype[j] == DOUBLE)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],localbuf[bufOffset[tid]+m]);
else if (vtype[j] == STRING)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) localbuf[bufOffset[tid]+m]]);
m ++;
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");

6
src/MPIIO/dump_xyz_mpiio.cpp
View File

@ -308,7 +308,7 @@ void DumpXYZMPIIO::write_string(int n, double *mybuf)
int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
{
MPI_Status mpiStatus;
double *localbuf = mybuf;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -343,7 +343,7 @@ int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none)
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
{
int tid = omp_get_thread_num();
int m=0;
@ -355,7 +355,7 @@ int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,typenames[static_cast<int> (mybuf[bufOffset[tid]+m+1])],mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,typenames[static_cast<int> (localbuf[bufOffset[tid]+m+1])],localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4]);
m += size_one;
}

4
src/Package.sh
View File

@ -78,9 +78,9 @@ elif (test $2 = "diff") then
echo " src/$file does not exist"
elif (! cmp -s $file ../$file) then
echo "************************************************"
echo "diff $1/$file src/$file "
echo "diff -u $1/$file src/$file "
echo "************************************************"
diff $file ../$file
diff -u $file ../$file
fi
done
fi

2
src/Purge.list
View File

@ -24,6 +24,8 @@ pair_dipole_sf.h
pair_dipole_sf.cpp
pair_dipole_sf_omp.h
pair_dipole_sf_omp.cpp
pair_dipole_sf_gpu.h
pair_dipole_sf_gpu.cpp
# deleted on Wed May 8 15:24:36 2013 +0000
compute_spec_atom.cpp
compute_spec_atom.h

2
src/RIGID/fix_shake.cpp
View File

@ -649,8 +649,6 @@ void FixShake::find_clusters()
tagint tagprev;
double massone;
tagint *buf;
MPI_Request request;
MPI_Status status;
if (me == 0 && screen) fprintf(screen,"Finding SHAKE clusters ...\n");

4
src/SHOCK/fix_append_atoms.cpp
View File

@ -315,7 +315,8 @@ int FixAppendAtoms::get_spatial()
if (domain->boxhi[2] - shockfront_loc < spatlead) advance = 1;
delete [] pos,val;
delete [] pos;
delete [] val;
}
advance_sum = 0;
@ -453,7 +454,6 @@ void FixAppendAtoms::pre_exchange()
double x[3];
double *sublo = domain->sublo;
double *subhi = domain->subhi;
double *mass = atom->mass;
int i,j,k,m;
for (k = klo; k <= khi; k++) {

3
src/USER-ATC/fix_atc.cpp
View File

@ -38,6 +38,7 @@
#include "stdio.h"
#include "string.h"
#include <sstream>
#include <string>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -288,7 +289,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
int me = ATC::LammpsInterface::instance()->comm_rank();
string groupName(arg[1]);
std::string groupName(arg[1]);
int igroup = group->find(groupName.c_str());
int atomCount = group->count(igroup);

7
src/USER-LB/fix_lb_rigid_pc_sphere.cpp
View File

@ -1332,7 +1332,7 @@ void FixLbRigidPCSphere::set_xv()
void FixLbRigidPCSphere::pre_neighbor()
{
int original,oldimage,newimage;
imageint original,oldimage,newimage;
for (int ibody = 0; ibody < nbody; ibody++) {
original = imagebody[ibody];
@ -1355,10 +1355,11 @@ void FixLbRigidPCSphere::pre_neighbor()
// adjust image flags of any atom in a rigid body whose xcm was remapped
int *atomimage = atom->image;
imageint *atomimage = atom->image;
int nlocal = atom->nlocal;
int ibody,idim,otherdims;
int ibody;
imageint idim,otherdims;
for (int i = 0; i < nlocal; i++) {
if (body[i] == -1) continue;

2
src/USER-LB/fix_lb_rigid_pc_sphere.h
View File

@ -78,7 +78,7 @@ class FixLbRigidPCSphere : public Fix {
double **torque_fluid;
double **torque_fluid_old;
double **rotate;
int *imagebody; // image flags of xcm of each rigid body
imageint *imagebody; // image flags of xcm of each rigid body
double **fflag; // flag for on/off of center-of-mass force
double **tflag; // flag for on/off of center-of-mass torque

1
src/USER-MISC/angle_cosine_shift_exp.cpp
View File

@ -303,7 +303,6 @@ double AngleCosineShiftExp::single(int type, int i1, int i2, int i3)
double s=sqrt(1.0-c*c);
double cccpsss=c*cost[type]+s*sint[type];
double cssmscc=c*sint[type]-s*cost[type];
if (doExpansion[type])
{

2
src/USER-REAXC/reaxc_ffield.cpp
View File

@ -52,7 +52,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* open force field file */
if ( (fp = fopen( ffield_file, "r" ) ) == NULL ) {
fprintf( stderr, "error opening the force filed file! terminating...\n" );
fprintf( stderr, "error opening the force field file! terminating...\n" );
MPI_Abort( comm, FILE_NOT_FOUND );
}

8
src/USER-REAXC/reaxc_tool_box.cpp
View File

@ -388,7 +388,7 @@ int Allocate_Tokenizer_Space( char **line, char **backup, char ***tokens )
int Tokenize( char* s, char*** tok )
{
char test[MAX_LINE];
char *sep = "\t \n!=";
const char *sep = (const char *)"\t \n!=";
char *word;
int count=0;
@ -405,7 +405,7 @@ int Tokenize( char* s, char*** tok )
/***************** taken from lammps ************************/
/* safe malloc */
void *smalloc( long n, char *name, MPI_Comm comm )
void *smalloc( long n, const char *name, MPI_Comm comm )
{
void *ptr;
@ -428,7 +428,7 @@ void *smalloc( long n, char *name, MPI_Comm comm )
/* safe calloc */
void *scalloc( int n, int size, char *name, MPI_Comm comm )
void *scalloc( int n, int size, const char *name, MPI_Comm comm )
{
void *ptr;
@ -458,7 +458,7 @@ void *scalloc( int n, int size, char *name, MPI_Comm comm )
/* safe free */
void sfree( void *ptr, char *name )
void sfree( void *ptr, const char *name )
{
if( ptr == NULL ) {
fprintf( stderr, "WARNING: trying to free the already NULL pointer %s!\n",

6
src/USER-REAXC/reaxc_tool_box.h
View File

@ -67,8 +67,8 @@ int Allocate_Tokenizer_Space( char**, char**, char*** );
int Tokenize( char*, char*** );
/* from lammps */
void *smalloc( long, char*, MPI_Comm );
void *scalloc( int, int, char*, MPI_Comm );
void sfree( void*, char* );
void *smalloc( long, const char*, MPI_Comm );
void *scalloc( int, int, const char*, MPI_Comm );
void sfree( void*, const char* );
#endif

110
src/balance.cpp
View File

@ -721,116 +721,6 @@ int Balance::adjust(int n, double *split)
return change;
}
/* ----------------------------------------------------------------------
OLD code: for local diffusion method that didn't work as well as RCB
adjust cuts between N slices in a dim via diffusive method
count = atoms per slice
split = current N+1 cuts, with 0.0 and 1.0 at end points
overwrite split with new cuts
diffusion means slices with more atoms than their neighbors "send" atoms,
by moving cut closer to sender, further from receiver
------------------------------------------------------------------------- */
void Balance::old_adjust(int iter, int n, bigint *count, double *split)
{
// need to allocate this if start using it again
double *cuts;
// damping factor
double damp = 0.5;
// loop over slices
// cut I is between 2 slices (I-1 and I) with counts
// cut I+1 is between 2 slices (I and I+1) with counts
// for a cut between 2 slices, only slice with larger count adjusts it
// special treatment of end slices with only 1 neighbor
bigint leftcount,mycount,rightcount;
double rho,target,targetleft,targetright;
for (int i = 0; i < n; i++) {
if (i == 0) leftcount = MAXBIGINT;
else leftcount = count[i-1];
mycount = count[i];
if (i == n-1) rightcount = MAXBIGINT;
else rightcount = count[i+1];
// middle slice is <= both left and right, so do nothing
// special case if 2 slices both have count = 0 -> no change in cut
if (mycount <= leftcount && mycount <= rightcount) {
if (leftcount == 0) cuts[i] = split[i];
if (rightcount == 0) cuts[i+1] = split[i+1];
continue;
}
// rho = density of atoms in the slice
rho = mycount / (split[i+1] - split[i]);
// middle slice has more atoms than left or right slice
// send atoms in that dir
if (mycount > leftcount) {
target = damp * 0.5*(mycount-leftcount);
cuts[i] = split[i] + target/rho;
}
if (mycount > rightcount) {
target = damp * 0.5*(mycount-rightcount);
cuts[i+1] = split[i+1] - target/rho;
}
/*
// middle slice has more atoms then left or right slice
// if delta from middle to top slice > delta between top and bottom slice
// then send atoms both dirs to bring all 3 slices to same count
// else bottom slice is very low, so send atoms only in that dir
if (mycount > leftcount && mycount > rightcount) {
if (mycount-MAX(leftcount,rightcount) >= fabs(leftcount-rightcount)) {
if (leftcount <= rightcount) {
targetleft = damp *
(rightcount-leftcount + (mycount-rightcount)/3.0);
targetright = damp * (mycount-rightcount)/3.0;
cuts[i] = split[i] + targetleft/rho;
cuts[i+1] = split[i+1] - targetright/rho;
} else {
targetleft = damp * (mycount-leftcount)/3.0;
targetright = damp *
(leftcount-rightcount + (mycount-leftcount)/3.0);
cuts[i] = split[i] + targetleft/rho;
cuts[i+1] = split[i+1] - targetright/rho;
}
} else if (leftcount < rightcount) {
target = damp * 0.5*(mycount-leftcount);
cuts[i] = split[i] + target/rho;
cuts[i+1] = split[i+1];
} else if (rightcount < leftcount) {
target = damp * 0.5*(mycount-rightcount);
cuts[i+1] = split[i+1] - target/rho;
cuts[i] = split[i];
}
// middle slice has more atoms than only left or right slice
// send atoms only in that dir
} else if (mycount > leftcount) {
target = damp * 0.5*(mycount-leftcount);
cuts[i] = split[i] + target/rho;
} else if (mycount > rightcount) {
target = damp * 0.5*(mycount-rightcount);
cuts[i+1] = split[i+1] - target/rho;
}
*/
}
// overwrite adjustable splits with new cuts
for (int i = 1; i < n; i++) split[i] = cuts[i];
}
/* ----------------------------------------------------------------------
binary search for where value falls in N-length vec
note that vec actually has N+1 values, but ignore last one

1
src/balance.h
View File

@ -68,7 +68,6 @@ class Balance : protected Pointers {
double imbalance_splits(int &);
void tally(int, int, double *);
int adjust(int, double *);
void old_adjust(int, int, bigint *, double *);
int binary(double, int, double *);
void debug_output(int, int, int, double *);
};

8
src/body.h
View File

@ -35,10 +35,10 @@ class Body : protected Pointers {
// methods implemented by child classes
virtual int pack_comm_body(class AtomVecBody::Bonus *, double *) {return 0;}
virtual int unpack_comm_body(class AtomVecBody::Bonus *, double *) {return 0;}
virtual int pack_border_body(class AtomVecBody::Bonus *, double *) {return 0;}
virtual int unpack_border_body(class AtomVecBody::Bonus *,
virtual int pack_comm_body(struct AtomVecBody::Bonus *, double *) {return 0;}
virtual int unpack_comm_body(struct AtomVecBody::Bonus *, double *) {return 0;}
virtual int pack_border_body(struct AtomVecBody::Bonus *, double *) {return 0;}
virtual int unpack_border_body(struct AtomVecBody::Bonus *,
double *) {return 0;}
virtual void data_body(int, int, int, char **, char **) = 0;

8
src/dump_cfg.cpp
View File

@ -273,9 +273,9 @@ void DumpCFG::write_lines(int n, double *mybuf)
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (j == 0) {
fprintf(fp,"%f \n",mybuf[m]);
fprintf(fp,"%f \n",mybuf[m]);
} else if (j == 1) {
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
@ -296,9 +296,9 @@ void DumpCFG::write_lines(int n, double *mybuf)
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (j == 0) {
fprintf(fp,"%f \n",mybuf[m]);
fprintf(fp,"%f \n",mybuf[m]);
} else if (j == 1) {
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2 && j <= 4) {
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
fprintf(fp,vformat[j],unwrap_coord);

2
src/dump_dcd.h
View File

@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class DumpDCD : public Dump {
public:
DumpDCD(LAMMPS *, int, char**);
~DumpDCD();
virtual ~DumpDCD();
private:
int natoms,ntotal;

2
src/dump_local.h
View File

@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class DumpLocal : public Dump {
public:
DumpLocal(LAMMPS *, int, char **);
~DumpLocal();
virtual ~DumpLocal();
private:
int nevery; // dump frequency to check Fix against

2
src/dump_xyz.h
View File

@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class DumpXYZ : public Dump {
public:
DumpXYZ(class LAMMPS *, int, char**);
~DumpXYZ();
virtual ~DumpXYZ();
protected:
int ntypes;

10
src/fix_adapt.cpp
View File

@ -200,8 +200,16 @@ void FixAdapt::init()
if (ad->which == PAIR) {
anypair = 1;
Pair *pair = NULL;
Pair *pair = force->pair_match(ad->pstyle,1);
if (lmp->suffix_enable) {
char psuffix[128];
strcpy(psuffix,ad->pstyle);
strcat(psuffix,"/");
strcat(psuffix,lmp->suffix);
pair = force->pair_match(psuffix,1);
}
if (pair == NULL) pair = force->pair_match(ad->pstyle,1);
if (pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL)

5
src/fix_wall_harmonic.h
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -29,9 +29,6 @@ class FixWallHarmonic : public FixWall {
FixWallHarmonic(class LAMMPS *, int, char **);
void precompute(int) {}
void wall_particle(int, int, double);
private:
double offset[6];
};
}

7
src/lmpwindows.h
View File

@ -37,9 +37,16 @@ inline double trunc(double x) {
}
// Windows version of mkdir function does not have permission flags
#ifndef S_IRWXU
# define S_IRWXU 0
#endif
#ifndef S_IRGRP
# define S_IRGRP 0
#endif
#ifndef S_IXGRP
# define S_IXGRP 0
#endif
inline int mkdir(const char *path, int){
return _mkdir(path);
}

2
src/main.cpp
View File

@ -27,8 +27,10 @@ int main(int argc, char **argv)
MPI_Init(&argc,&argv);
LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
lammps->input->file();
delete lammps;
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}

4
src/neighbor.cpp
View File

@ -320,7 +320,9 @@ void Neighbor::init()
special_flag[3] = 1;
else special_flag[3] = 2;
if (force->kspace) special_flag[1] = special_flag[2] = special_flag[3] = 2;
if (force->kspace || force->pair_match("coul/wolf",0)
|| force->pair_match("coul/dsf",0))
special_flag[1] = special_flag[2] = special_flag[3] = 2;
// maxwt = max multiplicative factor on atom indices stored in neigh list

1
src/pair_born_coul_wolf.cpp
View File

@ -37,6 +37,7 @@ using namespace MathConst;
PairBornCoulWolf::PairBornCoulWolf(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
single_enable = 0;
}
/* ---------------------------------------------------------------------- */

36
src/pair_coul_dsf.cpp
View File

@ -43,7 +43,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairCoulDSF::PairCoulDSF(LAMMPS *lmp) : Pair(lmp) {}
PairCoulDSF::PairCoulDSF(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
}
/* ---------------------------------------------------------------------- */
@ -59,7 +62,7 @@ PairCoulDSF::~PairCoulDSF()
void PairCoulDSF::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,jj,inum,jnum;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double r,rsq,r2inv,forcecoul,factor_coul;
double prefactor,erfcc,erfcd,e_self,t;
@ -72,7 +75,6 @@ void PairCoulDSF::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
@ -91,11 +93,10 @@ void PairCoulDSF::compute(int eflag, int vflag)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
if (evflag) {
if (eflag) {
e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
}
@ -109,20 +110,17 @@ void PairCoulDSF::compute(int eflag, int vflag)
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
erfcd = exp(-alpha*alpha*rsq);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
}
r = sqrt(rsq);
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
erfcd = exp(-alpha*alpha*rsq);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
fpair = forcecoul * r2inv;
f[i][0] += delx*fpair;
@ -135,10 +133,8 @@ void PairCoulDSF::compute(int eflag, int vflag)
}
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
} else ecoul = 0.0;
}
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
} else ecoul = 0.0;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);

5
src/pair_coul_wolf.cpp
View File

@ -34,7 +34,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairCoulWolf::PairCoulWolf(LAMMPS *lmp) : Pair(lmp) {}
PairCoulWolf::PairCoulWolf(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
}
/* ---------------------------------------------------------------------- */

15
src/pair_lj_cut_coul_dsf.cpp
View File

@ -43,7 +43,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairLJCutCoulDSF::PairLJCutCoulDSF(LAMMPS *lmp) : Pair(lmp) {}
PairLJCutCoulDSF::PairLJCutCoulDSF(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
}
/* ---------------------------------------------------------------------- */
@ -72,7 +75,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double prefactor,erfcc,erfcd,e_self,t;
double prefactor,erfcc,erfcd,t;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
@ -84,8 +87,8 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
@ -106,8 +109,8 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
jlist = firstneigh[i];
jnum = numneigh[i];
if (evflag) {
e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
if (eflag) {
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
}
@ -139,7 +142,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
}
} else forcecoul = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;