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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14128 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-10-21 18:29:37 +00:00
parent ddfb996d8e
commit 9a878cdd67
53 changed files with 289 additions and 181 deletions
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2
src/GRANULAR/fix_pour.cpp
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@ -671,7 +671,7 @@ void FixPour::pre_exchange()
if (ninserted_atoms) {
atom->natoms += ninserted_atoms;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds * ninserted_mols;

2
src/KSPACE/ewald_disp.cpp
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@ -52,7 +52,7 @@ EwaldDisp::EwaldDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
ewaldflag = dispersionflag = dipoleflag = 1;
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
memset(function, 0, EWALD_NORDER*sizeof(int));
memset(function, 0, EWALD_NFUNCS*sizeof(int));
kenergy = kvirial = NULL;
cek_local = cek_global = NULL;
ekr_local = NULL;

2
src/KSPACE/pppm_disp.cpp
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@ -245,7 +245,7 @@ void PPPMDisp::init()
int *ptr = pair ? (int *) pair->extract("ewald_order",tmp) : NULL;
double *p_cutoff = pair ? (double *) pair->extract("cut_coul",tmp) : NULL;
double *p_cutoff_lj = pair ? (double *) pair->extract("cut_LJ",tmp) : NULL;
if (!(ptr||*p_cutoff||*p_cutoff_lj))
if (!(ptr||p_cutoff||p_cutoff_lj))
error->all(FLERR,"KSpace style is incompatible with Pair style");
cutoff = *p_cutoff;
cutoff_lj = *p_cutoff_lj;

2
src/MANYBODY/pair_airebo.cpp
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@ -803,7 +803,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
if (vflag_atom)
v_tally3(atomi,atomj,atomk,fi,fj,delikS,deljkS);
} else {
} else if (npath == 4) {
fpair1 = dC*dwikS*wkmS*wmjS / rikS;
fi[0] = delikS[0]*fpair1;
fi[1] = delikS[1]*fpair1;

4
src/MANYBODY/pair_bop.cpp
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@ -5108,11 +5108,7 @@ void PairBOP::read_table(char *filename)
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
fgets(s,MAXLINE,fp);
if(nws==3) {
sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
} else {
sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
}
}
if(nws==3) {
for(i=0;i<bop_types;i++)

5
src/MANYBODY/pair_eam.cpp
View File

@ -79,6 +79,8 @@ PairEAM::~PairEAM()
memory->destroy(cutsq);
delete [] map;
delete [] type2frho;
map = NULL;
type2frho = NULL;
memory->destroy(type2rhor);
memory->destroy(type2z2r);
}
@ -91,6 +93,7 @@ PairEAM::~PairEAM()
memory->destroy(funcfl[i].zr);
}
memory->sfree(funcfl);
funcfl = NULL;
}
if (setfl) {
@ -101,6 +104,7 @@ PairEAM::~PairEAM()
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
delete setfl;
setfl = NULL;
}
if (fs) {
@ -111,6 +115,7 @@ PairEAM::~PairEAM()
memory->destroy(fs->rhor);
memory->destroy(fs->z2r);
delete fs;
fs = NULL;
}
memory->destroy(frho);

4
src/MC/fix_gcmc.cpp
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@ -1308,7 +1308,7 @@ void FixGCMC::attempt_molecule_insertion()
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
@ -1957,7 +1957,7 @@ void FixGCMC::attempt_molecule_insertion_full()
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;

2
src/MISC/fix_deposit.cpp
View File

@ -563,7 +563,7 @@ void FixDeposit::pre_exchange()
if (success) {
atom->natoms += natom;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds;

2
src/MISC/fix_oneway.cpp
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@ -43,7 +43,7 @@ FixOneWay::FixOneWay(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (nevery < 1) error->all(FLERR,"Illegal fix oneway command");
int len = strlen(arg[4]);
regionstr = new char[len];
regionstr = new char[len+1];
strcpy(regionstr,arg[4]);
if (strcmp(arg[5], "x") == 0) direction = X|PLUS;

6
src/MOLECULE/angle_cosine_periodic.cpp
View File

@ -57,7 +57,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
int i,i1,i2,i3,n,m,type,b_factor;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
double tn,tn_1,tn_2,un,un_1,un_2;
eangle = 0.0;
@ -120,10 +120,6 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
un_1 = 2.0;
un_2 = 0.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// force & energy
tn_2 = c;

4
src/MOLECULE/improper_umbrella.cpp
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@ -145,8 +145,8 @@ void ImproperUmbrella::compute(int eflag, int vflag)
}
}
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;

1
src/OPT/pair_eam_alloy_opt.h
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@ -28,6 +28,7 @@ namespace LAMMPS_NS {
class PairEAMAlloyOpt : public PairEAMAlloy, public PairEAMOpt {
public:
PairEAMAlloyOpt(class LAMMPS *);
virtual ~PairEAMAlloyOpt() {}
};
}

1
src/OPT/pair_eam_fs_opt.h
View File

@ -28,6 +28,7 @@ namespace LAMMPS_NS {
class PairEAMFSOpt : public PairEAMFS, public PairEAMOpt {
public:
PairEAMFSOpt(class LAMMPS *);
virtual ~PairEAMFSOpt() {}
};
}

4
src/REPLICA/neb.cpp
View File

@ -207,7 +207,7 @@ void NEB::run()
update->endstep = update->laststep = update->firststep + n1steps;
update->nsteps = n1steps;
update->max_eval = n1steps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps for NEB");
update->minimize->setup();
@ -275,7 +275,7 @@ void NEB::run()
update->endstep = update->laststep = update->firststep + n2steps;
update->nsteps = n2steps;
update->max_eval = n2steps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
update->minimize->init();

4
src/REPLICA/prd.cpp
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@ -220,7 +220,7 @@ void PRD::command(int narg, char **arg)
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
@ -568,7 +568,7 @@ void PRD::quench()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many iterations");
// full init works

6
src/REPLICA/tad.cpp
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@ -199,7 +199,7 @@ void TAD::command(int narg, char **arg)
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
@ -406,7 +406,7 @@ void TAD::command(int narg, char **arg)
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
}
if (me_universe == 0) fclose(ulogfile_neb);
if ((me_universe == 0) && ulogfile_neb) fclose(ulogfile_neb);
if (me == 0) {
if (screen) fprintf(screen,"\nTAD done\n");
@ -478,7 +478,7 @@ void TAD::quench()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many iterations");
// full init works

2
src/REPLICA/temper.cpp
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@ -107,7 +107,7 @@ void Temper::command(int narg, char **arg)
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();

2
src/SHOCK/fix_append_atoms.cpp
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@ -506,7 +506,7 @@ void FixAppendAtoms::pre_exchange()
if (addtotal) {
domain->reset_box();
atom->natoms += addtotal;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (atom->tag_enable) atom->tag_extend();
if (atom->map_style) {

10
src/SHOCK/fix_wall_piston.cpp
View File

@ -41,6 +41,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal fix wall/piston command");
randomt = NULL;
gfactor1 = gfactor2 = NULL;
tempflag = 0;
scaleflag = 1;
roughflag = 0;
@ -150,6 +151,15 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixWallPiston::~FixWallPiston()
{
delete[] gfactor2;
delete[] gfactor1;
delete randomt;
}
/* ---------------------------------------------------------------------- */
int FixWallPiston::setmask()
{
int mask = 0;

1
src/SHOCK/fix_wall_piston.h
View File

@ -26,6 +26,7 @@ namespace LAMMPS_NS {
class FixWallPiston : public Fix {
public:
FixWallPiston(class LAMMPS *, int, char **);
virtual ~FixWallPiston();
int setmask();
void post_integrate();
void initial_integrate(int);

40
src/USER-MISC/compute_basal_atom.cpp
View File

@ -243,7 +243,7 @@ void ComputeBasalAtom::compute_peratom()
j1[1]=2;
j1[2]=2;
}
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0;
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0.0;
for (j = 0; j < chi[0]; j++) {
for (k = j+1; k < chi[0]; k++) {
//get cross products
@ -261,27 +261,29 @@ void ComputeBasalAtom::compute_peratom()
y7[count] = y4[count]*copysign(1.0,z4[count]);
z7[count] = z4[count]*copysign(1.0,z4[count]);
//get average cross products
xmean5 = xmean5 + x5[count];
ymean5 = ymean5 + y5[count];
zmean5 = zmean5 + z5[count];
xmean6 = xmean6 + x6[count];
ymean6 = ymean6 + y6[count];
zmean6 = zmean6 + z6[count];
xmean7 = xmean7 + x7[count];
ymean7 = ymean7 + y7[count];
zmean6 = zmean6 + z7[count];
xmean5 += x5[count];
ymean5 += y5[count];
zmean5 += z5[count];
xmean6 += x6[count];
ymean6 += y6[count];
zmean6 += z6[count];
xmean7 += x7[count];
ymean7 += y7[count];
zmean6 += z7[count];
count++;
}
}
xmean5 = xmean5/count;
xmean6 = xmean6/count;
xmean7 = xmean7/count;
ymean5 = ymean5/count;
ymean6 = ymean6/count;
ymean7 = ymean7/count;
zmean5 = zmean5/count;
zmean6 = zmean6/count;
zmean7 = zmean7/count;
if (count > 0) {
xmean5 /= count;
xmean6 /= count;
xmean7 /= count;
ymean5 /= count;
ymean6 /= count;
ymean7 /= count;
zmean5 /= count;
zmean6 /= count;
zmean7 /= count;
}
var5 = var6 = var7 = 0.0;
//find standard deviations
for (j=0;j<count;j++){

69
src/USER-MISC/dihedral_table.cpp
View File

@ -81,7 +81,7 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
const double offdiag[], size_t o_stride,
const double b[], size_t b_stride,
double x[], size_t x_stride,
size_t N)
size_t N, bool warn)
{
int status = GSL_SUCCESS;
double * delta = (double *) malloc (N * sizeof (double));
@ -91,8 +91,15 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
double * z = (double *) malloc (N * sizeof (double));
if (delta == 0 || gamma == 0 || alpha == 0 || c == 0 || z == 0) {
cerr << "Internal Cyclic Spline Error: failed to allocate working space\n";
exit(GSL_ENOMEM);
if (warn)
fprintf(stderr,"Internal Cyclic Spline Error: failed to allocate working space\n");
if (delta) free(delta);
if (gamma) free(gamma);
if (alpha) free(alpha);
if (c) free(c);
if (z) free(z);
return GSL_ENOMEM;
}
else
{
@ -104,6 +111,11 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
if (N == 1)
{
x[0] = b[0] / diag[0];
free(delta);
free(gamma);
free(alpha);
free(c);
free(z);
return GSL_SUCCESS;
}
@ -165,21 +177,14 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
}
}
if (z != 0)
free (z);
if (c != 0)
free (c);
if (alpha != 0)
free (alpha);
if (gamma != 0)
free (gamma);
if (delta != 0)
free (delta);
if (status == GSL_EZERODIV) {
cerr <<"Internal Cyclic Spline Error: Matrix must be positive definite.\n";
exit(GSL_EZERODIV);
}
if ((status == GSL_EZERODIV) && warn)
fprintf(stderr, "Internal Cyclic Spline Error: Matrix must be positive definite.\n");
return status;
} //solve_cyc_tridiag()
@ -188,11 +193,11 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
static void cyc_spline(double const *xa,
static int cyc_spline(double const *xa,
double const *ya,
int n,
double period,
double *y2a)
double *y2a, bool warn)
{
double *diag = new double[n];
@ -234,18 +239,25 @@ static void cyc_spline(double const *xa,
((ya[i] - ya[im1]) / (xa[i] - xa_im1));
}
// Because this matix is tridiagonal (and cyclic), we can use the following
// Because this matrix is tridiagonal (and cyclic), we can use the following
// cheap method to invert it.
solve_cyc_tridiag(diag, 1,
if (solve_cyc_tridiag(diag, 1,
offdiag, 1,
rhs, 1,
y2a, 1,
n);
n, warn) != GSL_SUCCESS) {
if (warn)
fprintf(stderr,"Error in inverting matrix for splines.\n");
delete [] diag;
delete [] offdiag;
delete [] rhs;
return 1;
}
delete [] diag;
delete [] offdiag;
delete [] rhs;
return 0;
} // cyc_spline()
/* ---------------------------------------------------------------------- */
@ -913,6 +925,11 @@ void DihedralTable::coeff(int narg, char **arg)
tb->ffile[I] = ffile_tmp[i];
I++;
}
// clean up temporary storage
delete[] phifile_tmp;
delete[] ffile_tmp;
delete[] efile_tmp;
}
// spline read-in and compute r,e,f vectors within table
@ -1147,10 +1164,14 @@ void DihedralTable::spline_table(Table *tb)
memory->create(tb->e2file,tb->ninput,"dihedral:e2file");
memory->create(tb->f2file,tb->ninput,"dihedral:f2file");
cyc_spline(tb->phifile, tb->efile, tb->ninput, MY_2PI, tb->e2file);
if (cyc_spline(tb->phifile, tb->efile, tb->ninput,
MY_2PI,tb->e2file,comm->me == 0))
error->one(FLERR,"Error computing dihedral spline tables");
if (! tb->f_unspecified) {
cyc_spline(tb->phifile, tb->ffile, tb->ninput, MY_2PI, tb->f2file);
if (cyc_spline(tb->phifile, tb->ffile, tb->ninput,
MY_2PI, tb->f2file, comm->me == 0))
error->one(FLERR,"Error computing dihedral spline tables");
}
// CHECK to help make sure the user calculated forces in a way
@ -1302,9 +1323,9 @@ void DihedralTable::compute_table(Table *tb)
cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2);
cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2, comm->me == 0);
if (! tb->f_unspecified)
cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2);
cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2, comm->me == 0);
}
@ -1339,13 +1360,13 @@ void DihedralTable::param_extract(Table *tb, char *line)
else if (strcmp(word,"CHECKU") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkU_fname);
memory->create(checkU_fname,strlen(word),"dihedral_table:checkU");
memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU");
strcpy(checkU_fname, word);
}
else if (strcmp(word,"CHECKF") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkF_fname);
memory->create(checkF_fname,strlen(word),"dihedral_table:checkF");
memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF");
strcpy(checkF_fname, word);
}
// COMMENTING OUT: equilibrium angles are not supported

2
src/USER-MISC/fix_ave_spatial_sphere.cpp
View File

@ -827,7 +827,7 @@ void FixAveSpatialSphere::end_of_step()
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}

4
src/USER-MISC/fix_ipi.cpp
View File

@ -18,6 +18,7 @@
#include "mpi.h"
#include "stdio.h"
#include "string.h"
#include "stdlib.h"
#include "fix_ipi.h"
#include "atom.h"
#include "force.h"
@ -187,7 +188,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[1],"all"))
error->warning(FLERR,"Fix ipi always uses group all");
strcpy(host, arg[3]);
host = strdup(arg[3]);
port = force->inumeric(FLERR,arg[4]);
inet = ((narg > 5) && (strcmp(arg[5],"unix") ==0) ) ? 0 : 1;
@ -218,6 +219,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
FixIPI::~FixIPI()
{
if (bsize) delete[] buffer;
free(host);
modify->delete_compute("IPI_TEMP");
modify->delete_compute("IPI_PRESS");
}

2
src/USER-MISC/fix_ipi.h
View File

@ -34,7 +34,7 @@ class FixIPI : public Fix {
virtual void final_integrate();
protected:
char host[1024]; int port; int inet, master, hasdata;
char *host; int port; int inet, master, hasdata;
int ipisock, me; double *buffer; long bsize;
int kspace_flag;
};

4
src/USER-MISC/fix_srp.cpp
View File

@ -178,7 +178,9 @@ void FixSRP::setup_pre_force(int zz)
for (int n = 0; n < nbondlist; n++) {
// consider only the user defined bond type
if(bondlist[n][2] != btype) continue;
// btype of zero considers all bonds
if(btype > 0 && bondlist[n][2] != btype)
continue;
i = bondlist[n][0];
j = bondlist[n][1];

4
src/USER-MISC/fix_ti_spring.cpp
View File

@ -76,8 +76,8 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
t_switch = atoi(arg[4]); // Switching time.
t_equil = atoi(arg[5]); // Equilibration time.
t0 = update->ntimestep; // Initial time.
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
if (t_switch <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
if (t_equil <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Coupling parameter initialization.
sf = 1;

8
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -225,6 +225,10 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
t_surface_l = surface_l;
mult_factor = intensity;
duration = 0.0;
v_0_sq = v_0*v_0;
// error checks
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm number of nodes must be > 0");
surface_double = double(t_surface_l)*(domain->xprd/nxnodes);
if ((C_limit+esheat_0) < 0.0)
error->all(FLERR,"Fix ttm electronic_specific_heat must be >= 0.0");
@ -234,10 +238,6 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
if (gamma_s < 0.0) error->all(FLERR,"Fix ttm gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all(FLERR,"Fix ttm v_0 must be >= 0.0");
if (ionic_density <= 0.0) error->all(FLERR,"Fix ttm ionic_density must be > 0.0");
v_0_sq = v_0*v_0;
// error check
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all(FLERR,"Fix ttm number of nodes must be > 0");
if (seed <= 0) error->all(FLERR,"Invalid random number seed in fix ttm command");
if (surface_l < 0) error->all(FLERR,"Surface coordinates must be >= 0");
if (surface_l >= surface_r) error->all(FLERR, "Left surface coordinate must be less than right surface coordinate");

4
src/USER-MISC/improper_fourier.cpp
View File

@ -173,8 +173,8 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
}
}
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;

19
src/USER-MISC/pair_srp.cpp
View File

@ -59,6 +59,8 @@ static const char cite_srp[] =
" pages = {134903}\n"
"}\n\n";
static int srp_instance = 0;
/* ----------------------------------------------------------------------
set size of pair comms in constructor
---------------------------------------------------------------------- */
@ -71,6 +73,10 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
nextra = 1;
segment = NULL;
fix_id = strdup("XX_FIX_SRP");
fix_id[0] = '0' + srp_instance / 10;
fix_id[1] = '0' + srp_instance % 10;
++srp_instance;
}
/* ----------------------------------------------------------------------
@ -112,7 +118,8 @@ PairSRP::~PairSRP()
}
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix("mysrp");
if (modify->nfix) modify->delete_fix(fix_id);
free(fix_id);
}
/* ----------------------------------------------------------------------
@ -336,8 +343,14 @@ void PairSRP::settings(int narg, char **arg)
error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// wildcard
if (strcmp(arg[1],"*") == 0)
btype = 0;
else {
btype = force->inumeric(FLERR,arg[1]);
if (btype > atom->nbondtypes) error->all(FLERR,"Illegal pair_style command");
if ((btype > atom->nbondtypes) || (btype <= 0))
error->all(FLERR,"Illegal pair_style command");
}
// settings
midpoint = 0;
@ -426,7 +439,7 @@ void PairSRP::init_style()
// invoke here instead of constructor
// to make restart possible
char **fixarg = new char*[3];
fixarg[0] = (char *) "mysrp";
fixarg[0] = fix_id;
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "SRP";
modify->add_fix(3,fixarg);

1
src/USER-MISC/pair_srp.h
View File

@ -54,6 +54,7 @@ class PairSRP : public Pair {
int bptype;
int btype;
class Fix *f_srp;
char *fix_id;
int exclude,maxcount;
int **segment;
};

5
src/USER-MOLFILE/molfile_interface.cpp
View File

@ -756,10 +756,13 @@ int MolfileInterface::timestep(float *coords, float *vels,
*simtime = t->physical_time;
}
if (rv == MOLFILE_EOF)
if (rv == MOLFILE_EOF) {
delete t;
return 1;
}
}
delete t;
return 0;
}

6
src/USER-OMP/angle_cosine_periodic_omp.cpp
View File

@ -91,7 +91,7 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
int i,i1,i2,i3,n,m,type,b_factor;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
double tn,tn_1,tn_2,un,un_1,un_2;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
@ -149,10 +149,6 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
un_1 = 2.0;
un_2 = 0.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// force & energy
tn_2 = c;

4
src/USER-OMP/improper_fourier_omp.cpp
View File

@ -206,8 +206,8 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
}
}
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;

4
src/USER-OMP/improper_umbrella_omp.cpp
View File

@ -171,8 +171,8 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
}
}
if (c > 1.0) s = 1.0;
if (c < -1.0) s = -1.0;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;

1
src/USER-OMP/neigh_full_omp.cpp
View File

@ -599,7 +599,6 @@ void Neighbor::full_multi_omp(NeighList *list)
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;

2
src/USER-OMP/pair_airebo_omp.cpp
View File

@ -2250,7 +2250,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
if (vflag_atom)
v_tally3_thr(atomi,atomj,atomk,fi,fj,delikS,deljkS,thr);
} else {
} else if (npath == 4) {
fpair1 = dC*dwikS*wkmS*wmjS / rikS;
fi[0] = delikS[0]*fpair1;
fi[1] = delikS[1]*fpair1;

24
src/USER-OMP/pair_brownian_omp.cpp
View File

@ -48,6 +48,7 @@ PairBrownianOMP::PairBrownianOMP(LAMMPS *lmp) :
suffix_flag |= Suffix::OMP;
respa_enable = 0;
random_thr = NULL;
nthreads = 0;
}
/* ---------------------------------------------------------------------- */
@ -55,7 +56,7 @@ PairBrownianOMP::PairBrownianOMP(LAMMPS *lmp) :
PairBrownianOMP::~PairBrownianOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
@ -72,7 +73,6 @@ void PairBrownianOMP::compute(int eflag, int vflag)
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
@ -116,13 +116,24 @@ void PairBrownianOMP::compute(int eflag, int vflag)
}
}
// number of threads has changed. reallocate pool of pRNGs
if (nthreads != comm->nthreads) {
if (random_thr) {
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
if (!random_thr)
delete[] random_thr;
}
nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
for (int i=1; i < nthreads; ++i)
random_thr[i] = NULL;
// to ensure full compatibility with the serial Brownian style
// we use is random number generator instance for thread 0
random_thr[0] = random;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@ -137,9 +148,10 @@ void PairBrownianOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
if (flaglog) {
if (evflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
@ -395,8 +407,8 @@ double PairBrownianOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairBrownian::memory_usage();
bytes += comm->nthreads * sizeof(RanMars*);
bytes += comm->nthreads * sizeof(RanMars);
bytes += nthreads * sizeof(RanMars*);
bytes += nthreads * sizeof(RanMars);
return bytes;
}

1
src/USER-OMP/pair_brownian_omp.h
View File

@ -40,6 +40,7 @@ class PairBrownianOMP : public PairBrownian, public ThrOMP {
protected:
class RanMars **random_thr;
int nthreads;
private:
template <int LOGFLAG, int EVFLAG, int NEWTON_PAIR>

25
src/USER-OMP/pair_brownian_poly_omp.cpp
View File

@ -48,6 +48,7 @@ PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
suffix_flag |= Suffix::OMP;
respa_enable = 0;
random_thr = NULL;
nthreads = 0;
}
/* ---------------------------------------------------------------------- */
@ -55,7 +56,7 @@ PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
PairBrownianPolyOMP::~PairBrownianPolyOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
@ -72,7 +73,6 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
@ -117,12 +117,24 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
}
if (!random_thr)
// number of threads has changed. reallocate pool of pRNGs
if (nthreads != comm->nthreads) {
if (random_thr) {
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
}
nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
for (int i=1; i < nthreads; ++i)
random_thr[i] = NULL;
// to ensure full compatibility with the serial BrownianPoly style
// we use is random number generator instance for thread 0
random_thr[0] = random;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@ -137,9 +149,10 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
if (flaglog) {
if (evflag)
eval<1,1>(ifrom, ito, thr);
@ -384,8 +397,8 @@ double PairBrownianPolyOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairBrownianPoly::memory_usage();
bytes += comm->nthreads * sizeof(RanMars*);
bytes += comm->nthreads * sizeof(RanMars);
bytes += nthreads * sizeof(RanMars*);
bytes += nthreads * sizeof(RanMars);
return bytes;
}

1
src/USER-OMP/pair_brownian_poly_omp.h
View File

@ -40,6 +40,7 @@ class PairBrownianPolyOMP : public PairBrownianPoly, public ThrOMP {
protected:
class RanMars **random_thr;
int nthreads;
private:
template <int LOGFLAG, int EVFLAG>

3
src/USER-OMP/pair_dpd_omp.cpp
View File

@ -80,6 +80,7 @@ void PairDPDOMP::compute(int eflag, int vflag)
// we use the serial random number generator instance for thread 0
random_thr[0] = random;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
@ -93,7 +94,7 @@ void PairDPDOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && (tid > 0) && (random_thr[tid] == NULL))
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);

2
src/USER-OMP/pair_dpd_tstat_omp.cpp
View File

@ -93,7 +93,7 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && (tid > 0) && (random_thr[tid] == NULL))
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);

4
src/USER-OMP/thr_data.h
View File

@ -35,7 +35,7 @@ class ThrData {
public:
ThrData(int tid, class Timer *t);
~ThrData() {};
~ThrData() { delete _timer; _timer = NULL; };
void check_tid(int); // thread id consistency check
int get_tid() const { return _tid; }; // our thread id.
@ -140,7 +140,7 @@ class ThrData {
// disabled default methods
private:
ThrData() : _tid(-1) {};
ThrData() : _tid(-1), _timer(NULL) {};
};
////////////////////////////////////////////////////////////////////////

13
src/USER-PHONON/fix_phonon.h
View File

@ -31,6 +31,17 @@ FixStyle(phonon,FixPhonon)
#ifndef FIX_PHONON_H
#define FIX_PHONON_H
#include "lmptype.h"
#include "mpi.h"
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
#define MPI_FFT_SCALAR MPI_FLOAT
#else
typedef double FFT_SCALAR;
#define MPI_FFT_SCALAR MPI_DOUBLE
#endif
#include <complex>
#include "fix.h"
#include <map>
@ -72,7 +83,7 @@ class FixPhonon : public Fix {
int mynpt,mynq,fft_nsend;
int *fft_cnts, *fft_disp;
int fft_dim, fft_dim2;
double *fft_data;
FFT_SCALAR *fft_data;
tagint itag; // index variables
int idx, idq; // more index variables

1
src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
View File

@ -330,6 +330,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
int nall, countall;
MPI_Allreduce(&n, &nall, 1, MPI_INT, MPI_SUM, world);
MPI_Allreduce(&count, &countall, 1, MPI_INT, MPI_SUM, world);
if (countall < 1) countall = 1;
if (comm->me == 0) {
if (screen) {

41
src/compute_rdf.cpp
View File

@ -95,6 +95,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
typecount = new int[ntypes+1];
icount = new int[npairs];
jcount = new int[npairs];
duplicates = new int[npairs];
}
/* ---------------------------------------------------------------------- */
@ -113,13 +114,14 @@ ComputeRDF::~ComputeRDF()
delete [] typecount;
delete [] icount;
delete [] jcount;
delete [] duplicates;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::init()
{
int i,m;
int i,j,m;
if (force->pair) delr = force->pair->cutforce / nbin;
else error->all(FLERR,"Compute rdf requires a pair style be defined");
@ -143,12 +145,17 @@ void ComputeRDF::init()
// icount = # of I atoms participating in I,J pairs for each histogram
// jcount = # of J atoms participating in I,J pairs for each histogram
// duplicates = # of atoms in both groups I and J for each histogram
for (m = 0; m < npairs; m++) {
icount[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++) icount[m] += typecount[i];
jcount[m] = 0;
for (i = jlo[m]; i <= jhi[m]; i++) jcount[m] += typecount[i];
duplicates[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++)
for (j = jlo[m]; j <= jhi[m]; j++)
if (i == j) duplicates[m] += typecount[i];
}
int *scratch = new int[npairs];
@ -156,6 +163,8 @@ void ComputeRDF::init()
for (i = 0; i < npairs; i++) icount[i] = scratch[i];
MPI_Allreduce(jcount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) jcount[i] = scratch[i];
MPI_Allreduce(duplicates,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) duplicates[i] = scratch[i];
delete [] scratch;
// need an occasional half neighbor list
@ -265,25 +274,28 @@ void ComputeRDF::compute_array()
MPI_Allreduce(hist[0],histall[0],npairs*nbin,MPI_DOUBLE,MPI_SUM,world);
// convert counts to g(r) and coord(r) and copy into output array
// nideal = # of J atoms surrounding single I atom in a single bin
// assuming J atoms are at uniform density
// vfrac = fraction of volume in shell m
// npairs = number of pairs, corrected for duplicates
// duplicates = pairs in which both atoms are the same
double constant,nideal,gr,ncoord,rlower,rupper;
double constant,vfrac,gr,ncoord,rlower,rupper,normfac;
if (domain->dimension == 3) {
constant = 4.0*MY_PI / (3.0*domain->xprd*domain->yprd*domain->zprd);
for (m = 0; m < npairs; m++) {
normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
- static_cast<double>(duplicates[m])/icount[m] : 0.0;
ncoord = 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
nideal = constant *
(rupper*rupper*rupper - rlower*rlower*rlower) * jcount[m];
if (icount[m]*nideal != 0.0)
gr = histall[m][ibin] / (icount[m]*nideal);
vfrac = constant * (rupper*rupper*rupper - rlower*rlower*rlower);
if (vfrac * normfac != 0.0)
gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
ncoord += gr*nideal;
if (icount[m] != 0)
ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}
@ -294,14 +306,17 @@ void ComputeRDF::compute_array()
for (m = 0; m < npairs; m++) {
ncoord = 0.0;
normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
- static_cast<double>(duplicates[m])/icount[m] : 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
nideal = constant * (rupper*rupper - rlower*rlower) * jcount[m];
if (icount[m]*nideal != 0.0)
gr = histall[m][ibin] / (icount[m]*nideal);
vfrac = constant * (rupper*rupper - rlower*rlower);
if (vfrac * normfac != 0.0)
gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
ncoord += gr*nideal;
if (icount[m] != 0)
ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}

1
src/compute_rdf.h
View File

@ -45,6 +45,7 @@ class ComputeRDF : public Compute {
int *typecount;
int *icount,*jcount;
int *duplicates;
class NeighList *list; // half neighbor list
};

2
src/fix_ave_spatial.cpp
View File

@ -888,7 +888,7 @@ void FixAveSpatial::end_of_step()
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}

2
src/fix_ave_time.cpp
View File

@ -907,7 +907,7 @@ void FixAveTime::invoke_vector(bigint ntimestep)
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}

3
src/info.cpp
View File

@ -104,6 +104,7 @@ void Info::command(int narg, char **arg)
++idx;
} else if ((idx+1 < narg) && (strncmp(arg[idx],"out",3) == 0)
&& (strncmp(arg[idx+1],"screen",3) == 0)) {
if ((out != screen) && (out != logfile)) fclose(out);
out = screen;
idx += 2;
} else if ((idx+1 < narg) && (strncmp(arg[idx],"out",3) == 0)
@ -547,7 +548,7 @@ bool Info::is_available(const char *category, const char *name)
int match = 0;
if (strcmp(category,"command") == 0) {
if (input->command_map->find(name) != input->command_map->end());
if (input->command_map->find(name) != input->command_map->end())
match = 1;
} else if (strcmp(category,"compute") == 0) {

1
src/pair.cpp
View File

@ -119,6 +119,7 @@ Pair::~Pair()
{
num_tally_compute = 0;
memory->sfree((void *)list_tally_compute);
list_tally_compute = NULL;
if (copymode) return;

3
src/velocity.cpp
View File

@ -364,7 +364,8 @@ void Velocity::create(double t_desired, int seed)
// no-bias compute calculates temp only for new thermal velocities
double t;
if (bias_flag == 0) t = temperature->compute_scalar();
if ((bias_flag == 0) || (temperature_nobias == NULL))
t = temperature->compute_scalar();
else t = temperature_nobias->compute_scalar();
rescale(t,t_desired);