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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13889 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-08-18 21:13:14 +00:00
parent 21dd53e50d
commit 916fc0f1cb
11 changed files with 27 additions and 27 deletions
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7
src/MANYBODY/pair_polymorphic.cpp
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@ -79,8 +79,9 @@ PairPolymorphic::~PairPolymorphic()
void PairPolymorphic::compute(int eflag, int vflag)
{
tagint itag,jtag;
int i,j,k,ii,jj,kk,inum,jnum;
int itag,jtag,iel,jel,kel,iparam_ij,iparam_ik,iparam_ijk;
int iel,jel,kel,iparam_ij,iparam_ik,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2,r0,r1,r2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
@ -94,7 +95,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
int *tag = atom->tag;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@ -512,7 +513,7 @@ void PairPolymorphic::read_file(char *file, char** elements)
// open file on proc 0
FILE *fp=NULL;
if (comm->me == 0) {
fp = fopen(file,"r");
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open polymorphic potential file %s",file);

11
src/USER-SMD/atom_vec_smd.cpp
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@ -146,7 +146,6 @@ void AtomVecSMD::grow_reset() {
radius = atom->radius;
rmass = atom->rmass;
molecule = atom->molecule;
vfrac = atom->vfrac;
x0 = atom->x0;
contact_radius = atom->contact_radius;
@ -657,7 +656,7 @@ void AtomVecSMD::unpack_border_vel(int n, int first, double *buf) {
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i; // 10
molecule[i] = (tagint) ubuf(buf[m++]).i; // 10
radius[i] = buf[m++];
rmass[i] = buf[m++];
@ -698,7 +697,7 @@ int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) {
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++]; // 3
molecule[i] = (int) ubuf(buf[m++]).i; // 4
molecule[i] = (tagint) ubuf(buf[m++]).i; // 4
radius[i] = buf[m++];
rmass[i] = buf[m++];
vfrac[i] = buf[m++];
@ -790,7 +789,7 @@ int AtomVecSMD::unpack_exchange(double *buf) {
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11
molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
@ -920,7 +919,7 @@ int AtomVecSMD::unpack_restart(double *buf) {
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11
molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
@ -1034,7 +1033,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR, "Invalid atom type in Atoms section of data file");
molecule[nlocal] = atoi(values[2]);
molecule[nlocal] = ATOTAGINT(values[2]);
if (molecule[nlocal] <= 0)
error->one(FLERR, "Invalid molecule in Atoms section of data file");

2
src/USER-SMD/atom_vec_smd.h
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@ -88,7 +88,7 @@ class AtomVecSMD : public AtomVec {
double **x,**v,**f;
double *radius,*rmass;
int *molecule;
tagint *molecule;
double *vfrac,**x0,*contact_radius, **smd_data_9, *e, *de, **vest;
double **tlsph_stress;
double *eff_plastic_strain;

2
src/USER-SMD/fix_smd_move_triangulated_surface.cpp
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@ -255,7 +255,7 @@ void FixSMDMoveTriSurf::initial_integrate(int vflag) {
double **v = atom->v;
double **vest = atom->vest;
double **smd_data_9 = atom->smd_data_9;
int *mol = atom->molecule;
tagint *mol = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;

2
src/USER-SMD/fix_smd_wall_surface.cpp
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@ -437,7 +437,7 @@ void FixSMDWallSurface::read_triangles(int pass) {
* due to calling grow() in create_atoms() above;
*/
int *mol = atom->molecule;
tagint *mol = atom->molecule;
int *type = atom->type;
double *radius = atom->radius;
double *contact_radius = atom->contact_radius;

12
src/USER-SMD/pair_smd_tlsph.cpp
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@ -137,7 +137,7 @@ PairTlsph::~PairTlsph() {
---------------------------------------------------------------------- */
void PairTlsph::PreCompute() {
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double *vfrac = atom->vfrac;
double *radius = atom->radius;
double **x0 = atom->x0;
@ -145,7 +145,7 @@ void PairTlsph::PreCompute() {
double **v = atom->vest; // extrapolated velocities corresponding to current positions
double **vint = atom->v; // Velocity-Verlet algorithm velocities
double *damage = atom->damage;
int *tag = atom->tag;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int jnum, jj, i, j, itype, idim;
@ -417,7 +417,7 @@ void PairTlsph::compute(int eflag, int vflag) {
}
void PairTlsph::ComputeForces(int eflag, int vflag) {
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double **x = atom->x;
double **v = atom->vest;
double **x0 = atom->x0;
@ -702,7 +702,7 @@ void PairTlsph::ComputeForces(int eflag, int vflag) {
shape matrix correction
------------------------------------------------------------------------- */
void PairTlsph::AssembleStress() {
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double *eff_plastic_strain = atom->eff_plastic_strain;
double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
double **tlsph_stress = atom->smd_stress;
@ -1842,7 +1842,7 @@ void *PairTlsph::extract(const char *str, int &i) {
int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
int i, j, m;
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double *damage = atom->damage;
double *eff_plastic_strain = atom->eff_plastic_strain;
double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
@ -1885,7 +1885,7 @@ int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, in
void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
int i, m, last;
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double *damage = atom->damage;
double *eff_plastic_strain = atom->eff_plastic_strain;
double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;

2
src/USER-SMD/pair_smd_triangulated_surface.cpp
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@ -101,7 +101,7 @@ void PairTriSurf::compute(int eflag, int vflag) {
else
evflag = vflag_fdotr = 0;
int *mol = atom->molecule;
tagint *mol = atom->molecule;
double **f = atom->f;
double **smd_data_9 = atom->smd_data_9;
double **x = atom->x;

6
src/atom_vec_tri.cpp
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@ -1433,7 +1433,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
// size = length of one edge
double c2mc1[2],c3mc1[3];
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double size = MAX(MathExtra::len3(c2mc1),MathExtra::len3(c3mc1));
@ -1557,7 +1557,7 @@ int AtomVecTri::data_vel_hybrid(int m, char **values)
void AtomVecTri::pack_data(double **buf)
{
double c2mc1[2],c3mc1[3],norm[3];
double c2mc1[3],c3mc1[3],norm[3];
double area;
int nlocal = atom->nlocal;
@ -1595,7 +1595,7 @@ int AtomVecTri::pack_data_hybrid(int i, double *buf)
else buf[1] = ubuf(1).d;
if (tri[i] < 0) buf[2] = rmass[i];
else {
double c2mc1[2],c3mc1[3],norm[3];
double c2mc1[3],c3mc1[3],norm[3];
MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
MathExtra::sub3(bonus[tri[i]].c3,bonus[tri[i]].c1,c3mc1);
MathExtra::cross3(c2mc1,c3mc1,norm);

6
src/delete_atoms.cpp
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@ -722,9 +722,9 @@ void DeleteAtoms::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
if (atom->molecular == 0)
error->all(FLERR,"Cannot delete_atoms mol yes for "
"non-molecular systems");
if (atom->molecule_flag == 0)
error->all(FLERR,"Delete_atoms mol yes requires "
"atom attribute molecule");
if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mol_flag = 0;
else error->all(FLERR,"Illegal delete_atoms command");

2
src/math_extra.cpp
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@ -61,7 +61,7 @@ int mldivide3(const double m[3][3], const double *v, double *ans)
}
}
while (aug[p][i] == 0.0 && p < 3) p++;
while (p < 3 && aug[p][i] == 0.0) p++;
if (p == 3) return 1;
else

2
src/set.cpp
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@ -642,7 +642,7 @@ void Set::set(int keyword)
double *c1 = avec_tri->bonus[atom->tri[i]].c1;
double *c2 = avec_tri->bonus[atom->tri[i]].c2;
double *c3 = avec_tri->bonus[atom->tri[i]].c3;
double c2mc1[2],c3mc1[3];
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double norm[3];