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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10167 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-06-28 19:36:17 +00:00
parent 1cda7f63aa
commit 3428df4c4b
6 changed files with 29 additions and 35 deletions
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2
src/RIGID/fix_rigid_nh.cpp
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@ -612,7 +612,7 @@ void FixRigidNH::final_integrate()
// sum over atoms to get force and torque on rigid body // sum over atoms to get force and torque on rigid body
int *image = atom->image; tagint *image = atom->image;
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;

4
src/RIGID/fix_rigid_nh.h
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@ -1,4 +1,4 @@
/* ---------------------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
@ -72,7 +72,7 @@ class FixRigidNH : public FixRigid {
int tcomputeflag,pcomputeflag; int tcomputeflag,pcomputeflag;
void couple(); void couple();
void remap(); virtual void remap();
void nhc_temp_integrate(); void nhc_temp_integrate();
void nhc_press_integrate(); void nhc_press_integrate();

11
src/USER-OMP/dihedral_nharmonic_omp.cpp
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@ -87,7 +87,7 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3]; double edihedral,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2; double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2; double b2mag,b3mag2,b3mag,ctmp,c_,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s12,c,p,pd,a11,a22; double c2mag,sc1,sc2,s1,s12,c,p,pd,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2; double a33,a12,a13,a23,sx2,sy2,sz2;
double s2,sin2; double s2,sin2;
@ -201,14 +201,15 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// force & energy // force & energy
// p = sum (i=1,n) a_i * c**(i-1) // p = sum (i=1,n) a_i * c**(i-1)
// pd = dp/dc // pd = dp/dc
c_ = c;
p = a[type][0]; p = a[type][0];
pd = a[type][1]; pd = a[type][1];
for (int i = 1; i < nterms[type]-1; i++) { for (int i = 1; i < nterms[type]-1; i++) {
p += c * a[type][i]; p += c_ * a[type][i];
pd += c * static_cast<double>(i+1) * a[type][i+1]; pd += c_ * static_cast<double>(i+1) * a[type][i+1];
c *= c; c_ *= c;
} }
p += c * a[type][nterms[type]-1]; p += c_ * a[type][nterms[type]-1];
if (EFLAG) edihedral = p; if (EFLAG) edihedral = p;

14
src/pair_table.cpp
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@ -179,15 +179,15 @@ void PairTable::compute(int eflag, int vflag)
void PairTable::allocate() void PairTable::allocate()
{ {
allocated = 1; allocated = 1;
int nt = atom->ntypes; const int nt = atom->ntypes + 1;
memory->create(setflag,nt+1,nt+1,"pair:setflag"); memory->create(setflag,nt,nt,"pair:setflag");
for (int i = 1; i <= nt; i++) memory->create(cutsq,nt,nt,"pair:cutsq");
for (int j = i; j <= nt; j++) memory->create(tabindex,nt,nt,"pair:tabindex");
setflag[i][j] = 0;
memory->create(cutsq,nt+1,nt+1,"pair:cutsq"); memset(&setflag[0][0],0,nt*nt*sizeof(int));
memory->create(tabindex,nt+1,nt+1,"pair:tabindex"); memset(&cutsq[0][0],0,nt*nt*sizeof(double));
memset(&tabindex[0][0],0,nt*nt*sizeof(int));
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

9
src/special.cpp
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@ -54,11 +54,9 @@ Special::~Special()
void Special::build() void Special::build()
{ {
int i,j,k,m,n,size; int i,j,k,size;
int max,maxall,nbuf; int max,maxall,nbuf;
int *buf; int *buf;
MPI_Request request;
MPI_Status status;
MPI_Barrier(world); MPI_Barrier(world);
@ -637,8 +635,6 @@ void Special::combine()
void Special::angle_trim() void Special::angle_trim()
{ {
int i,j,m,n; int i,j,m,n;
MPI_Request request;
MPI_Status status;
int *num_angle = atom->num_angle; int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral; int *num_dihedral = atom->num_dihedral;
@ -760,8 +756,6 @@ void Special::angle_trim()
void Special::dihedral_trim() void Special::dihedral_trim()
{ {
int i,j,m,n; int i,j,m,n;
MPI_Request request;
MPI_Status status;
int *num_dihedral = atom->num_dihedral; int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1; int **dihedral_atom1 = atom->dihedral_atom1;
@ -826,7 +820,6 @@ void Special::dihedral_trim()
// delete 1-4 neighbors if they are not flagged in dflag // delete 1-4 neighbors if they are not flagged in dflag
int offset;
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
m = 0; m = 0;
for (j = 0; j < nspecial[i][2]; j++) for (j = 0; j < nspecial[i][2]; j++)

24
src/write_data.cpp
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@ -286,8 +286,8 @@ void WriteData::atoms()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
double **buf; double **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my atom data into buf // pack my atom data into buf
@ -339,8 +339,8 @@ void WriteData::velocities()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
double **buf; double **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my velocity data into buf // pack my velocity data into buf
@ -390,8 +390,8 @@ void WriteData::bonds()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
int **buf; int **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my bond data into buf // pack my bond data into buf
@ -443,8 +443,8 @@ void WriteData::angles()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
int **buf; int **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my angle data into buf // pack my angle data into buf
@ -514,8 +514,8 @@ void WriteData::dihedrals()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
int **buf; int **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my dihedral data into buf // pack my dihedral data into buf
@ -585,8 +585,8 @@ void WriteData::impropers()
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
int **buf; int **buf;
if (me == 0) memory->create(buf,maxrow,ncol,"write_data:buf"); if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,sendrow,ncol,"write_data:buf"); else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my improper data into buf // pack my improper data into buf