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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9413 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-02-08 18:09:25 +00:00
parent 9907a91db9
commit a62be73ba7
8 changed files with 67 additions and 38 deletions
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5
src/CLASS2/bond_class2.cpp
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@ -197,12 +197,15 @@ void BondClass2::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double BondClass2::single(int type, double rsq, int i, int j)
double BondClass2::single(int type, double rsq, int i, int j, double &fforce)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double dr2 = dr*dr;
double dr3 = dr2*dr;
double dr4 = dr3*dr;
double de_bond = 2.0*k2[type]*dr + 3.0*k3[type]*dr2 + 4.0*k4[type]*dr3;
if (r > 0.0) fforce = -de_bond/r;
else fforce = 0.0;
return (k2[type]*dr2 + k3[type]*dr3 + k4[type]*dr4);
}

2
src/CLASS2/bond_class2.h
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@ -34,7 +34,7 @@ class BondClass2 : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
double single(int, double, int, int);
double single(int, double, int, int, double &);
protected:
double *r0,*k2,*k3,*k4;

3
src/MC/fix_bond_swap.cpp
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@ -650,8 +650,9 @@ double FixBondSwap::pair_eng(int i, int j)
double FixBondSwap::bond_eng(int btype, int i, int j)
{
double tmp;
double rsq = dist_rsq(i,j);
return force->bond->single(btype,rsq,i,j);
return force->bond->single(btype,rsq,i,j,tmp);
}
/* ---------------------------------------------------------------------- */

63
src/compute_bond_local.cpp
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@ -27,6 +27,8 @@ using namespace LAMMPS_NS;
#define DELTA 10000
enum{DIST,ENG,FORCE};
/* ---------------------------------------------------------------------- */
ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
@ -42,17 +44,22 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
dflag = eflag = -1;
nvalues = 0;
bstyle = new int[nvalues];
int i;
nvalues = 0;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"dist") == 0) dflag = nvalues++;
else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++;
if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST;
else if (strcmp(arg[iarg],"eng") == 0) bstyle[nvalues++] = ENG;
else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE;
else error->all(FLERR,"Invalid keyword in compute bond/local command");
}
// set singleflag if need to call bond->single()
singleflag = 0;
for (int i = 0; i < nvalues; i++)
if (bstyle[i] != DIST) singleflag = 1;
nmax = 0;
vector = NULL;
array = NULL;
@ -64,6 +71,7 @@ ComputeBondLocal::~ComputeBondLocal()
{
memory->destroy(vector);
memory->destroy(array);
delete [] bstyle;
}
/* ---------------------------------------------------------------------- */
@ -109,7 +117,8 @@ int ComputeBondLocal::compute_bonds(int flag)
{
int i,m,n,atom1,atom2;
double delx,dely,delz,rsq;
double *dbuf,*ebuf;
double *dbuf,*ebuf,*fbuf;
double *ptr;
double **x = atom->x;
int *num_bond = atom->num_bond;
@ -120,22 +129,10 @@ int ComputeBondLocal::compute_bonds(int flag)
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
if (flag) {
if (nvalues == 1) {
if (dflag >= 0) dbuf = vector;
if (eflag >= 0) ebuf = vector;
} else {
if (dflag >= 0 && array) dbuf = &array[0][dflag];
else dbuf = NULL;
if (eflag >= 0 && array) ebuf = &array[0][eflag];
else ebuf = NULL;
}
}
Bond *bond = force->bond;
double eng,fbond;
m = n = 0;
double fforce; // unused
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & groupbit)) continue;
for (i = 0; i < num_bond[atom1]; i++) {
@ -150,13 +147,29 @@ int ComputeBondLocal::compute_bonds(int flag)
delz = x[atom1][2] - x[atom2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (dflag >= 0) dbuf[n] = sqrt(rsq);
if (eflag >= 0) {
if (singleflag) {
if (bond_type[atom1][i] > 0)
ebuf[n] = bond->single(bond_type[atom1][i],rsq,atom1,atom2,fforce);
else ebuf[n] = 0.0;
eng = bond->single(bond_type[atom1][i],rsq,atom1,atom2,fbond);
else eng = fbond = 0.0;
}
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (bstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fbond;
break;
}
}
n += nvalues;
}
m++;

2
src/compute_bond_local.h
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@ -35,6 +35,8 @@ class ComputeBondLocal : public Compute {
private:
int nvalues,dflag,eflag;
int ncount;
int *bstyle;
int singleflag;
int nmax;
double *vector;

12
src/fix.h
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@ -122,6 +122,7 @@ class Fix : protected Pointers {
virtual void final_integrate_respa(int, int) {}
virtual void min_setup_pre_exchange() {}
virtual void min_setup_pre_neighbor() {}
virtual void min_setup_pre_force(int) {}
virtual void min_pre_exchange() {}
virtual void min_pre_force(int) {}
@ -189,11 +190,12 @@ namespace FixConst {
static const int POST_FORCE_RESPA = 1<<12;
static const int FINAL_INTEGRATE_RESPA = 1<<13;
static const int MIN_PRE_EXCHANGE = 1<<14;
static const int MIN_PRE_FORCE = 1<<15;
static const int MIN_POST_FORCE = 1<<16;
static const int MIN_ENERGY = 1<<17;
static const int POST_RUN = 1<<18;
static const int FIX_CONST_LAST = 1<<19;
static const int MIN_PRE_NEIGHBOR = 1<<15;
static const int MIN_PRE_FORCE = 1<<16;
static const int MIN_POST_FORCE = 1<<17;
static const int MIN_ENERGY = 1<<18;
static const int POST_RUN = 1<<19;
static const int FIX_CONST_LAST = 1<<20;
}
}

10
src/modify.cpp
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@ -56,8 +56,9 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
list_initial_integrate_respa = list_post_integrate_respa = NULL;
list_pre_force_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
list_min_pre_exchange = list_min_pre_force =
list_min_post_force = list_min_energy = NULL;
list_min_pre_exchange = list_pre_neighbor = NULL;
list_min_pre_force = list_min_post_force = NULL;
list_min_energy = NULL;
end_of_step_every = NULL;
@ -104,6 +105,7 @@ Modify::~Modify()
delete [] list_post_force_respa;
delete [] list_final_integrate_respa;
delete [] list_min_pre_exchange;
delete [] list_min_pre_neighbor;
delete [] list_min_pre_force;
delete [] list_min_post_force;
delete [] list_min_energy;
@ -150,6 +152,7 @@ void Modify::init()
n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_PRE_NEIGHBOR,n_min_pre_neighbor,list_min_pre_neighbor);
list_init(MIN_PRE_FORCE,n_min_pre_force,list_min_pre_force);
list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);
list_init(MIN_ENERGY,n_min_energy,list_min_energy);
@ -255,6 +258,9 @@ void Modify::setup_pre_neighbor()
if (update->whichflag == 1)
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_pre_neighbor[i]]->setup_pre_neighbor();
else if (update->whichflag == 2)
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_min_pre_neighbor[i]]->min_setup_pre_neighbor();
}
/* ----------------------------------------------------------------------

8
src/modify.h
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@ -27,7 +27,8 @@ class Modify : protected Pointers {
int n_final_integrate,n_end_of_step,n_thermo_energy;
int n_initial_integrate_respa,n_post_integrate_respa;
int n_pre_force_respa,n_post_force_respa,n_final_integrate_respa;
int n_min_pre_exchange,n_min_pre_force,n_min_post_force,n_min_energy;
int n_min_pre_exchange,n_min_pre_neighbor;
int n_min_pre_force,n_min_post_force,n_min_energy;
int restart_pbc_any; // 1 if any fix sets restart_pbc
int nfix_restart_global; // stored fix global info from restart file
@ -110,8 +111,9 @@ class Modify : protected Pointers {
int *list_initial_integrate_respa,*list_post_integrate_respa;
int *list_pre_force_respa,*list_post_force_respa;
int *list_final_integrate_respa;
int *list_min_pre_exchange,*list_min_pre_force;
int *list_min_post_force,*list_min_energy;
int *list_min_pre_exchange,*list_min_pre_neighbor;
int *list_min_pre_force,*list_min_post_force;
int *list_min_energy;
int *end_of_step_every;