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Small changes to fix adapt for solid free energies 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9150 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2012-12-12 22:30:41 +00:00
parent 6c074e8c7e
commit dba5a5ad3f
4 changed files with 108 additions and 14 deletions
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91
src/compute_ti.cpp
View File

@ -16,6 +16,7 @@
------------------------------------------------------------------------- */
#include "mpi.h"
#include "atom.h"
#include "string.h"
#include "compute_ti.h"
#include "update.h"
@ -40,18 +41,23 @@ ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal compute ti command");
peflag = 1;
peratom_flag = 1;
peatomflag = 1;
scalar_flag = 1;
extscalar = 1;
timeflag = 1;
// terms come in triplets
// changed to quadruplets to include atom type
nterms = (narg-3) / 3;
if (narg != 3*nterms + 3) error->all(FLERR,"Illegal compute ti command");
nterms = (narg-3) / 4;
if (narg != 4*nterms + 3) error->all(FLERR,"Illegal compute ti command");
which = new int[nterms];
ivar1 = new int[nterms];
ivar2 = new int[nterms];
ilo = new int[nterms];
ihi = new int[nterms];
var1 = new char*[nterms];
var2 = new char*[nterms];
pptr = new Pair*[nterms];
@ -65,15 +71,17 @@ ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute ti command");
if (iarg+4 > narg) error->all(FLERR,"Illegal compute ti command");
if (strcmp(arg[iarg],"kspace") == 0) which[nterms] = KSPACE;
else if (strcmp(arg[iarg],"tail") == 0) which[nterms] = TAIL;
else {
which[nterms] = PAIR;
int n = strlen(arg[iarg]) + 1;
pstyle[nterms] = new char[n];
strcpy(pstyle[nterms],arg[iarg]);
}
which[nterms] = PAIR;}
int n = strlen(arg[iarg]) + 1;
pstyle[nterms] = new char[n];
strcpy(pstyle[nterms],arg[iarg]);
force->bounds(arg[iarg+1],atom->ntypes,ilo[nterms],ihi[nterms]);
iarg += 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
@ -105,6 +113,8 @@ ComputeTI::~ComputeTI()
delete [] ivar2;
delete [] var1;
delete [] var2;
delete [] ilo;
delete [] ihi;
delete [] pptr;
delete [] pstyle;
}
@ -153,22 +163,79 @@ double ComputeTI::compute_scalar()
double dUdl = 0.0;
for (int m = 0; m < nterms; m++) {
int total_flag = 0;
if ((ihi[m]-ilo[m])==atom->ntypes) total_flag = 1;
eng = 0.0;
value1 = input->variable->compute_equal(ivar1[m]);
value2 = input->variable->compute_equal(ivar2[m]);
if (value1 == 0.0) continue;
if (which[m] == PAIR) {
eng = pptr[m]->eng_vdwl + pptr[m]->eng_coul;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
int ntypes = atom->ntypes;
int *mask = atom->mask;
if (total_flag) {
eng = pptr[m]->eng_vdwl + pptr[m]->eng_coul;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
}
else {
int nlocal = atom->nlocal;
int npair = nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *eatom = pptr[m]->eatom;
if (force->newton) npair += atom->nghost;
for(int i = 0; i < npair; i++)
{
if ((ilo[m]<=type[i])&(ihi[m]>=type[i]))
eng += eatom[i];
}
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
}
dUdl += engall/value1 * value2;
} else if (which[m] == TAIL) {
double vol = domain->xprd*domain->yprd*domain->zprd;
eng = force->pair->etail / vol;
if (total_flag)
eng = force->pair->etail / vol;
else {
eng = 0;
for (int it = 1; it <= atom->ntypes; it++) {
int jt;
if ((it >= ilo[m])&&(it <=ihi[m])) jt = it;
else jt = ilo[m];
for (; jt <=ihi[m];jt++) {
if ((force->pair->tail_flag)&&(force->pair->setflag[it][jt])) {
double cut = force->pair->init_one(it,jt);
eng += force->pair->etail_ij;
}
if (it !=jt) eng += force->pair->etail_ij;
}
}
eng /= vol;
}
dUdl += eng/value1 * value2;
} else if (which[m] == KSPACE) {
eng = force->kspace->energy;
int ntypes = atom->ntypes;
int *mask = atom->mask;
if (total_flag)
eng = force->kspace->energy;
else {
int nlocal = atom->nlocal;
int npair = nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *eatom = force->kspace->eatom;
eng = 0;
for(int i = 0; i < nlocal; i++)
if ((ilo[m]<=type[i])&(ihi[m]>=type[i]))
eng += eatom[i];
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
eng = engall;
}
dUdl += eng/value1 * value2;
}
}

20
src/fix_adapt.cpp
View File

@ -33,7 +33,7 @@ using namespace FixConst;
using namespace MathConst;
enum{PAIR,KSPACE,ATOM};
enum{DIAMETER};
enum{DIAMETER,CHARGE};
/* ---------------------------------------------------------------------- */
@ -71,6 +71,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
nadapt = 0;
diamflag = 0;
chgflag = 0;
iarg = 4;
while (iarg < narg) {
@ -110,6 +111,9 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (strcmp(arg[iarg+1],"diameter") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].aparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
@ -229,6 +233,10 @@ void FixAdapt::init()
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
if (ad->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"Fix adapt requires atom attribute charge");
}
}
}
@ -334,6 +342,16 @@ void FixAdapt::change_settings()
radius[i]*radius[i]*radius[i] * density;
}
}
} else if (ad->aparam == CHARGE) {
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// cout<<"Fix adapt called now!\n";
// cout<<" Charge of atom: "<<i<<" is: "<<value;
q[i] = value;
}
}
}
}

5
src/fix_adapt.h
View File

@ -27,6 +27,7 @@ namespace LAMMPS_NS {
class FixAdapt : public Fix {
public:
int diamflag; // 1 if atom diameters will vary, for AtomVecGranular
int chgflag;
FixAdapt(class LAMMPS *, int, char **);
~FixAdapt();
@ -99,4 +100,8 @@ E: Fix adapt requires atom attribute diameter
The atom style being used does not specify an atom diameter.
E: Fix adapt requires atom attribute charge
The atom style being used does not specify an atom charge.
*/

6
src/pair_gauss.cpp
View File

@ -217,7 +217,11 @@ void PairGauss::coeff(int narg, char **arg)
double PairGauss::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
// This error is triggered when ti is performed on lj/cut tail
// in presence of extra atom type for tether sites
// "i = 2 j = 1 ERROR: All pair coeffs are not set (pair_gauss.cpp:223)"
// if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);
else offset[i][j] = 0.0;