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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1272 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-01-02 19:24:46 +00:00
parent 428ca84042
commit b2e9f7dc10
145 changed files with 2801 additions and 2615 deletions
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10
src/ASPHERE/compute_temp_asphere.cpp
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@ -29,6 +29,9 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
@ -41,7 +44,8 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -110,6 +114,8 @@ void ComputeTempAsphere::recount()
double ComputeTempAsphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;
@ -163,6 +169,8 @@ void ComputeTempAsphere::compute_vector()
{
int i;
invoked |= INVOKED_VECTOR;
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;

4
src/ASPHERE/fix_npt_asphere.cpp
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@ -172,18 +172,16 @@ void FixNPTASphere::final_integrate()
t_current = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) double ptmp = ptemperature->compute_scalar();
double tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->add_step(update->ntimestep+1);
pressure->addstep(update->ntimestep+1);
// update eta_dot

4
src/CLASS2/bond_class2.cpp
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@ -198,12 +198,12 @@ void BondClass2::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondClass2::single(int type, double rsq, int i, int j, double &eng)
double BondClass2::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double dr2 = dr*dr;
double dr3 = dr2*dr;
double dr4 = dr3*dr;
eng = k2[type]*dr2 + k3[type]*dr3 + k4[type]*dr4;
return (k2[type]*dr2 + k3[type]*dr3 + k4[type]*dr4);
}

2
src/CLASS2/bond_class2.h
View File

@ -28,7 +28,7 @@ class BondClass2 : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double *r0,*k2,*k3,*k4;

17
src/CLASS2/pair_lj_class2.cpp
View File

@ -354,9 +354,9 @@ void PairLJClass2::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, int eflag,
One &one)
double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;
@ -365,12 +365,9 @@ void PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
one.fforce = factor_lj*forcelj*r2inv;
fforce = factor_lj*forcelj*r2inv;
if (eflag) {
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
one.eng_coul = 0.0;
}
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
return factor_lj*philj;
}

2
src/CLASS2/pair_lj_class2.h
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@ -30,7 +30,7 @@ class PairLJClass2 : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
private:
double cut_global;

30
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -412,9 +412,10 @@ void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul,
double factor_lj, int eflag, One &one)
double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcecoul,forcelj,phicoul,philj;
@ -428,17 +429,18 @@ void PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
one.fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
one.eng_coul = factor_coul*phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng += factor_lj*philj;
}
return eng;
}

2
src/CLASS2/pair_lj_class2_coul_cut.h
View File

@ -31,7 +31,7 @@ class PairLJClass2CoulCut : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
private:
double cut_lj_global,cut_coul_global;

32
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -423,9 +423,10 @@ void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul,
double factor_lj, int eflag, One &one)
double PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,r3inv,r6inv,grij,expm2,t,erfc,prefactor;
double forcecoul,forcelj,phicoul,philj;
@ -447,20 +448,21 @@ void PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
one.fforce = (forcecoul + factor_lj*forcelj) * r2inv;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/CLASS2/pair_lj_class2_coul_long.h
View File

@ -31,7 +31,7 @@ class PairLJClass2CoulLong : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
private:

39
src/COLLOID/pair_colloid.cpp
View File

@ -351,9 +351,8 @@ double PairColloid::init_one(int i, int j)
offset[j][i] = offset[i][j] = 0.0;
if (offset_flag) {
One one;
single(0,0,i,j,cutsq[i][j],0.0,1.0,1,one);
offset[j][i] = offset[i][j] = one.eng_vdwl;
double tmp;
offset[j][i] = offset[i][j] = single(0,0,i,j,cutsq[i][j],0.0,1.0,tmp);
}
return cut[i][j];
@ -443,9 +442,9 @@ void PairColloid::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairColloid::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, int eflag,
One &one)
double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double K[9],h[4],g[4];
double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
@ -455,9 +454,9 @@ void PairColloid::single(int i, int j, int itype, int jtype, double rsq,
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
one.fforce = factor_lj*forcelj*r2inv;
if (eflag) phi = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce = factor_lj*forcelj*r2inv;
phi = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
case SMALL_LARGE:
@ -470,13 +469,12 @@ void PairColloid::single(int i, int j, int itype, int jtype, double rsq,
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
one.fforce = 4.0/15.0*r*fR*factor_lj *
fforce = 4.0/15.0*r*fR*factor_lj *
(2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6] - 5.0)/K[0];
if (eflag)
phi = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
phi = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
break;
case LARGE_LARGE:
@ -510,16 +508,11 @@ void PairColloid::single(int i, int j, int itype, int jtype, double rsq,
dUR = phi/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
one.fforce = factor_lj*(dUR+dUA)/r;
if (eflag)
phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
offset[itype][jtype];
fforce = factor_lj*(dUR+dUA)/r;
phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
offset[itype][jtype];
break;
}
if (eflag) {
one.eng_vdwl = factor_lj*phi;
one.eng_coul = 0.0;
}
return factor_lj*phi;
}

2
src/COLLOID/pair_colloid.h
View File

@ -30,7 +30,7 @@ class PairColloid : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
private:
double cut_global;

13
src/DIPOLE/compute_temp_dipole.cpp
View File

@ -23,9 +23,9 @@
using namespace LAMMPS_NS;
// moment of inertia for a sphere
#define INERTIA 0.4
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INERTIA 0.4 // moment of inertia for a sphere
/* ---------------------------------------------------------------------- */
@ -39,7 +39,8 @@ ComputeTempDipole::ComputeTempDipole(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -87,6 +88,8 @@ void ComputeTempDipole::recount()
double ComputeTempDipole::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **v = atom->v;
double *mass = atom->mass;
double **omega = atom->omega;
@ -116,6 +119,8 @@ void ComputeTempDipole::compute_vector()
{
int i;
invoked |= INVOKED_VECTOR;
double **v = atom->v;
double *mass = atom->mass;
double **omega = atom->omega;

22
src/DPD/pair_dpd.cpp
View File

@ -260,7 +260,7 @@ void PairDPD::init_style()
// using different random numbers
if (force->newton_pair == 0 && comm->me == 0) error->warning(
"DPD potential needs newton pair on for momentum conservation");
"Pair style dpd needs newton pair on for momentum conservation");
int irequest = neighbor->request(this);
}
@ -370,27 +370,21 @@ void PairDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, int eflag,
One &one)
double PairDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
r = sqrt(rsq);
if (r < EPSILON) {
one.fforce = 0.0;
if (eflag) one.eng_vdwl = one.eng_coul = 0.0;
return;
fforce = 0.0;
return 0.0;
}
rinv = 1.0/r;
wd = 1.0 - r/cut[itype][jtype];
fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
one.fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
if (eflag) {
phi = a0[itype][jtype] * r * (1.0 - 0.5*r/cut[itype][jtype]);
one.eng_vdwl = factor_dpd*phi;
one.eng_coul = 0.0;
}
phi = a0[itype][jtype] * r * (1.0 - 0.5*r/cut[itype][jtype]);
return factor_dpd*phi;
}

2
src/DPD/pair_dpd.h
View File

@ -31,7 +31,7 @@ class PairDPD : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
private:
double cut_global,temperature;

31
src/KSPACE/pair_buck_coul_long.cpp
View File

@ -394,9 +394,10 @@ void PairBuckCoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairBuckCoulLong::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
double PairBuckCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,grij,expm2,t,erfc,prefactor;
double forcecoul,forcebuck,phicoul,phibuck;
@ -418,20 +419,20 @@ void PairBuckCoulLong::single(int i, int j, int itype, int jtype,
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
one.fforce = (forcecoul + factor_lj*forcebuck) * r2inv;
fforce = (forcecoul + factor_lj*forcebuck) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
one.eng_vdwl = factor_lj*phibuck;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
eng += factor_lj*phibuck;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/KSPACE/pair_buck_coul_long.h
View File

@ -31,7 +31,7 @@ class PairBuckCoulLong : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
private:

28
src/KSPACE/pair_coul_long.cpp
View File

@ -512,10 +512,10 @@ void PairCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
void PairCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
double PairCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,phicoul;
@ -545,19 +545,17 @@ void PairCoulLong::single(int i, int j, int itype, int jtype,
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
one.fforce = forcecoul * r2inv;
fforce = forcecoul * r2inv;
if (eflag) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
one.eng_vdwl = 0.0;
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
return phicoul;
}
/* ---------------------------------------------------------------------- */

2
src/KSPACE/pair_coul_long.h
View File

@ -31,7 +31,7 @@ class PairCoulLong : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
private:

52
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -1127,10 +1127,10 @@ void PairLJCharmmCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double switch1,switch2,fraction,table,forcecoul,forcelj,phicoul,philj;
@ -1174,29 +1174,31 @@ void PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
one.fforce = (forcecoul + factor_lj*forcelj) * r2inv;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/KSPACE/pair_lj_charmm_coul_long.h
View File

@ -32,7 +32,7 @@ class PairLJCharmmCoulLong : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void compute_inner();
void compute_middle();

46
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -1080,10 +1080,10 @@ void PairLJCutCoulLong::free_tables()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
double PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,forcelj,phicoul,philj;
@ -1115,29 +1115,33 @@ void PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
one.fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/KSPACE/pair_lj_cut_coul_long.h
View File

@ -32,7 +32,7 @@ class PairLJCutCoulLong : public Pair {
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
virtual void single(int, int, int, int, double, double, double, int, One &);
virtual double single(int, int, int, int, double, double, double, double &);
void compute_inner();
void compute_middle();

3
src/MANYBODY/pair_airebo.h
View File

@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class PairAIREBO : public Pair {
public:
PairAIREBO(class LAMMPS *);
virtual ~PairAIREBO();
~PairAIREBO();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
@ -31,7 +31,6 @@ class PairAIREBO : public Pair {
void read_restart(FILE *) {}
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
void single(int, int, int, int, double, double, double, int, One &) {}
private:
int me;

13
src/MANYBODY/pair_eam.cpp
View File

@ -764,9 +764,9 @@ void PairEAM::grab(FILE *fp, int n, double *list)
/* ---------------------------------------------------------------------- */
void PairEAM::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
double PairEAM::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
int m;
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
@ -791,12 +791,9 @@ void PairEAM::single(int i, int j, int itype, int jtype,
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
one.fforce = -psip*recip;
fforce = -psip*recip;
if (eflag) {
one.eng_vdwl = phi;
one.eng_coul = 0.0;
}
return phi;
}
/* ---------------------------------------------------------------------- */

2
src/MANYBODY/pair_eam.h
View File

@ -27,7 +27,7 @@ class PairEAM : public Pair {
virtual void coeff(int, char **);
void init_style();
double init_one(int, int);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);

5
src/MOLECULE/angle_hybrid.cpp
View File

@ -259,9 +259,8 @@ void AngleHybrid::read_restart(FILE *fp)
double AngleHybrid::single(int type, int i1, int i2, int i3)
{
if (styles[map[type]])
return styles[map[type]]->single(type,i1,i2,i3);
else return 0.0;
if (styles[map[type]]) return styles[map[type]]->single(type,i1,i2,i3);
return 0.0;
}
/* ----------------------------------------------------------------------

6
src/MOLECULE/bond_fene.cpp
View File

@ -217,7 +217,7 @@ void BondFENE::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondFENE::single(int type, double rsq, int i, int j, double &eng)
double BondFENE::single(int type, double rsq, int i, int j)
{
double r0sq = r0[type] * r0[type];
double rlogarg = 1.0 - rsq/r0sq;
@ -234,11 +234,13 @@ void BondFENE::single(int type, double rsq, int i, int j, double &eng)
rlogarg = 0.1;
}
eng = -0.5 * k[type]*r0sq*log(rlogarg);
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type]) {
double sr2,sr6;
sr2 = sigma[type]*sigma[type]/rsq;
sr6 = sr2*sr2*sr2;
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
return eng;
}

2
src/MOLECULE/bond_fene.h
View File

@ -28,7 +28,7 @@ class BondFENE : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double TWO_1_3;

6
src/MOLECULE/bond_fene_expand.cpp
View File

@ -228,7 +228,7 @@ void BondFENEExpand::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondFENEExpand::single(int type, double rsq, int i, int j, double &eng)
double BondFENEExpand::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double rshift = r - shift[type];
@ -248,11 +248,13 @@ void BondFENEExpand::single(int type, double rsq, int i, int j, double &eng)
rlogarg = 0.1;
}
eng = -0.5 * k[type]*r0sq*log(rlogarg);
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type]) {
double sr2,sr6;
sr2 = sigma[type]*sigma[type]/rshiftsq;
sr6 = sr2*sr2*sr2;
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
return eng;
}

2
src/MOLECULE/bond_fene_expand.h
View File

@ -28,7 +28,7 @@ class BondFENEExpand : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double TWO_1_3;

4
src/MOLECULE/bond_harmonic.cpp
View File

@ -177,10 +177,10 @@ void BondHarmonic::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondHarmonic::single(int type, double rsq, int i, int j, double &eng)
double BondHarmonic::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double rk = k[type] * dr;
eng = rk*dr;
return rk*dr;
}

2
src/MOLECULE/bond_harmonic.h
View File

@ -28,7 +28,7 @@ class BondHarmonic : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double *k,*r0;

5
src/MOLECULE/bond_hybrid.cpp
View File

@ -263,9 +263,10 @@ void BondHybrid::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondHybrid::single(int type, double rsq, int i, int j, double &eng)
double BondHybrid::single(int type, double rsq, int i, int j)
{
if (styles[map[type]]) styles[map[type]]->single(type,rsq,i,j,eng);
if (styles[map[type]]) return styles[map[type]]->single(type,rsq,i,j);
return 0.0;
}
/* ----------------------------------------------------------------------

4
src/MOLECULE/bond_morse.cpp
View File

@ -187,10 +187,10 @@ void BondMorse::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondMorse::single(int type, double rsq, int i, int j, double &eng)
double BondMorse::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double ralpha = exp(-alpha[type]*dr);
eng = d0[type]*(1-ralpha)*(1-ralpha);
return d0[type]*(1-ralpha)*(1-ralpha);
}

2
src/MOLECULE/bond_morse.h
View File

@ -28,7 +28,7 @@ class BondMorse : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double *d0,*alpha,*r0;

4
src/MOLECULE/bond_nonlinear.cpp
View File

@ -182,12 +182,12 @@ void BondNonlinear::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondNonlinear::single(int type, double rsq, int i, int j, double &eng)
double BondNonlinear::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double drsq = dr*dr;
double lamdasq = lamda[type]*lamda[type];
double denom = lamdasq - drsq;
eng = epsilon[type] * drsq / denom;
return epsilon[type] * drsq / denom;
}

2
src/MOLECULE/bond_nonlinear.h
View File

@ -28,7 +28,7 @@ class BondNonlinear : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double *epsilon,*r0,*lamda;

19
src/MOLECULE/bond_quartic.cpp
View File

@ -58,7 +58,6 @@ void BondQuartic::compute(int eflag, int vflag)
int i1,i2,n,m,type,itype,jtype;
double delx,dely,delz,ebond,fbond,evdwl,fpair;
double r,rsq,dr,r2,ra,rb,sr2,sr6;
Pair::One one;
ebond = evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@ -158,9 +157,8 @@ void BondQuartic::compute(int eflag, int vflag)
jtype = atom->type[i2];
if (rsq < cutsq[itype][jtype]) {
force->pair->single(i1,i2,itype,jtype,rsq,1.0,1.0,eflag,one);
fpair = -one.fforce;
if (eflag) evdwl = -(one.eng_vdwl + one.eng_coul);
evdwl = -force->pair->single(i1,i2,itype,jtype,rsq,1.0,1.0,fpair);
fpair = -fpair;
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fpair;
@ -299,12 +297,12 @@ void BondQuartic::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondQuartic::single(int type, double rsq, int i, int j, double &eng)
double BondQuartic::single(int type, double rsq, int i, int j)
{
double r,dr,r2,ra,rb,sr2,sr6;
eng = 0.0;
if (type <= 0) return;
if (type <= 0) return 0.0;
double eng = 0.0;
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
@ -313,9 +311,8 @@ void BondQuartic::single(int type, double rsq, int i, int j, double &eng)
int jtype = atom->type[j];
if (rsq < force->pair->cutsq[itype][jtype]) {
Pair::One one;
force->pair->single(i,j,itype,jtype,rsq,1.0,1.0,1,one);
eng = -one.eng_coul - one.eng_vdwl;
double tmp;
eng = -force->pair->single(i,j,itype,jtype,rsq,1.0,1.0,tmp);
}
// quartic bond
@ -334,4 +331,6 @@ void BondQuartic::single(int type, double rsq, int i, int j, double &eng)
sr6 = sr2*sr2*sr2;
eng += 4.0*sr6*(sr6-1.0) + 1.0;
}
return eng;
}

2
src/MOLECULE/bond_quartic.h
View File

@ -29,7 +29,7 @@ class BondQuartic : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
private:
double TWO_1_3;

6
src/MOLECULE/improper_harmonic.cpp
View File

@ -162,9 +162,9 @@ void ImproperHarmonic::compute(int eflag, int vflag)
sy2 = a22*vb2y + a23*vb3y + a12*vb1y;
sz2 = a22*vb2z + a23*vb3z + a12*vb1z;
f1[0] = a12*vb2x + a13*vb3x + a11*vb1x;
f1[1] = a12*vb2y + a13*vb3y + a11*vb1y;
f1[2] = a12*vb2z + a13*vb3z + a11*vb1z;
f1[0] = a12*vb2x + a13*vb3x + a11*vb1x;
f1[1] = a12*vb2y + a13*vb3y + a11*vb1y;
f1[2] = a12*vb2z + a13*vb3z + a11*vb1z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];

51
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
View File

@ -436,10 +436,10 @@ void PairLJCharmmCoulCharmm::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul,
double factor_lj,
int eflag, One &one)
double PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,switch1,switch2,forcecoul,forcelj,phicoul,philj;
@ -466,29 +466,30 @@ void PairLJCharmmCoulCharmm::single(int i, int j, int itype, int jtype,
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
one.fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
(cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
denom_coul;
phicoul *= switch1;
}
one.eng_coul = factor_coul*phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
(cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
denom_coul;
phicoul *= switch1;
}
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/MOLECULE/pair_lj_charmm_coul_charmm.h
View File

@ -31,7 +31,7 @@ class PairLJCharmmCoulCharmm : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
virtual void single(int, int, int, int, double, double, double, int, One &);
virtual double single(int, int, int, int, double, double, double, double &);
virtual void *extract(char *);
protected:

53
src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
View File

@ -157,10 +157,12 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulCharmmImplicit::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul,
double factor_lj,
int eflag, One &one)
double PairLJCharmmCoulCharmmImplicit::single(int i, int j,
int itype, int jtype,
double rsq,
double factor_coul,
double factor_lj,
double &fforce)
{
double r2inv,r6inv,switch1,switch2,forcecoul,forcelj,phicoul,philj;
@ -187,29 +189,30 @@ void PairLJCharmmCoulCharmmImplicit::single(int i, int j, int itype, int jtype,
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
one.fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*r2inv;
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
(cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
denom_coul;
phicoul *= switch1;
}
one.eng_coul = factor_coul*phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*r2inv;
if (rsq > cut_coul_innersq) {
switch1 = (cut_coulsq-rsq) * (cut_coulsq-rsq) *
(cut_coulsq + 2.0*rsq - 3.0*cut_coul_innersq) /
denom_coul;
phicoul *= switch1;
}
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */

2
src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
View File

@ -22,7 +22,7 @@ class PairLJCharmmCoulCharmmImplicit : public PairLJCharmmCoulCharmm {
public:
PairLJCharmmCoulCharmmImplicit(class LAMMPS *);
void compute(int, int);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
};

4
src/USER-ACKLAND/compute_ackland_atom.cpp
View File

@ -34,6 +34,7 @@
using namespace LAMMPS_NS;
enum{UNKNOWN,BCC,FCC,HCP,ICO};
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
@ -93,6 +94,7 @@ void ComputeAcklandAtom::init_list(int id, NeighList *ptr)
}
/* ---------------------------------------------------------------------- */
void ComputeAcklandAtom::compute_peratom()
{
int i,j,ii,jj,k,n,inum,jnum;
@ -100,6 +102,8 @@ void ComputeAcklandAtom::compute_peratom()
int *ilist,*jlist,*numneigh,**firstneigh;
int chi[8];
invoked |= INVOKED_PERATOM;
// grow structure array if necessary
if (atom->nlocal > nmax) {

30
src/USER-EWALDN/pair_buck_coul.cpp
View File

@ -1116,24 +1116,24 @@ void PairBuckCoul::free_tables()
/* ---------------------------------------------------------------------- */
void PairBuckCoul::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_buck,
int eflag, One &one)
double PairBuckCoul::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_buck,
double &fforce)
{
double f, r, r2inv, r6inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
r = sqrt(rsq);
r2inv = 1.0/rsq;
one.eng_coul = 0.0;
double eng = 0.0;
if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
f = s*(1.0-factor_coul)/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
if (eflag) one.eng_coul = t-f;
eng += t-f;
}
else { // table real space
register float t = rsq;
@ -1141,12 +1141,10 @@ void PairBuckCoul::single(int i, int j, int itype, int jtype,
register double f = (rsq-rtable[k])*drtable[k], qiqj = q[i]*q[j];
t = (1.0-factor_coul)*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) one.eng_coul = qiqj*(etable[k]+f*detable[k]-t);
eng += qiqj*(etable[k]+f*detable[k]-t);
}
}
else force_coul = 0.0;
} else force_coul = 0.0;
one.eng_vdwl = 0.0;
if (rsq < cut_bucksq[itype][jtype]) { // buckingham
register double expr = factor_buck*exp(-sqrt(rsq)*rhoinv[itype][jtype]);
r6inv = r2inv*r2inv*r2inv;
@ -1155,18 +1153,18 @@ void PairBuckCoul::single(int i, int j, int itype, int jtype,
x2 = a2*exp(-x2)*buck_c[itype][jtype];
force_buck = buck1[itype][jtype]*r*expr-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*buck2[itype][jtype];
if (eflag) one.eng_vdwl = buck_a[itype][jtype]*expr-
eng += buck_a[itype][jtype]*expr-
g6*((a2+1.0)*a2+0.5)*x2+t*buck_c[itype][jtype];
}
else { // cut
force_buck =
buck1[itype][jtype]*r*expr-factor_buck*buck_c[itype][jtype]*r6inv;
if (eflag) one.eng_vdwl = buck_a[itype][jtype]*expr-
factor_buck*(buck_c[itype][jtype]*r6inv-offset[itype][jtype]);
eng += buck_a[itype][jtype]*expr-
factor_buck*(buck_c[itype][jtype]*r6inv-offset[itype][jtype]);
}
}
else force_buck = 0.0;
} else force_buck = 0.0;
one.fforce = (force_coul+force_buck)*r2inv;
fforce = (force_coul+force_buck)*r2inv;
return eng;
}

2
src/USER-EWALDN/pair_buck_coul.h
View File

@ -36,7 +36,7 @@ class PairBuckCoul : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
void compute_inner();

31
src/USER-EWALDN/pair_lj_coul.cpp
View File

@ -1107,23 +1107,23 @@ void PairLJCoul::free_tables()
/* ---------------------------------------------------------------------- */
void PairLJCoul::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
double PairLJCoul::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv, r6inv, force_coul, force_lj;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
double eng = 0.0;
r2inv = 1.0/rsq;
one.eng_coul = 0.0;
if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
r = s*(1.0-factor_coul)/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
if (eflag) one.eng_coul = t-r;
eng += t-r;
}
else { // table real space
register float t = rsq;
@ -1131,12 +1131,10 @@ void PairLJCoul::single(int i, int j, int itype, int jtype,
register double f = (rsq-rtable[k])*drtable[k], qiqj = q[i]*q[j];
t = (1.0-factor_coul)*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) one.eng_coul = qiqj*(etable[k]+f*detable[k]-t);
eng += qiqj*(etable[k]+f*detable[k]-t);
}
}
else force_coul = 0.0;
} else force_coul = 0.0;
one.eng_vdwl = 0.0;
if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
r6inv = r2inv*r2inv*r2inv;
if (ewald_order&64) { // long-range
@ -1144,17 +1142,16 @@ void PairLJCoul::single(int i, int j, int itype, int jtype,
x2 = a2*exp(-x2)*lj4[itype][jtype];
force_lj = factor_lj*(r6inv *= r6inv)*lj1[itype][jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
if (eflag) one.eng_vdwl = factor_lj*r6inv*lj3[itype][jtype]-
eng += factor_lj*r6inv*lj3[itype][jtype]-
g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
}
else { // cut
force_lj = factor_lj*r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
if (eflag) one.eng_vdwl = factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
lj4[itype][jtype])-offset[itype][jtype]);
eng += factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
lj4[itype][jtype])-offset[itype][jtype]);
}
}
else force_lj = 0.0;
} else force_lj = 0.0;
one.fforce = (force_coul+force_lj)*r2inv;
fforce = (force_coul+force_lj)*r2inv;
return eng;
}

2
src/USER-EWALDN/pair_lj_coul.h
View File

@ -35,7 +35,7 @@ class PairLJCoul : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
void compute_inner();

2
src/bond.h
View File

@ -38,7 +38,7 @@ class Bond : protected Pointers {
virtual double equilibrium_distance(int) = 0;
virtual void write_restart(FILE *) = 0;
virtual void read_restart(FILE *) = 0;
virtual void single(int, double, int, int, double &) = 0;
virtual double single(int, double, int, int) = 0;
virtual double memory_usage();
protected:

2
src/bond_hybrid.h
View File

@ -32,7 +32,7 @@ class BondHybrid : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double &);
double single(int, double, int, int);
double memory_usage();
private:

16
src/compute.cpp
View File

@ -14,6 +14,7 @@
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "compute.h"
#include "group.h"
#include "domain.h"
@ -32,12 +33,18 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (narg < 3) error->all("Illegal compute command");
// compute ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all("Compute ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find compute group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
@ -53,10 +60,9 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
scalar_flag = vector_flag = peratom_flag = 0;
tempflag = pressflag = peflag = 0;
pressatomflag = peatomflag = 0;
id_pre = NULL;
timeflag = 0;
invoked = 0;
npre = 0;
id_pre = NULL;
comm_forward = comm_reverse = 0;
// set modify defaults
@ -76,8 +82,6 @@ Compute::~Compute()
{
delete [] id;
delete [] style;
for (int i = 0; i < npre; i++) delete [] id_pre[i];
delete [] id_pre;
memory->sfree(tlist);
@ -117,7 +121,7 @@ void Compute::modify_params(int narg, char **arg)
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
void Compute::add_step(int ntimestep)
void Compute::addstep(int ntimestep)
{
// i = location in list to insert ntimestep
@ -149,7 +153,7 @@ void Compute::add_step(int ntimestep)
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
int Compute::match_step(int ntimestep)
int Compute::matchstep(int ntimestep)
{
for (int i = ntime-1; i >= 0; i--) {
if (ntimestep < tlist[i]) return 0;

16
src/compute.h
View File

@ -33,8 +33,10 @@ class Compute : protected Pointers {
int size_vector; // N = size of global vector
int peratom_flag; // 0/1 if compute_peratom() function exists
int size_peratom; // 0 = scalar_atom, N = size of vector_atom
int extscalar; // 0/1 if scalar is intensive/extensive
int extvector; // 0/1/-1 if vector is all int/ext/extlist
int *extlist; // list of 0/1 int/ext for each vec component
int extensive; // 0/1 if scalar,vector are intensive/extensive values
int tempflag; // 1 if Compute can be used as temperature
// must have both compute_scalar, compute_vector
int pressflag; // 1 if Compute can be used as pressure (uses virial)
@ -43,17 +45,17 @@ class Compute : protected Pointers {
int peflag; // 1 if Compute calculates PE (uses Force energies)
int peatomflag; // 1 if Compute calculates per-atom PE
char *id_pre; // ID of pre-compute the Compute may store
int timeflag; // 1 if Compute stores list of timesteps it's called on
int ntime; // # of entries in time list
int maxtime; // max # of entries time list can hold
int *tlist; // time list of steps the Compute is called on
int invoked; // 1 if Compute was invoked (e.g. by a variable)
int invoked; // set when Compute is invoked, to avoid re-invoking
double dof; // degrees-of-freedom for temperature
int npre; // # of computes to compute before this one
char **id_pre; // IDs of Computes to compute before this one
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
@ -71,8 +73,8 @@ class Compute : protected Pointers {
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
void add_step(int);
int match_step(int);
void addstep(int);
int matchstep(int);
virtual double memory_usage() {return 0.0;}

211
src/compute_attribute_atom.cpp
View File

@ -1,211 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_attribute_atom.h"
#include "atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{X,Y,Z,XU,YU,ZU,VX,VY,VZ,FX,FY,FZ,XYZ,V,F};
/* --------------------------------------------------------------------- */
ComputeAttributeAtom::ComputeAttributeAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute ke/atom command");
peratom_flag = 1;
size_peratom = 0;
if (strcmp(arg[3],"x") == 0) which = X;
else if (strcmp(arg[3],"y") == 0) which = Y;
else if (strcmp(arg[3],"z") == 0) which = Z;
else if (strcmp(arg[3],"xu") == 0) which = XU;
else if (strcmp(arg[3],"yu") == 0) which = YU;
else if (strcmp(arg[3],"zu") == 0) which = ZU;
else if (strcmp(arg[3],"vx") == 0) which = VX;
else if (strcmp(arg[3],"vy") == 0) which = VY;
else if (strcmp(arg[3],"vz") == 0) which = VZ;
else if (strcmp(arg[3],"fx") == 0) which = FX;
else if (strcmp(arg[3],"fy") == 0) which = FY;
else if (strcmp(arg[3],"fz") == 0) which = FZ;
else if (strcmp(arg[3],"xyz") == 0) {
which = XYZ;
size_peratom = 3;
} else if (strcmp(arg[3],"v") == 0) {
which = V;
size_peratom = 3;
} else if (strcmp(arg[3],"f") == 0) {
which = F;
size_peratom = 3;
} else error->all("Illegal compute attribute/atom command");
nmax = 0;
s_attribute = NULL;
v_attribute = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeAttributeAtom::~ComputeAttributeAtom()
{
memory->sfree(s_attribute);
memory->destroy_2d_double_array(v_attribute);
}
/* ---------------------------------------------------------------------- */
void ComputeAttributeAtom::compute_peratom()
{
// grow attribute array if necessary
if (atom->nlocal > nmax) {
if (size_peratom == 0) {
memory->sfree(s_attribute);
nmax = atom->nmax;
s_attribute = (double *)
memory->smalloc(nmax*sizeof(double),
"compute/attribute/atom:s_attribute");
scalar_atom = s_attribute;
} else {
memory->destroy_2d_double_array(v_attribute);
nmax = atom->nmax;
v_attribute =
memory->create_2d_double_array(nmax,size_peratom,
"compute/attribute/atom:v_attribute");
vector_atom = v_attribute;
}
}
// fill attribute vector with appropriate atom value
// or simply set pointer to exisitng atom vector
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
if (which == X) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = x[i][0];
else s_attribute[i] = 0.0;
} else if (which == Y) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = x[i][1];
else s_attribute[i] = 0.0;
} else if (which == Z) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = x[i][2];
else s_attribute[i] = 0.0;
} else if (which == XU) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
s_attribute[i] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
else s_attribute[i] = 0.0;
} else if (which == YU) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
s_attribute[i] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
else s_attribute[i] = 0.0;
} else if (which == ZU) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
s_attribute[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
else s_attribute[i] = 0.0;
} else if (which == VX) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = v[i][0];
else s_attribute[i] = 0.0;
} else if (which == VY) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = v[i][1];
else s_attribute[i] = 0.0;
} else if (which == VZ) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = v[i][2];
else s_attribute[i] = 0.0;
} else if (which == FX) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = f[i][0];
else s_attribute[i] = 0.0;
} else if (which == FY) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = f[i][1];
else s_attribute[i] = 0.0;
} else if (which == FZ) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_attribute[i] = f[i][2];
else s_attribute[i] = 0.0;
} else if (which == XYZ) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v_attribute[i][0] = x[i][0];
v_attribute[i][1] = x[i][1];
v_attribute[i][2] = x[i][2];
} else {
v_attribute[i][0] = 0.0;
v_attribute[i][1] = 0.0;
v_attribute[i][2] = 0.0;
}
} else if (which == V) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v_attribute[i][0] = v[i][0];
v_attribute[i][1] = v[i][1];
v_attribute[i][2] = v[i][2];
} else {
v_attribute[i][0] = 0.0;
v_attribute[i][1] = 0.0;
v_attribute[i][2] = 0.0;
}
} else if (which == F) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v_attribute[i][0] = f[i][0];
v_attribute[i][1] = f[i][1];
v_attribute[i][2] = f[i][2];
} else {
v_attribute[i][0] = 0.0;
v_attribute[i][1] = 0.0;
v_attribute[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeAttributeAtom::memory_usage()
{
double bytes = 0.0;
if (size_peratom == 0) bytes = nmax * sizeof(double);
else bytes = size_peratom * nmax * sizeof(double);
return bytes;
}

36
src/compute_attribute_atom.h
View File

@ -1,36 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef COMPUTE_ATTRIBUTE_ATOM_H
#define COMPUTE_ATTRIBUTE_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeAttributeAtom : public Compute {
public:
ComputeAttributeAtom(class LAMMPS *, int, char **);
~ComputeAttributeAtom();
void init() {}
void compute_peratom();
double memory_usage();
private:
int which,allocate,nmax;
double *s_attribute,**v_attribute;
};
}
#endif

4
src/compute_centro_atom.cpp
View File

@ -27,6 +27,8 @@
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
@ -89,6 +91,8 @@ void ComputeCentroAtom::compute_peratom()
int *ilist,*jlist,*numneigh,**firstneigh;
double pairs[66];
invoked |= INVOKED_PERATOM;
// grow centro array if necessary
if (atom->nlocal > nmax) {

4
src/compute_coord_atom.cpp
View File

@ -27,6 +27,8 @@
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
@ -88,6 +90,8 @@ void ComputeCoordAtom::compute_peratom()
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
invoked |= INVOKED_PERATOM;
// grow coordination array if necessary
if (atom->nlocal > nmax) {

4
src/compute_ke_atom.cpp
View File

@ -22,6 +22,8 @@
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
ComputeKEAtom::ComputeKEAtom(LAMMPS *lmp, int narg, char **arg) :
@ -58,6 +60,8 @@ void ComputeKEAtom::init()
void ComputeKEAtom::compute_peratom()
{
invoked |= INVOKED_PERATOM;
// grow ke array if necessary
if (atom->nlocal > nmax) {

8
src/compute_pe.cpp
View File

@ -28,6 +28,8 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
/* ---------------------------------------------------------------------- */
ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) :
@ -62,7 +64,7 @@ ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) :
// settings
scalar_flag = 1;
extensive = 1;
extscalar = 1;
peflag = 1;
timeflag = 1;
}
@ -71,9 +73,9 @@ ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) :
double ComputePE::compute_scalar()
{
invoked = 1;
double one = 0.0;
invoked |= INVOKED_SCALAR;
double one = 0.0;
if (pairflag && force->pair)
one += force->pair->eng_vdwl + force->pair->eng_coul;

4
src/compute_pe_atom.cpp
View File

@ -26,6 +26,8 @@
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
@ -74,7 +76,7 @@ void ComputePEAtom::compute_peratom()
{
int i;
invoked = 1;
invoked |= INVOKED_PERATOM;
// grow local energy array if necessary

46
src/compute_pressure.cpp
View File

@ -30,6 +30,9 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
@ -40,21 +43,19 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
pressflag = 1;
timeflag = 1;
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
npre = 1;
id_pre = new char*[1];
int n = strlen(arg[3]) + 1;
id_pre[0] = new char[n];
strcpy(id_pre[0],arg[3]);
int icompute = modify->find_compute(id_pre[0]);
id_pre = new char[n];
strcpy(id_pre,arg[3]);
int icompute = modify->find_compute(id_pre);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
if (modify->compute[icompute]->tempflag == 0)
error->all("Compute pressure temp ID does not compute temperature");
@ -109,7 +110,7 @@ void ComputePressure::init()
// set temperature used by pressure
int icompute = modify->find_compute(id_pre[0]);
int icompute = modify->find_compute(id_pre);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
temperature = modify->compute[icompute];
@ -153,16 +154,25 @@ void ComputePressure::init()
/* ----------------------------------------------------------------------
compute total pressure, averaged over Pxx, Pyy, Pzz
assume temperature has already been computed
------------------------------------------------------------------------- */
double ComputePressure::compute_scalar()
{
invoked |= INVOKED_SCALAR;
// invoke temperature it it hasn't been already
double t;
if (keflag) {
if (temperature->invoked & INVOKED_SCALAR) t = temperature->scalar;
else t = temperature->compute_scalar();
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(3,3);
if (keflag)
scalar = (temperature->dof * boltz * temperature->scalar +
scalar = (temperature->dof * boltz * t +
virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
@ -170,7 +180,7 @@ double ComputePressure::compute_scalar()
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(2,2);
if (keflag)
scalar = (temperature->dof * boltz * temperature->scalar +
scalar = (temperature->dof * boltz * t +
virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
@ -186,11 +196,21 @@ double ComputePressure::compute_scalar()
void ComputePressure::compute_vector()
{
invoked |= INVOKED_VECTOR;
// invoke temperature it it hasn't been already
double *ke_tensor;
if (keflag) {
if (!(temperature->invoked & INVOKED_VECTOR))
temperature->compute_vector();
ke_tensor = temperature->vector;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(6,3);
if (keflag) {
double *ke_tensor = temperature->vector;
for (int i = 0; i < 6; i++)
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
} else
@ -200,7 +220,6 @@ void ComputePressure::compute_vector()
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(4,2);
if (keflag) {
double *ke_tensor = temperature->vector;
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
@ -219,7 +238,6 @@ void ComputePressure::virial_compute(int n, int ndiag)
int i,j;
double v[6],*vcomponent;
invoked = 1;
for (i = 0; i < n; i++) v[i] = 0.0;
// sum contributions to virial from forces and fixes

5
src/compute_rotate_dipole.cpp
View File

@ -20,6 +20,7 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INERTIA3D 0.4 // moments of inertia for sphere and disk
#define INERTIA2D 0.5
@ -34,7 +35,7 @@ ComputeRotateDipole::ComputeRotateDipole(LAMMPS *lmp, int narg, char **arg) :
error->all("Compute rotate/dipole requires atom attributes dipole, omega");
scalar_flag = 1;
extensive = 1;
extscalar = 1;
inertia = NULL;
}
@ -68,6 +69,8 @@ void ComputeRotateDipole::init()
double ComputeRotateDipole::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double *dipole = atom->dipole;
double **omega = atom->omega;
int *type = atom->type;

5
src/compute_rotate_gran.cpp
View File

@ -21,6 +21,7 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INERTIA3D 0.4 // moments of inertia for sphere and disk
#define INERTIA2D 0.5
@ -36,7 +37,7 @@ ComputeRotateGran::ComputeRotateGran(LAMMPS *lmp, int narg, char **arg) :
"radius, rmass, omega");
scalar_flag = 1;
extensive = 1;
extscalar = 1;
}
/* ---------------------------------------------------------------------- */
@ -51,6 +52,8 @@ void ComputeRotateGran::init()
double ComputeRotateGran::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **omega = atom->omega;
double *radius = atom->radius;
double *rmass = atom->rmass;

4
src/compute_stress_atom.cpp
View File

@ -27,6 +27,8 @@
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 4
/* ---------------------------------------------------------------------- */
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
@ -78,7 +80,7 @@ void ComputeStressAtom::compute_peratom()
{
int i,j;
invoked = 1;
invoked |= INVOKED_PERATOM;
// grow local stress array if necessary

305
src/compute_sum.cpp
View File

@ -12,16 +12,27 @@
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "compute_sum.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_PERATOM 4
enum{X,V,F,COMPUTE,FIX,VARIABLE};
/* ---------------------------------------------------------------------- */
ComputeSum::ComputeSum(LAMMPS *lmp, int narg, char **arg) :
@ -29,74 +40,171 @@ ComputeSum::ComputeSum(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 4) error->all("Illegal compute sum command");
// store pre-compute IDs
// parse remaining values
npre = narg - 3;
id_pre = new char*[npre];
for (int i = 0; i < npre; i++) {
int iarg = i + 3;
int n = strlen(arg[iarg]) + 1;
id_pre[i] = new char[n];
strcpy(id_pre[i],arg[iarg]);
which = new int[narg-3];
argindex = new int[narg-3];
ids = new char*[narg-3];
value2index = new int[narg-3];
nvalues = 0;
int iarg = 3;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal compute sum command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else error->all("Illegal compute sum command");
iarg++;
}
compute = new Compute*[npre];
// setup and error check
// all sub-computes must be peratom
// check consistency of sub-computes for scalar & vector output
int icompute;
for (int i = 0; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Compute sum compute is not a per-atom compute");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for compute sum does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Compute sum compute does not calculate per-atom values");
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
error->all("Compute sum compute does not calculate a per-atom scalar");
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
error->all("Compute sum compute does not calculate a per-atom vector");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for compute sum does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Compute sum fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom != 0)
error->all("Compute sum fix does not calculate a per-atom scalar");
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
error->all("Compute sum fix does not calculate a per-atom vector");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for compute sum does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Compute sum variable is not atom-style variable");
}
}
peratom_flag = 0;
extensive = 0;
// this compute produces either a scalar or vector
icompute = modify->find_compute(id_pre[0]);
int size = modify->compute[icompute]->size_peratom;
if (size == 0) {
if (nvalues == 1) {
scalar_flag = 1;
extscalar = 1;
vector = NULL;
onevec = NULL;
} else {
vector_flag = 1;
size_vector = size;
size_vector = nvalues;
extvector = 1;
vector = new double[size_vector];
onevec = new double[size_vector];
}
for (int i = 1; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (modify->compute[icompute]->size_peratom != size)
error->all("Inconsistent sizes of compute sum compute quantities");
}
maxatom = 0;
varatom = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSum::~ComputeSum()
{
delete [] compute;
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
delete [] vector;
delete [] onevec;
memory->sfree(varatom);
}
/* ---------------------------------------------------------------------- */
void ComputeSum::init()
{
// set ptrs to Computes used as pre-computes by this compute
// set indices and check validity of all computes,fixes,variables
for (int i = 0; i < npre; i++) {
int icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
compute[i] = modify->compute[icompute];
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for compute sum does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for compute sum does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for compute sum does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
@ -104,31 +212,10 @@ void ComputeSum::init()
double ComputeSum::compute_scalar()
{
int i;
// invoke all the pre-computes
// this is the only compute that does this
// done b/c pre-computes are per-atom and this compute is not
for (int icompute = 0; icompute < npre; icompute++)
compute[icompute]->compute_peratom();
// compute scalar quantity by summing over atom scalars
// only include atoms in group
int *mask = atom->mask;
int nlocal = atom->nlocal;
double one = 0.0;
for (int icompute = 0; icompute < npre; icompute++) {
double *scalar_atom = compute[icompute]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += scalar_atom[i];
}
invoked |= INVOKED_SCALAR;
double one = compute_one(0);
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
return scalar;
}
@ -136,30 +223,100 @@ double ComputeSum::compute_scalar()
void ComputeSum::compute_vector()
{
int i,j;
invoked |= INVOKED_VECTOR;
// invoke all the pre-computes
// this is the only compute that does this
// done b/c pre-computes are per-atom and this compute is not
for (int m = 0; m < nvalues; m++) onevec[m] = compute_one(m);
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
}
for (int icompute = 0; icompute < npre; icompute++)
compute[icompute]->compute_peratom();
/* ---------------------------------------------------------------------- */
// compute vector quantity by summing over atom vectors
double ComputeSum::compute_one(int m)
{
int i;
// invoke the appropriate attribute,compute,fix,variable
// compute scalar quantity by summing over atom scalars
// only include atoms in group
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (j = 0; j < size_vector; j++) onevec[j] = 0.0;
int n = value2index[m];
int j = argindex[m];
double one = 0.0;
for (int icompute = 0; icompute < npre; icompute++) {
double **vector_atom = compute[icompute]->vector_atom;
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
for (j = 0; j < size_vector; j++)
onevec[j] += vector_atom[i][j];
if (mask[i] & groupbit) one += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
if (!(modify->compute[n]->invoked & INVOKED_PERATOM))
modify->compute[n]->compute_peratom();
if (j == 0) {
double *compute_scalar = modify->compute[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += compute_scalar[i];
} else {
double **compute_vector = modify->compute[n]->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += compute_vector[i][jm1];
}
// access fix fields, check if frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[n]->peratom_freq)
error->all("Fix used in compute sum not computed at compatible time");
if (j == 0) {
double *fix_scalar = modify->fix[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += fix_scalar[i];
} else {
double **fix_vector = modify->fix[n]->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += fix_vector[i][jm1];
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (nlocal > maxatom) {
maxatom = atom->nmax;
memory->sfree(varatom);
varatom = (double *)
memory->smalloc(maxatom*sizeof(double),"compute/sum:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += varatom[i];
}
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
return one;
}
/* ----------------------------------------------------------------------
memory usage of varatom
------------------------------------------------------------------------- */
double ComputeSum::memory_usage()
{
double bytes = maxatom * sizeof(double);
return bytes;
}

10
src/compute_sum.h
View File

@ -25,10 +25,18 @@ class ComputeSum : public Compute {
void init();
double compute_scalar();
void compute_vector();
double memory_usage();
private:
int nvalues;
int *which,*argindex,*value2index;
char **ids;
double *onevec;
class Compute **compute;
int maxatom;
double *varatom;
double compute_one(int);
};
}

166
src/compute_sum_atom.cpp
View File

@ -1,166 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_sum_atom.h"
#include "atom.h"
#include "modify.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSumAtom::ComputeSumAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal compute sum/atom command");
// store pre-compute IDs
npre = narg - 3;
id_pre = new char*[npre];
for (int i = 0; i < npre; i++) {
int iarg = i + 3;
int n = strlen(arg[iarg]) + 1;
id_pre[i] = new char[n];
strcpy(id_pre[i],arg[iarg]);
}
compute = new Compute*[npre];
// all sub-computes must be peratom
// check consistency of sub-computes for scalar & vector output
int icompute;
for (int i = 0; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Compute sum/atom compute is not a per-atom compute");
}
peratom_flag = 1;
icompute = modify->find_compute(id_pre[0]);
size_peratom = modify->compute[icompute]->size_peratom;
for (int i = 1; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (modify->compute[icompute]->size_peratom != size_peratom)
error->all("Inconsistent sizes of compute sum/atom compute quantities");
}
// values generated by this compute
nmax = 0;
s_value = NULL;
v_value = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSumAtom::~ComputeSumAtom()
{
delete [] compute;
memory->sfree(s_value);
memory->destroy_2d_double_array(v_value);
}
/* ---------------------------------------------------------------------- */
void ComputeSumAtom::init()
{
// set ptrs to Computes used as pre-computes by this compute
for (int i = 0; i < npre; i++) {
int icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
compute[i] = modify->compute[icompute];
}
}
/* ---------------------------------------------------------------------- */
void ComputeSumAtom::compute_peratom()
{
int i,j,m;
// grow sum array if necessary
if (atom->nlocal > nmax) {
nmax = atom->nmax;
if (size_peratom == 0) {
memory->sfree(s_value);
s_value = (double *)
memory->smalloc(nmax*sizeof(double),"compute/sum/atom:s_value");
scalar_atom = s_value;
} else {
memory->destroy_2d_double_array(v_value);
v_value = memory->create_2d_double_array(nmax,size_peratom,
"compute/sum/atom:v_value");
vector_atom = v_value;
}
}
// sum over pre-computes
// pre-computes of the pre-computes are not invoked
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (size_peratom == 0) {
double *scalar = compute[0]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_value[i] = scalar[i];
else s_value[i] = 0.0;
for (m = 1; m < npre; m++) {
scalar = compute[m]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_value[i] += scalar[i];
}
} else {
double **vector = compute[0]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
for (j = 0; j < size_peratom; j++)
v_value[i][j] = vector[i][j];
else
for (j = 0; j < size_peratom; j++)
v_value[i][j] = 0.0;
for (m = 1; m < npre; m++) {
vector = compute[m]->vector_atom;
for (j = 0; j < size_peratom; j++)
if (mask[i] & groupbit) v_value[i][j] += vector[i][j];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeSumAtom::memory_usage()
{
double bytes = 0.0;
if (size_peratom == 0) bytes = nmax * sizeof(double);
else bytes = nmax*size_peratom * sizeof(double);
return bytes;
}

37
src/compute_sum_atom.h
View File

@ -1,37 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef COMPUTE_SUM_ATOM_H
#define COMPUTE_SUM_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeSumAtom : public Compute {
public:
ComputeSumAtom(class LAMMPS *, int, char **);
~ComputeSumAtom();
void init();
void compute_peratom();
double memory_usage();
private:
int nmax;
class Compute **compute;
double *s_value,**v_value;
};
}
#endif

10
src/compute_temp.cpp
View File

@ -23,6 +23,9 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
@ -32,7 +35,8 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -70,6 +74,8 @@ void ComputeTemp::recount()
double ComputeTemp::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -102,6 +108,8 @@ void ComputeTemp::compute_vector()
{
int i;
invoked |= INVOKED_VECTOR;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;

9
src/compute_temp_deform.cpp
View File

@ -30,6 +30,8 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
/* ---------------------------------------------------------------------- */
@ -41,7 +43,8 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -95,6 +98,8 @@ double ComputeTempDeform::compute_scalar()
{
double lamda[3],vstream[3],vthermal[3];
invoked |= INVOKED_SCALAR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -153,6 +158,8 @@ void ComputeTempDeform::compute_vector()
{
double lamda[3],vstream[3],vthermal[3];
invoked |= INVOKED_VECTOR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;

10
src/compute_temp_partial.cpp
View File

@ -23,6 +23,9 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
@ -36,7 +39,8 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -74,6 +78,8 @@ void ComputeTempPartial::recount()
double ComputeTempPartial::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -107,6 +113,8 @@ void ComputeTempPartial::compute_vector()
{
int i;
invoked |= INVOKED_VECTOR;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;

10
src/compute_temp_ramp.cpp
View File

@ -29,6 +29,9 @@ using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
@ -101,7 +104,8 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -141,6 +145,8 @@ double ComputeTempRamp::compute_scalar()
{
double fraction,vramp,vthermal[3];
invoked |= INVOKED_SCALAR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -181,6 +187,8 @@ void ComputeTempRamp::compute_vector()
int i;
double fraction,vramp,vthermal[3];
invoked |= INVOKED_VECTOR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;

10
src/compute_temp_region.cpp
View File

@ -22,6 +22,9 @@
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
@ -34,7 +37,8 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = vector_flag = 1;
size_vector = 6;
extensive = 0;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[6];
@ -58,6 +62,8 @@ void ComputeTempRegion::init()
double ComputeTempRegion::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -102,6 +108,8 @@ void ComputeTempRegion::compute_vector()
{
int i;
invoked |= INVOKED_VECTOR;
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;

65
src/compute_variable.cpp
View File

@ -1,65 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "compute_variable.h"
#include "input.h"
#include "variable.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeVariable::ComputeVariable(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute variable command");
// store variable name
int n = strlen(arg[3]) + 1;
varname = new char[n];
strcpy(varname,arg[3]);
scalar_flag = 1;
extensive = 0;
}
/* ---------------------------------------------------------------------- */
ComputeVariable::~ComputeVariable()
{
delete [] varname;
}
/* ---------------------------------------------------------------------- */
void ComputeVariable::init()
{
// check if variable exists
int ivariable = input->variable->find(varname);
if (ivariable < 0)
error->all("Could not find compute variable name");
}
/* ---------------------------------------------------------------------- */
double ComputeVariable::compute_scalar()
{
scalar = atof(input->variable->retrieve(varname));
return scalar;
}

34
src/compute_variable.h
View File

@ -1,34 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef COMPUTE_VARIABLE_H
#define COMPUTE_VARIABLE_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeVariable : public Compute {
public:
ComputeVariable(class LAMMPS *, int, char **);
~ComputeVariable();
void init();
double compute_scalar();
private:
char *varname;
};
}
#endif

94
src/compute_variable_atom.cpp
View File

@ -1,94 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_variable_atom.h"
#include "atom.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeVariableAtom::ComputeVariableAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute variable/atom command");
// store variable name
int n = strlen(arg[3]) + 1;
varname = new char[n];
strcpy(varname,arg[3]);
peratom_flag = 1;
size_peratom = 0;
nmax = 0;
result = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeVariableAtom::~ComputeVariableAtom()
{
delete [] varname;
memory->sfree(result);
}
/* ---------------------------------------------------------------------- */
void ComputeVariableAtom::init()
{
// set ivariable used by this compute and check if it exists
ivariable = input->variable->find(varname);
if (ivariable < 0)
error->all("Could not find compute variable name");
}
/* ---------------------------------------------------------------------- */
void ComputeVariableAtom::compute_peratom()
{
// grow result array if necessary
if (atom->nlocal > nmax) {
memory->sfree(result);
nmax = atom->nmax;
result = (double *) memory->smalloc(nmax*sizeof(double),
"compute/variable/atom:result");
scalar_atom = result;
}
// parse variable once to create parse tree
// evaluate tree for all atoms, will be zero for atoms not in group
// free parse tree memory stored by Variable
input->variable->build_parse_tree(ivariable);
input->variable->evaluate_parse_tree(igroup,result);
input->variable->free_parse_tree();
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeVariableAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

37
src/compute_variable_atom.h
View File

@ -1,37 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef COMPUTE_VARIABLE_ATOM_H
#define COMPUTE_VARIABLE_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeVariableAtom : public Compute {
public:
ComputeVariableAtom(class LAMMPS *, int, char **);
~ComputeVariableAtom();
void init();
void compute_peratom();
double memory_usage();
private:
int nmax,ivariable;
char *varname;
double *result;
};
}
#endif

183
src/dump_custom.cpp
View File

@ -40,6 +40,8 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
#define INVOKED_PERATOM 4 // same as in computes
/* ---------------------------------------------------------------------- */
DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
@ -247,7 +249,7 @@ int DumpCustom::count()
{
int i;
// grow choose and variable storage arrays if needed
// grow choose and variable vbuf arrays if needed
int nlocal = atom->nlocal;
if (nlocal > maxlocal) {
@ -267,21 +269,18 @@ int DumpCustom::count()
}
// invoke Computes for per-atom dump quantities
// only if not already invoked
if (ncompute)
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
for (i = 0; i < ncompute; i++)
if (!(compute[i]->invoked & INVOKED_PERATOM))
compute[i]->compute_peratom();
// invoke Variables for per-atom dump quantities
// parse variable once to create parse tree
// evaluate tree for all atoms, will be zero for atoms not in group
// free parse tree memory stored by Variable
// evaluate atom-style Variables for per-atom dump quantities
if (nvariable)
for (i = 0; i < nvariable; i++) {
input->variable->build_parse_tree(variable[i]);
input->variable->evaluate_parse_tree(igroup,vbuf[i]);
input->variable->free_parse_tree();
}
for (i = 0; i < nvariable; i++)
input->variable->compute_atom(variable[i],igroup,vbuf[i],1,0);
// choose all local atoms for output
@ -722,7 +721,6 @@ void DumpCustom::parse_fields(int narg, char **arg)
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// if Compute has pre-computes, first add them to list
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_compute;
@ -752,9 +750,6 @@ void DumpCustom::parse_fields(int narg, char **arg)
argindex[i] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->npre)
for (int ic = 0; ic < modify->compute[n]->npre; ic++)
int tmp = add_compute(modify->compute[n]->id_pre[ic]);
field2index[i] = add_compute(suffix);
delete [] suffix;
@ -806,8 +801,8 @@ void DumpCustom::parse_fields(int narg, char **arg)
n = input->variable->find(suffix);
if (n < 0) error->all("Could not find dump custom variable name");
if (input->variable->peratom(n) == 0)
error->all("Dump custom variable does not compute peratom info");
if (input->variable->atomstyle(n) == 0)
error->all("Dump custom variable is not atom-style variable");
field2index[i] = add_variable(suffix);
delete [] suffix;
@ -983,7 +978,6 @@ int DumpCustom::modify_param(int narg, char **arg)
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2index and argindex arrays, since access is beyond nfield
// if Compute has pre-computes, first add them to list
else if (strncmp(arg[1],"c_",2) == 0) {
thresh_array[nthresh] = COMPUTE;
@ -1020,9 +1014,6 @@ int DumpCustom::modify_param(int narg, char **arg)
argindex[nfield+nthresh] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->npre)
for (int ic = 0; ic < modify->compute[n]->npre; ic++)
int tmp = add_compute(modify->compute[n]->id_pre[ic]);
field2index[nfield+nthresh] = add_compute(suffix);
delete [] suffix;
@ -1087,8 +1078,8 @@ int DumpCustom::modify_param(int narg, char **arg)
n = input->variable->find(suffix);
if (n < 0) error->all("Could not find dump custom variable name");
if (input->variable->peratom(n) == 0)
error->all("Dump custom variable does not compute peratom info");
if (input->variable->atomstyle(n) == 0)
error->all("Dump custom variable is not atom-style variable");
field2index[nfield+nthresh] = add_variable(suffix);
delete [] suffix;
@ -1129,11 +1120,80 @@ double DumpCustom::memory_usage()
return bytes;
}
// ----------------------------------------------------------------------
// one method for every keyword dump custom can output
// the atom quantity is packed into buf starting at n with stride size_one
// customize by adding a method
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
extraction of Compute, Fix, Variable results
------------------------------------------------------------------------- */
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2index[n]]->scalar_atom;
double **array = compute[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fix(int n)
{
double *vector = fix[field2index[n]]->scalar_atom;
double **array = fix[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_variable(int n)
{
double *vector = vbuf[field2index[n]];
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
}
/* ----------------------------------------------------------------------
one method for every keyword dump custom can output
the atom quantity is packed into buf starting at n with stride size_one
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
@ -1597,70 +1657,3 @@ void DumpCustom::pack_tqz(int n)
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2index[n]]->scalar_atom;
double **array = compute[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fix(int n)
{
double *vector = fix[field2index[n]]->scalar_atom;
double **array = fix[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_variable(int n)
{
double *vector = vbuf[field2index[n]];
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
}

9
src/fix.cpp
View File

@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "string.h"
#include "ctype.h"
#include "fix.h"
#include "group.h"
#include "error.h"
@ -22,11 +23,19 @@ using namespace LAMMPS_NS;
Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
// fix ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all("Fix ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find fix group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;

4
src/fix.h
View File

@ -38,7 +38,9 @@ class Fix : protected Pointers {
int vector_flag; // 0/1 if compute_vector() function exists
int size_vector; // N = size of global vector
int scalar_vector_freq; // frequency compute s/v data is available at
int extensive; // 0/1 if s/v are intensive/extensive values
int extscalar; // 0/1 if scalar is intensive/extensive
int extvector; // 0/1/-1 if vector is all int/ext/extlist
int *extlist; // list of 0/1 int/ext for each vec component
int peratom_flag; // 0/1 if per-atom data is stored
int size_peratom; // 0 = scalar_atom, N = size of vector_atom

331
src/fix_ave_atom.cpp
View File

@ -18,25 +18,99 @@
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{X,V,F,COMPUTE,FIX,VARIABLE};
#define INVOKED_PERATOM 4 // same as in computes
/* ---------------------------------------------------------------------- */
FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all("Illegal fix ave/atom command");
if (narg < 7) error->all("Illegal fix ave/atom command");
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
peratom_freq = atoi(arg[5]);
int n = strlen(arg[6]) + 1;
id_compute = new char[n];
strcpy(id_compute,arg[6]);
// parse remaining values
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/atom command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else error->all("Illegal fix ave/atom command");
iarg++;
}
// setup and error check
@ -45,24 +119,49 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
(nrepeat-1)*nevery >= peratom_freq)
error->all("Illegal fix ave/atom command");
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Compute ID for fix ave/atom does not exist");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/atom compute does not calculate per-atom values");
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
error->all("Fix ave/atom compute does not calculate a per-atom scalar");
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
error->all("Fix ave/atom compute does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom)
error->all("Fix ave/atom compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/atom fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom != 0)
error->all("Fix ave/atom fix does not calculate a per-atom scalar");
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
error->all("Fix ave/atom fix does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom)
error->all("Fix ave/atom fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/atom variable is not atom-style variable");
}
}
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/atom compute does not calculate per-atom info");
// this fix produces either a per-atom scalar or vector
peratom_flag = 1;
// setup list of computes to call, including pre-computes
ncompute = 1 + modify->compute[icompute]->npre;
compute = new Compute*[ncompute];
if (nvalues == 1) size_peratom = 0;
else size_peratom = nvalues;
// perform initial allocation of atom-based array
// register with Atom class
size_peratom = modify->compute[icompute]->size_peratom;
scalar = NULL;
vector = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
@ -70,12 +169,9 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
// zero the array since dump may access it on timestep 0
int nlocal = atom->nlocal;
if (size_peratom == 0)
for (int i = 0; i < nlocal; i++) scalar[i] = 0.0;
else
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < size_peratom; m++)
vector[i][m] = 0.0;
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < nvalues; m++)
vector[i][m] = 0.0;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of peratom_freq and nrepeat = 1
@ -89,12 +185,11 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += peratom_freq;
// set timestep for all computes that store invocation times
// since don't know a priori which are invoked by this fix
// add nvalid to ALL computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can just set timestep for ones actually invoked
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->add_step(nvalid);
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
@ -105,9 +200,12 @@ FixAveAtom::~FixAveAtom()
atom->delete_callback(id,0);
delete [] id_compute;
delete [] compute;
memory->sfree(scalar);
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy_2d_double_array(vector);
}
@ -124,29 +222,49 @@ int FixAveAtom::setmask()
void FixAveAtom::init()
{
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Compute ID for fix ave/atom does not exist");
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/atom does not exist");
value2index[m] = icompute;
ncompute = 0;
if (modify->compute[icompute]->npre)
for (int i = 0; i < modify->compute[icompute]->npre; i++) {
int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
if (ic < 0)
error->all("Precompute ID of compute for fix ave/atom does not exist");
compute[ncompute++] = modify->compute[ic];
}
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/atom does not exist");
value2index[m] = ifix;
compute[ncompute++] = modify->compute[icompute];
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/atom not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/atom does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveAtom::setup()
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveAtom::end_of_step()
{
int i,m;
int i,j,m,n;
// skip if not step which requires doing something
@ -156,32 +274,70 @@ void FixAveAtom::end_of_step()
int nlocal = atom->nlocal;
if (irepeat == 0) {
if (size_peratom == 0)
for (i = 0; i < nlocal; i++) scalar[i] = 0.0;
else
for (i = 0; i < nlocal; i++)
for (m = 0; m < size_peratom; m++)
vector[i][m] = 0.0;
}
if (irepeat == 0)
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
vector[i][m] = 0.0;
// accumulate results of compute to local copy
// accumulate results of attributes,computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
int *mask = atom->mask;
if (size_peratom == 0) {
double *compute_scalar = compute[ncompute-1]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) scalar[i] += compute_scalar[i];
} else {
double **compute_vector = compute[ncompute-1]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
for (m = 0; m < size_peratom; m++)
vector[i][m] += compute_vector[i][m];
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked & INVOKED_PERATOM)) compute->compute_peratom();
if (j == 0) {
double *compute_scalar = compute->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += compute_scalar[i];
} else {
int jm1 = j - 1;
double **compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += compute_vector[i][jm1];
}
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
if (j == 0) {
double *fix_scalar = modify->fix[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += fix_scalar[i];
} else {
int jm1 = j - 1;
double **fix_vector = modify->fix[n]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += fix_vector[i][jm1];
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE)
input->variable->compute_atom(n,igroup,&vector[0][m],nvalues,1);
}
// done if irepeat < nrepeat
@ -201,13 +357,9 @@ void FixAveAtom::end_of_step()
// average the final result for the Nfreq timestep
double repeat = nrepeat;
if (size_peratom == 0)
for (i = 0; i < nlocal; i++)
scalar[i] /= repeat;
else
for (i = 0; i < nlocal; i++)
for (m = 0; m < size_peratom; m++)
vector[i][m] /= repeat;
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
vector[i][m] /= repeat;
}
/* ----------------------------------------------------------------------
@ -217,8 +369,7 @@ void FixAveAtom::end_of_step()
double FixAveAtom::memory_usage()
{
double bytes;
if (size_peratom == 0) bytes = atom->nmax * sizeof(double);
else bytes = atom->nmax*size_peratom * sizeof(double);
bytes = atom->nmax*nvalues * sizeof(double);
return bytes;
}
@ -228,15 +379,10 @@ double FixAveAtom::memory_usage()
void FixAveAtom::grow_arrays(int nmax)
{
if (size_peratom == 0) {
scalar = (double *) memory->srealloc(scalar,nmax*sizeof(double),
"fix_ave/atom:scalar");
scalar_atom = scalar;
} else {
vector = memory->grow_2d_double_array(vector,nmax,size_peratom,
"fix_ave/atom:vector");
vector_atom = vector;
}
vector = memory->grow_2d_double_array(vector,nmax,nvalues,
"fix_ave/atom:vector");
vector_atom = vector;
scalar_atom = vector[0];
}
/* ----------------------------------------------------------------------
@ -245,11 +391,8 @@ void FixAveAtom::grow_arrays(int nmax)
void FixAveAtom::copy_arrays(int i, int j)
{
if (size_peratom == 0)
scalar[j] = scalar[i];
else
for (int m = 0; m <= size_peratom; m++)
vector[j][m] = vector[i][m];
for (int m = 0; m < nvalues; m++)
vector[j][m] = vector[i][m];
}
/* ----------------------------------------------------------------------
@ -258,13 +401,8 @@ void FixAveAtom::copy_arrays(int i, int j)
int FixAveAtom::pack_exchange(int i, double *buf)
{
if (size_peratom == 0) {
buf[0] = scalar[i];
return 1;
}
for (int m = 0; m <= size_peratom; m++) buf[m] = vector[i][m];
return size_peratom;
for (int m = 0; m < nvalues; m++) buf[m] = vector[i][m];
return nvalues;
}
/* ----------------------------------------------------------------------
@ -273,11 +411,6 @@ int FixAveAtom::pack_exchange(int i, double *buf)
int FixAveAtom::unpack_exchange(int nlocal, double *buf)
{
if (size_peratom == 0) {
scalar[nlocal] = buf[0];
return 1;
}
for (int m = 0; m <= size_peratom; m++) vector[nlocal][m] = buf[m];
return size_peratom;
for (int m = 0; m < nvalues; m++) vector[nlocal][m] = buf[m];
return nvalues;
}

10
src/fix_ave_atom.h
View File

@ -25,6 +25,7 @@ class FixAveAtom : public Fix {
~FixAveAtom();
int setmask();
void init();
void setup();
void end_of_step();
double memory_usage();
@ -34,12 +35,11 @@ class FixAveAtom : public Fix {
int unpack_exchange(int, double *);
private:
int nrepeat,irepeat,nvalid;
char *id_compute;
int ncompute;
class Compute **compute;
int nvalues;
int nrepeat,nvalid,irepeat;
int *which,*argindex,*value2index;
char **ids;
double *scalar;
double **vector;
};

563
src/fix_ave_spatial.cpp
View File

@ -24,26 +24,28 @@
#include "lattice.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
enum{DENSITY_MASS,DENSITY_NUM,COMPUTE,FIX};
enum{X,V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
enum{ONE,RUNNING,WINDOW};
#define BIG 1000000000
#define INVOKED_PERATOM 4 // same as in computes
/* ---------------------------------------------------------------------- */
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all("Illegal fix ave/spatial command");
if (narg < 10) error->all("Illegal fix ave/spatial command");
MPI_Comm_rank(world,&me);
@ -62,34 +64,96 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[7],"center") == 0) originflag = CENTER;
if (strcmp(arg[7],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD) origin = atof(arg[6]);
if (originflag == COORD) origin = atof(arg[7]);
delta = atof(arg[8]);
if (strcmp(arg[9],"density") == 0) {
if (strcmp(arg[10],"mass") == 0) which = DENSITY_MASS;
else if (strcmp(arg[10],"number") == 0) which = DENSITY_NUM;
else error->all("Illegal fix ave/spatial command");
} else if (strcmp(arg[9],"compute") == 0) {
which = COMPUTE;
int n = strlen(arg[10]) + 1;
id_compute = new char[n];
strcpy(id_compute,arg[10]);
} else if (strcmp(arg[9],"fix") == 0) {
which = FIX;
int n = strlen(arg[10]) + 1;
id_fix = new char[n];
strcpy(id_fix,arg[10]);
} else error->all("Illegal fix ave/spatial command");
// parse values until one isn't recognized
// parse optional args
which = new int[narg-9];
argindex = new int[narg-9];
ids = new char*[narg-9];
value2index = new int[narg-9];
nvalues = 0;
int iarg = 9;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"density/number") == 0) {
which[nvalues] = DENSITY_NUMBER;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
which[nvalues] = DENSITY_MASS;
argindex[nvalues++] = 0;
} else if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/spatial command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
// optional args
normflag = ALL;
scaleflag = BOX;
fp = NULL;
ave = ONE;
int iarg = 11;
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
@ -131,11 +195,71 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
} else error->all("Illegal fix ave/spatial command");
}
// if density, no normalization by atom count should be done
// thus ALL and SAMPLE should give same answer, but code does normalize
// thus only ALL is computed correctly, so force norm to be ALL
// setup and error check
if (which == DENSITY_MASS || which == DENSITY_NUM) normflag = ALL;
if (nevery <= 0) error->all("Illegal fix ave/spatial command");
if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not calculate per-atom values");
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
error->all("Fix ave/spatial compute does not calculate a per-atom scalar");
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
error->all("Fix ave/spatial compute does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom)
error->all("Fix ave/spatial compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/spatial fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom != 0)
error->all("Fix ave/spatial fix does not calculate a per-atom scalar");
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
error->all("Fix ave/spatial fix does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom)
error->all("Fix ave/spatial fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/spatial variable is not atom-style variable");
}
}
// print header into file
if (fp && me == 0) {
fprintf(fp,"Spatial-averaged data for fix %s and group %s\n",id,arg[1]);
fprintf(fp,"TimeStep Number-of-layers\n");
fprintf(fp,"Layer Coordinate Natoms");
for (int i = 0; i < nvalues; i++)
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
else fprintf(fp," %s",arg[9+i]);
fprintf(fp,"\n");
}
// this fix produces a global vector
// set size_vector to BIG since compute_vector() checks bounds on-the-fly
vector_flag = 1;
size_vector = BIG;
scalar_vector_freq = nfreq;
extvector = 0;
// setup scaling
@ -162,60 +286,6 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
delta *= scale;
if (originflag == COORD) origin *= scale;
// setup and error check
if (nevery <= 0) error->all("Illegal fix ave/spatial command");
if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
// nvalues = # of quantites per line of output file
// for COMPUTE, setup list of computes to call, including pre-computes
nvalues = 1;
compute = NULL;
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not calculate per-atom info");
nvalues = size_peratom = modify->compute[icompute]->size_peratom;
if (nvalues == 0) nvalues = 1;
ncompute = 1 + modify->compute[icompute]->npre;
compute = new Compute*[ncompute];
}
if (which == FIX) {
int ifix = modify->find_fix(id_fix);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/spatial fix does not calculate per-atom info");
nvalues = size_peratom = modify->fix[ifix]->size_peratom;
if (nvalues == 0) nvalues = 1;
}
// print header into file
if (fp && me == 0) {
fprintf(fp,"Spatial-averaged data for fix %s, group %s, and %s %s\n",
id,group->names[igroup],arg[10],arg[11]);
fprintf(fp,"TimeStep Number-of-layers (one per snapshot)\n");
fprintf(fp,"Layer Coord Atoms Value(s) (one per layer)\n");
}
// enable this fix to produce a global vector
// set size_vector to BIG since compute_vector() will check bounds
vector_flag = 1;
size_vector = BIG;
scalar_vector_freq = nfreq;
extensive = 0;
// initializations
irepeat = 0;
@ -228,6 +298,12 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
values_one = values_many = values_sum = values_total = NULL;
values_list = NULL;
maxatomvar = 0;
varatom = NULL;
maxatomlayer = 0;
layer = NULL;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of nfreq and nrepeat = 1
// else backup from next multiple of nfreq
@ -239,24 +315,24 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
// set timestep for all computes that store invocation times
// since don't know a priori which are invoked by this fix
// add nvalid to ALL computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can just set timestep for ones actually invoked
if (which == COMPUTE)
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->add_step(nvalid);
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveSpatial::~FixAveSpatial()
{
if (which == COMPUTE) delete [] id_compute;
if (which == FIX) delete [] id_fix;
if (fp && me == 0) fclose(fp);
delete [] which;
delete [] argindex;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
delete [] compute;
if (fp && me == 0) fclose(fp);
memory->sfree(coord);
memory->sfree(count_one);
@ -269,6 +345,9 @@ FixAveSpatial::~FixAveSpatial()
memory->destroy_2d_double_array(values_sum);
memory->destroy_2d_double_array(values_total);
memory->destroy_3d_double_array(values_list);
memory->sfree(varatom);
memory->sfree(layer);
}
/* ---------------------------------------------------------------------- */
@ -291,36 +370,32 @@ void FixAveSpatial::init()
error->all("Fix ave/spatial settings invalid with changing box");
}
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
ncompute = 0;
if (modify->compute[icompute]->npre)
for (int i = 0; i < modify->compute[icompute]->npre; i++) {
int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
if (ic < 0)
error->all("Precompute ID for fix ave/spatial does not exist");
compute[ncompute++] = modify->compute[ic];
}
compute[ncompute++] = modify->compute[icompute];
}
// set ptr to fix ID
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
if (which == FIX) {
int ifix = modify->find_fix(id_fix);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
fix = modify->fix[ifix];
if (nevery % fix->peratom_freq)
error->all("Fix ave/spatial and fix not computed at compatible times");
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
value2index[m] = ifix;
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/spatial not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
@ -337,7 +412,7 @@ void FixAveSpatial::setup()
void FixAveSpatial::end_of_step()
{
int i,j,m,ilayer;
int i,j,m,n,ilayer;
double lo,hi;
// skip if not step which requires doing something
@ -448,107 +523,129 @@ void FixAveSpatial::end_of_step()
for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0;
}
// perform the computation for one sample
// sum within each layer, only include atoms in fix group
// assign each atom to a layer
// insure array index is within bounds (since atoms can be outside box)
// if scaleflag = REDUCED, box coords -> lamda coords before computing layer
// if scaleflag = REDUCED, box coords -> lamda coords
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// DENSITY_MASS adds mass to values
if (which == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (mass) values_one[ilayer][0] += mass[type[i]];
else values_one[ilayer][0] += rmass[i];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// DENSITY_NUM adds 1 to values
} else if (which == DENSITY_NUM) {
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
values_one[ilayer][0] += 1.0;
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// COMPUTE adds its scalar or vector quantity to values
} else if (which == COMPUTE) {
modify->clearstep_compute();
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
double *scalar = compute[ncompute-1]->scalar_atom;
double **vector = compute[ncompute-1]->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// FIX adds its scalar or vector quantity to values
} else if (which == FIX) {
double *scalar = fix->scalar_atom;
double **vector = fix->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
if (nlocal > maxatomlayer) {
maxatomlayer = atom->nmax;
memory->sfree(layer);
layer = (int *)
memory->smalloc(maxatomlayer*sizeof(int),"ave/spatial:layer");
}
// average a single sample
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
layer[i] = ilayer;
count_one[ilayer] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// perform the computation for one sample
// accumulate results of attributes,computes,fixes,variables to local copy
// sum within each layer, only include atoms in fix group
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
// X,V,F adds coords,velocities,forces to values
if (which[m] == X || which[m] == V || which[m] == F) {
double **attribute;
if (which[m] == X) attribute = x;
else if (which[m] == V) attribute = atom->v;
else attribute = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[layer[i]][m] += attribute[i][j];
// DENSITY_NUMBER adds 1 to values
} else if (which[m] == DENSITY_NUMBER) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[layer[i]][m] += 1.0;
// DENSITY_MASS adds mass to values
} else if (which[m] == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mass) values_one[layer[i]][m] += mass[type[i]];
else values_one[layer[i]][m] += rmass[i];
// COMPUTE adds its scalar or vector component to values
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked & INVOKED_PERATOM)) compute->compute_peratom();
double *scalar = compute->scalar_atom;
double **vector = compute->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (j == 0) values_one[layer[i]][m] += scalar[i];
else values_one[layer[i]][m] += vector[i][jm1];
// FIX adds its scalar or vector component to values
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
double *scalar = modify->fix[n]->scalar_atom;
double **vector = modify->fix[n]->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (j == 0) values_one[layer[i]][m] += scalar[i];
else values_one[layer[i]][m] += vector[i][jm1];
}
// VARIABLE adds its per-atom quantities to values
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (nlocal > maxatomvar) {
maxatomvar = atom->nmax;
memory->sfree(varatom);
varatom = (double *)
memory->smalloc(maxatomvar*sizeof(double),"ave/spatial:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[layer[i]][m] += varatom[i];
}
}
// process a single sample
// if normflag = ALL, accumulate values,count separately to many
// if normflag = SAMPLE, one = value/count, accumulate one to many
// exception is SAMPLE density: no normalization by atom count
if (normflag == ALL) {
for (m = 0; m < nlayers; m++) {
@ -560,8 +657,11 @@ void FixAveSpatial::end_of_step()
MPI_Allreduce(count_one,count_many,nlayers,MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_many[m][j] += values_one[m][j]/count_many[m];
for (j = 0; j < nvalues; j++) {
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
values_many[m][j] += values_one[m][j];
else values_many[m][j] += values_one[m][j]/count_many[m];
}
count_sum[m] += count_many[m];
}
}
@ -572,16 +672,18 @@ void FixAveSpatial::end_of_step()
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
if (which == COMPUTE) modify->addstep_compute(nvalid);
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
if (which == COMPUTE) modify->addstep_compute(nvalid);
modify->addstep_compute(nvalid);
// time average across samples
// if density, also normalize by volume
// if normflag = ALL, final is total value / total count
// if normflag = SAMPLE, final is sum of ave / repeat
// exception is ALL density: normalized by repeat, not total count
double repeat = nrepeat;
@ -592,7 +694,9 @@ void FixAveSpatial::end_of_step()
for (m = 0; m < nlayers; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_sum[m][j] /= count_sum[m];
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
values_sum[m][j] /= repeat;
else values_sum[m][j] /= count_sum[m];
count_sum[m] /= repeat;
}
} else {
@ -605,10 +709,12 @@ void FixAveSpatial::end_of_step()
}
}
if (which == DENSITY_MASS || which == DENSITY_NUM) {
for (m = 0; m < nlayers; m++)
values_sum[m][0] *= count_sum[m] / layer_volume;
}
// density is additionally normalized by layer volume
for (j = 0; j < nvalues; j++)
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
for (m = 0; m < nlayers; m++)
values_sum[m][j] /= layer_volume;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
@ -667,13 +773,24 @@ void FixAveSpatial::end_of_step()
/* ----------------------------------------------------------------------
return Nth vector value
since values_sum is 2d array, map N into ilayer and ivalue
if ilayer >= nlayers, just return 0, since nlayers can vary with time
if ilayer exceeds current layers, return 0.0 instead of generate an error
------------------------------------------------------------------------- */
double FixAveSpatial::compute_vector(int n)
{
int ivalue = n % nvalues;
int ilayer = n / nvalues;
if (ilayer < nlayers && norm) return values_total[ilayer][ivalue]/norm;
return 0.0;
if (ilayer >= nlayers) return 0.0;
return values_total[ilayer][ivalue]/norm;
}
/* ----------------------------------------------------------------------
memory usage of varatom and layer
------------------------------------------------------------------------- */
double FixAveSpatial::memory_usage()
{
double bytes = maxatomvar * sizeof(double);
bytes += maxatomlayer * sizeof(int);
return bytes;
}

23
src/fix_ave_spatial.h
View File

@ -28,26 +28,31 @@ class FixAveSpatial : public Fix {
void setup();
void end_of_step();
double compute_vector(int);
double memory_usage();
private:
int me;
int nrepeat,nfreq,irepeat,nvalid;
int dim,originflag,which,normflag;
int me,nvalues;
int nrepeat,nfreq,nvalid,irepeat;
int dim,originflag,normflag;
double origin,delta;
char *id_compute,*id_fix;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
int nlayers,nvalues,ave,nwindow;
int maxlayer,scaleflag,size_peratom;
int nlayers,ave,nwindow;
int maxlayer,scaleflag;
double xscale,yscale,zscale;
double layer_volume;
double *coord;
double *count_one,*count_many,*count_sum;
double **values_one,**values_many,**values_sum;
double offset,invdelta;
int ncompute;
class Compute **compute;
class Fix *fix;
int maxatomvar;
double *varatom;
int maxatomlayer;
int *layer;
int norm,iwindow,window_limit;
double *count_total;

375
src/fix_ave_time.cpp
View File

@ -22,21 +22,25 @@
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX};
enum{SCALAR,VECTOR,BOTH};
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING,WINDOW};
#define INVOKED_SCALAR 1 // same as in computes
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all("Illegal fix ave/time command");
if (narg < 7) error->all("Illegal fix ave/time command");
MPI_Comm_rank(world,&me);
@ -44,37 +48,55 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
if (strcmp(arg[6],"compute") == 0) which = COMPUTE;
else if (strcmp(arg[6],"fix") == 0) which = FIX;
else error->all("Illegal fix ave/time command");
// parse values until one isn't recognized
int n = strlen(arg[7]) + 1;
id = new char[n];
strcpy(id,arg[7]);
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/time command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
// option defaults
sflag = 1;
vflag = 0;
fp = NULL;
ave = ONE;
// optional args
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
if (strcmp(arg[iarg+1],"scalar") == 0) {
sflag = 1;
vflag = 0;
} else if (strcmp(arg[iarg+1],"vector") == 0) {
sflag = 0;
vflag = 1;
} else if (strcmp(arg[iarg+1],"both") == 0) sflag = vflag = 1;
else error->all("Illegal fix ave/time command");
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
@ -107,85 +129,108 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/time command");
int icompute,ifix;
if (which == COMPUTE) {
icompute = modify->find_compute(id);
if (icompute < 0) error->all("Compute ID for fix ave/time does not exist");
} else {
ifix = modify->find_fix(id);
if (ifix < 0) error->all("Fix ID for fix ave/time does not exist");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all("Fix ave/time compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all("Fix ave/time compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (argindex[i] && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/time fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all("Fix ave/time fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/time does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all("Fix ave/time variable is not equal-style variable");
}
}
if (which == COMPUTE) {
if (sflag && modify->compute[icompute]->scalar_flag == 0)
error->all("Fix ave/time compute does not calculate a scalar");
if (vflag && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector");
} else {
if (sflag && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/time fix does not calculate a scalar");
if (vflag && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a vector");
}
// setup list of computes to call, including pre-computes
compute = NULL;
if (which == COMPUTE) {
ncompute = 1 + modify->compute[icompute]->npre;
compute = new Compute*[ncompute];
} else ncompute = 0;
// print header into file
if (fp && me == 0) {
if (which == COMPUTE)
fprintf(fp,"Time-averaged data for fix %s, group %s, and compute %s\n",
id,group->names[modify->compute[icompute]->igroup],id);
else
fprintf(fp,"Time-averaged data for fix %s, group %s, and fix %s\n",
id,group->names[modify->fix[ifix]->igroup],id);
if (sflag and !vflag)
fprintf(fp,"TimeStep Value\n");
else if (!sflag and vflag)
fprintf(fp,"TimeStep Vector-values\n");
else if (!sflag and vflag)
fprintf(fp,"TimeStep Scalar-value Vector-values\n");
fprintf(fp,"Time-averaged data for fix %s\n",id);
fprintf(fp,"TimeStep");
for (int i = 0; i < nvalues; i++)
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
fprintf(fp,"\n");
}
// allocate memory for averaging
// allocate and initialize memory for averaging
vector = vector_total = NULL;
if (vflag) {
if (which == COMPUTE) size_vector = modify->compute[icompute]->size_vector;
else size_vector = modify->fix[ifix]->size_vector;
vector = new double[size_vector];
vector_total = new double[size_vector];
}
vector = new double[nvalues];
vector_total = new double[nvalues];
for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
scalar_list = NULL;
vector_list = NULL;
if (sflag && ave == WINDOW) scalar_list = new double[nwindow];
if (vflag && ave == WINDOW)
vector_list = memory->create_2d_double_array(nwindow,size_vector,
if (ave == WINDOW)
vector_list = memory->create_2d_double_array(nwindow,nvalues,
"ave/time:vector_list");
// enable this fix to produce a global scalar and/or vector
// this fix produces either a global scalar or vector
// intensive/extensive flags set by compute,fix,variable that produces value
if (sflag) scalar_flag = 1;
if (vflag) vector_flag = 1;
scalar_vector_freq = nfreq;
if (which == COMPUTE) extensive = modify->compute[icompute]->extensive;
else extensive = modify->fix[ifix]->extensive;
extlist = NULL;
if (nvalues == 1) {
scalar_flag = 1;
if (which[0] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (argindex[0] == 0) extscalar = compute->extscalar;
else if (compute->extvector >= 0) extscalar = compute->extvector;
else extscalar = compute->extlist[argindex[0]-1];
} else if (which[0] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (argindex[0] == 0) extscalar = fix->extscalar;
else if (fix->extvector >= 0) extscalar = fix->extvector;
else extscalar = fix->extlist[argindex[0]-1];
} else if (which[0] == VARIABLE)
extscalar = 0;
} else {
vector_flag = 1;
size_vector = nvalues;
extvector = -1;
extlist = new int[nvalues];
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[i] == 0) extlist[i] = compute->extscalar;
else if (compute->extvector >= 0) extlist[i] = compute->extvector;
else extlist[i] = compute->extlist[argindex[i]-1];
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) extlist[i] = fix->extscalar;
else if (fix->extvector >= 0) extlist[i] = fix->extvector;
else extlist[i] = fix->extlist[argindex[i]-1];
} else if (which[i] == VARIABLE)
extlist[i] = 0;
}
}
// initializations
// set scalar and vector total to zero since they accumulate
// set vector total to zero since it accumulates
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
scalar_total = 0.0;
if (vflag) for (int i = 0; i < size_vector; i++) vector_total[i] = 0.0;
for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of nfreq and nrepeat = 1
@ -198,24 +243,27 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
// set timestep for all computes that store invocation times
// since don't know a priori which are invoked by this fix
// add nvalid to ALL computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can just set timestep for ones actually invoked
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->add_step(nvalid);
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveTime::~FixAveTime()
{
delete [] id;
delete [] which;
delete [] argindex;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
delete [] extlist;
if (fp && me == 0) fclose(fp);
delete [] compute;
delete [] vector;
delete [] vector_total;
delete [] scalar_list;
memory->destroy_2d_double_array(vector_list);
}
@ -232,36 +280,33 @@ int FixAveTime::setmask()
void FixAveTime::init()
{
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
if (which == COMPUTE) {
int icompute = modify->find_compute(id);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
ncompute = 0;
if (modify->compute[icompute]->npre)
for (int i = 0; i < modify->compute[icompute]->npre; i++) {
int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
if (ic < 0)
error->all("Precompute ID for fix ave/time does not exist");
compute[ncompute++] = modify->compute[ic];
}
compute[ncompute++] = modify->compute[icompute];
}
// set ptr to fix ID
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
if (which == FIX) {
int ifix = modify->find_fix(id);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
fix = modify->fix[ifix];
if (nevery % fix->scalar_vector_freq)
error->all("Fix ave/time and fix not computed at compatible times");
int ilist = 0;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
value2index[i] = ifix;
if (nevery % modify->fix[ifix]->scalar_vector_freq)
error->all("Fix for fix ave/time not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/time does not exist");
value2index[i] = ivariable;
}
}
}
@ -278,7 +323,8 @@ void FixAveTime::setup()
void FixAveTime::end_of_step()
{
int i;
int i,j,k,m;
double tmp;
// skip if not step which requires doing something
@ -286,33 +332,44 @@ void FixAveTime::end_of_step()
// zero if first step
if (irepeat == 0) {
scalar = 0.0;
if (vflag)
for (i = 0; i < size_vector; i++) vector[i] = 0.0;
}
if (irepeat == 0)
for (i = 0; i < nvalues; i++) vector[i] = 0.0;
// accumulate results of compute or fix to local copy
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
if (which == COMPUTE) {
modify->clearstep_compute();
modify->clearstep_compute();
if (sflag) {
double value;
for (i = 0; i < ncompute; i++) value = compute[i]->compute_scalar();
scalar += value;
}
if (vflag) {
for (i = 0; i < ncompute; i++) compute[i]->compute_vector();
double *cvector = compute[ncompute-1]->vector;
for (i = 0; i < size_vector; i++) vector[i] += cvector[i];
}
int ilist = 0;
} else {
if (sflag) scalar += fix->compute_scalar();
if (vflag)
for (i = 0; i < size_vector; i++)
vector[i] += fix->compute_vector(i);
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (compute->invoked & INVOKED_SCALAR) vector[i] += compute->scalar;
else vector[i] += compute->compute_scalar();
} else {
if (!(compute->invoked & INVOKED_VECTOR)) compute->compute_vector();
vector[i] += compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
vector[i] += modify->fix[m]->compute_scalar();
else
vector[i] += modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
vector[i] += input->variable->compute_equal(m);
}
// done if irepeat < nrepeat
@ -321,46 +378,36 @@ void FixAveTime::end_of_step()
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
if (which == COMPUTE) modify->addstep_compute(nvalid);
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
if (which == COMPUTE) modify->addstep_compute(nvalid);
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
if (sflag) scalar /= repeat;
if (vflag) for (i = 0; i < size_vector; i++) vector[i] /= repeat;
for (i = 0; i < nvalues; i++) vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
if (sflag) scalar_total = scalar;
if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] = vector[i];
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
if (sflag) scalar_total += scalar;
if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] += vector[i];
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
if (sflag) {
scalar_total += scalar;
if (window_limit) scalar_total -= scalar_list[iwindow];
scalar_list[iwindow] = scalar;
}
if (vflag) {
for (i = 0; i < size_vector; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
@ -376,9 +423,7 @@ void FixAveTime::end_of_step()
if (fp && me == 0) {
fprintf(fp,"%d",update->ntimestep);
if (sflag) fprintf(fp," %g",scalar_total/norm);
if (vflag)
for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector_total[i]/norm);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm);
fprintf(fp,"\n");
fflush(fp);
}
@ -391,7 +436,7 @@ void FixAveTime::end_of_step()
double FixAveTime::compute_scalar()
{
if (norm) return scalar_total/norm;
if (norm) return vector_total[0]/norm;
return 0.0;
}

16
src/fix_ave_time.h
View File

@ -31,20 +31,16 @@ class FixAveTime : public Fix {
double compute_vector(int);
private:
int me;
int nrepeat,nfreq,nvalid,irepeat,which,ifix;
char *id;
int me,nvalues;
int nrepeat,nfreq,nvalid,irepeat;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
int sflag,vflag,ave,nwindow,nsum;
double scalar,*vector;
int ncompute;
class Compute **compute;
class Fix *fix;
int ave,nwindow,nsum;
double *vector;
int norm,iwindow,window_limit;
double scalar_total;
double *scalar_list;
double *vector_total;
double **vector_list;
};

5
src/fix_drag.cpp
View File

@ -33,7 +33,7 @@ FixDrag::FixDrag(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = 3;
scalar_vector_freq = 1;
extensive = 1;
extvector = 1;
xflag = yflag = zflag = 1;
@ -46,6 +46,9 @@ FixDrag::FixDrag(LAMMPS *lmp, int narg, char **arg) :
f_mag = atof(arg[6]);
delta = atof(arg[7]);
force_flag = 0;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
}
/* ---------------------------------------------------------------------- */

3
src/fix_dt_reset.cpp
View File

@ -47,7 +47,8 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = 1;
scalar_vector_freq = 1;
extensive = 0;
extscalar = 0;
extvector = 0;
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix dt/reset command");

6
src/fix_indent.cpp
View File

@ -42,7 +42,8 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = 3;
scalar_vector_freq = 1;
extensive = 1;
extscalar = 1;
extvector = 1;
k = atof(arg[3]);
@ -103,6 +104,9 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) :
r0_start *= zscale;
}
} else error->all("Illegal fix indent command");
indenter_flag = 0;
indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0;
}
/* ---------------------------------------------------------------------- */

27
src/fix_nph.cpp
View File

@ -48,7 +48,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
box_change = 1;
scalar_flag = 1;
scalar_vector_freq = 1;
extensive = 1;
extscalar = 1;
double p_period[3];
if (strcmp(arg[3],"xyz") == 0) {
@ -242,7 +242,6 @@ void FixNPH::init()
}
// set temperature and pressure ptrs
// set ptemperature only if pressure's id_pre[0] is not id_temp
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix nph does not exist");
@ -252,14 +251,6 @@ void FixNPH::init()
if (icompute < 0) error->all("Press ID for fix nph does not exist");
pressure = modify->compute[icompute];
if (strcmp(id_temp,pressure->id_pre[0]) == 0) ptemperature = NULL;
else {
icompute = modify->find_compute(pressure->id_pre[0]);
if (icompute < 0)
error->all("Temp ID of press ID for fix nph does not exist");
ptemperature = modify->compute[icompute];
}
// set timesteps and frequencies
// Nkt = initial value for piston mass and energy conservation
// guesstimate a unit-dependent t_initial if actual T = 0.0
@ -323,18 +314,16 @@ void FixNPH::setup()
double tmp = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) tmp = ptemperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->add_step(update->ntimestep+1);
pressure->addstep(update->ntimestep+1);
}
/* ----------------------------------------------------------------------
@ -438,18 +427,16 @@ void FixNPH::final_integrate()
double tmp = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) tmp = ptemperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->add_step(update->ntimestep+1);
pressure->addstep(update->ntimestep+1);
// update omega_dot
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
@ -752,13 +739,13 @@ int FixNPH::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPH is not for group all");
// reset id_pre[0] of pressure to new temp ID
// reset id_pre of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
delete [] modify->compute[icompute]->id_pre[0];
modify->compute[icompute]->id_pre[0] = new char[n];
strcpy(modify->compute[icompute]->id_pre[0],id_temp);
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
return 2;

2
src/fix_nph.h
View File

@ -56,7 +56,7 @@ class FixNPH : public Fix {
double *step_respa;
char *id_temp,*id_press;
class Compute *temperature,*pressure,*ptemperature;
class Compute *temperature,*pressure;
int tflag,pflag;
void couple();

27
src/fix_npt.cpp
View File

@ -47,7 +47,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
box_change = 1;
scalar_flag = 1;
scalar_vector_freq = 1;
extensive = 1;
extscalar = 1;
t_start = atof(arg[3]);
t_stop = atof(arg[4]);
@ -252,7 +252,6 @@ void FixNPT::init()
}
// set temperature and pressure ptrs
// set ptemperature only if pressure's id_pre[0] is not id_temp
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix npt does not exist");
@ -262,14 +261,6 @@ void FixNPT::init()
if (icompute < 0) error->all("Press ID for fix npt does not exist");
pressure = modify->compute[icompute];
if (strcmp(id_temp,pressure->id_pre[0]) == 0) ptemperature = NULL;
else {
icompute = modify->find_compute(pressure->id_pre[0]);
if (icompute < 0)
error->all("Temp ID of press ID for fix npt does not exist");
ptemperature = modify->compute[icompute];
}
// set timesteps and frequencies
dtv = update->dt;
@ -325,18 +316,16 @@ void FixNPT::setup()
t_current = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) double ptmp = ptemperature->compute_scalar();
double tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->add_step(update->ntimestep+1);
pressure->addstep(update->ntimestep+1);
}
/* ----------------------------------------------------------------------
@ -448,18 +437,16 @@ void FixNPT::final_integrate()
t_current = temperature->compute_scalar();
if (press_couple == 0) {
if (ptemperature) double ptmp = ptemperature->compute_scalar();
double tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
if (ptemperature) ptemperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->add_step(update->ntimestep+1);
pressure->addstep(update->ntimestep+1);
// update eta_dot
@ -781,13 +768,13 @@ int FixNPT::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPT is not for group all");
// reset id_pre[0] of pressure to new temp ID
// reset id_pre of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
delete [] modify->compute[icompute]->id_pre[0];
modify->compute[icompute]->id_pre[0] = new char[n];
strcpy(modify->compute[icompute]->id_pre[0],id_temp);
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
return 2;

2
src/fix_npt.h
View File

@ -62,7 +62,7 @@ class FixNPT : public Fix {
double *step_respa;
char *id_temp,*id_press;
class Compute *temperature,*pressure,*ptemperature;
class Compute *temperature,*pressure;
int tflag,pflag;
void couple();

2
src/fix_nvt.cpp
View File

@ -41,7 +41,7 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
restart_global = 1;
scalar_flag = 1;
scalar_vector_freq = 1;
extensive = 1;
extscalar = 1;
t_start = atof(arg[3]);
t_stop = atof(arg[4]);

4
src/fix_orient_fcc.cpp
View File

@ -48,7 +48,7 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
scalar_vector_freq = 1;
extensive = 1;
extscalar = 1;
nstats = atoi(arg[3]);
direction_of_motion = atoi(arg[4]);
@ -149,6 +149,8 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
if (use_xismooth) comm_forward = 62;
else comm_forward = 50;
added_energy = 0.0;
}
/* ---------------------------------------------------------------------- */

2
src/fix_print.cpp
View File

@ -101,7 +101,7 @@ void FixPrint::end_of_step()
// make a copy of string to work on
// substitute for $ variables (no printing)
// append a newline and print final copy
// variable evaluation may invoke a compute that affects Verlet::eflag,vflag
// variable evaluation may invoke computes so wrap with clear/add
modify->clearstep_compute();

5
src/fix_set_force.cpp
View File

@ -31,7 +31,7 @@ FixSetForce::FixSetForce(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = 3;
scalar_vector_freq = 1;
extensive = 1;
extvector = 1;
flagx = flagy = flagz = 1;
if (strcmp(arg[3],"NULL") == 0) flagx = 0;
@ -40,6 +40,9 @@ FixSetForce::FixSetForce(LAMMPS *lmp, int narg, char **arg) :
else yvalue = atof(arg[4]);
if (strcmp(arg[5],"NULL") == 0) flagz = 0;
else zvalue = atof(arg[5]);
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
}
/* ---------------------------------------------------------------------- */

5
src/fix_spring.cpp
View File

@ -41,7 +41,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
size_vector = 3;
scalar_vector_freq = 1;
extensive = 1;
extvector = 1;
if (strcmp(arg[3],"tether") == 0) {
if (narg != 9) error->all("Illegal fix spring command");
@ -78,6 +78,9 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
if (r0 < 0) error->all("R0 < 0 for fix spring command");
} else error->all("Illegal fix spring command");
force_flag = 0;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
}
/* ---------------------------------------------------------------------- */

4
src/fix_temp_rescale.cpp
View File

@ -42,7 +42,7 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
scalar_vector_freq = nevery;
extensive = 1;
extscalar = 1;
t_start = atof(arg[4]);
t_end = atof(arg[5]);
@ -109,6 +109,8 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
}
delete [] newarg;
tflag = 1;
energy = 0.0;
}
/* ---------------------------------------------------------------------- */

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