jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12621 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-10-07 23:03:23 +00:00
parent 48baa5ba69
commit 166a9c5bc7
15 changed files with 184 additions and 57 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
src/KSPACE/ewald.cpp
View File

@ -439,7 +439,7 @@ void Ewald::compute(int eflag, int vflag)
energy += ug[k] * (sfacrl_all[k]*sfacrl_all[k] +
sfacim_all[k]*sfacim_all[k]);
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

2
src/KSPACE/msm.cpp
View File

@ -576,7 +576,7 @@ void MSM::compute(int eflag, int vflag)
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

2
src/KSPACE/pppm.cpp
View File

@ -677,7 +677,7 @@ void PPPM::compute(int eflag, int vflag)
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

2
src/KSPACE/pppm_cg.cpp
View File

@ -218,7 +218,7 @@ void PPPMCG::compute(int eflag, int vflag)
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

2
src/KSPACE/pppm_disp.cpp
View File

@ -1135,7 +1135,7 @@ void PPPMDisp::compute(int eflag, int vflag)
energy_1 *= 0.5*volume;
energy_6 *= 0.5*volume;
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

2
src/KSPACE/pppm_stagger.cpp
View File

@ -212,7 +212,7 @@ void PPPMStagger::compute(int eflag, int vflag)
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
if (atom->natoms != natoms_original) {
if (qsum_update_flag || (atom->natoms != natoms_original)) {
qsum_qsq(0);
natoms_original = atom->natoms;
}

1
src/QEQ/fix_qeq.cpp
View File

@ -262,6 +262,7 @@ void FixQEq::reallocate_matrix()
void FixQEq::init_list(int id, NeighList *ptr)
{
list = ptr;
if (force->kspace) force->kspace->qsum_update_flag = 1;
}
/* ---------------------------------------------------------------------- */

2
src/QEQ/fix_qeq_dynamic.cpp
View File

@ -30,6 +30,7 @@
#include "force.h"
#include "group.h"
#include "pair.h"
#include "kspace.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
@ -167,6 +168,7 @@ void FixQEqDynamic::pre_force(int vflag)
}
}
if (force->kspace) force->kspace->setup();
}
/* ---------------------------------------------------------------------- */

3
src/QEQ/fix_qeq_point.cpp
View File

@ -28,6 +28,7 @@
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "kspace.h"
#include "group.h"
#include "respa.h"
#include "memory.h"
@ -82,6 +83,8 @@ void FixQEqPoint::pre_force(int vflag)
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->setup();
}
/* ---------------------------------------------------------------------- */

3
src/QEQ/fix_qeq_shielded.cpp
View File

@ -28,6 +28,7 @@
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "kspace.h"
#include "group.h"
#include "respa.h"
#include "memory.h"
@ -125,6 +126,8 @@ void FixQEqShielded::pre_force(int vflag)
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->setup();
}
/* ---------------------------------------------------------------------- */

4
src/QEQ/fix_qeq_slater.cpp
View File

@ -28,9 +28,9 @@
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "kspace.h"
#include "group.h"
#include "pair.h"
#include "kspace.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
@ -101,6 +101,8 @@ void FixQEqSlater::pre_force(int vflag)
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->setup();
}
/* ---------------------------------------------------------------------- */

202
src/USER-FEP/fix_adapt_fep.cpp
View File

@ -20,13 +20,14 @@
#include "stdlib.h"
#include "fix_adapt_fep.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "group.h"
#include "modify.h"
#include "force.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "kspace.h"
#include "fix_store.h"
#include "input.h"
#include "variable.h"
#include "math_const.h"
@ -40,8 +41,6 @@ using namespace MathConst;
enum{PAIR,KSPACE,ATOM};
enum{DIAMETER,CHARGE};
#undef ADAPT_DEBUG
/* ---------------------------------------------------------------------- */
FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
@ -51,6 +50,8 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
nevery = force->inumeric(FLERR,arg[3]);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt/fep command");
dynamic_group_allow = 1;
// count # of adaptations
nadapt = 0;
@ -169,6 +170,8 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
for (int m = 0; m < nadapt; m++)
if (adapt[m].which == PAIR)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
id_fix_diam = id_fix_chg = NULL;
}
/* ---------------------------------------------------------------------- */
@ -184,6 +187,13 @@ FixAdaptFEP::~FixAdaptFEP()
}
}
delete [] adapt;
// check nfix in case all fixes have already been deleted
if (id_fix_diam && modify->nfix) modify->delete_fix(id_fix_diam);
if (id_fix_chg && modify->nfix) modify->delete_fix(id_fix_chg);
delete [] id_fix_diam;
delete [] id_fix_chg;
}
/* ---------------------------------------------------------------------- */
@ -196,12 +206,92 @@ int FixAdaptFEP::setmask()
return mask;
}
/* ----------------------------------------------------------------------
if need to restore per-atom quantities, create new fix STORE styles
------------------------------------------------------------------------- */
void FixAdaptFEP::post_constructor()
{
if (!resetflag) return;
if (!diamflag && !chgflag) return;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
// new fix group = group for this fix
id_fix_diam = NULL;
id_fix_chg = NULL;
char **newarg = new char*[5];
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "1";
newarg[4] = (char *) "1";
if (diamflag) {
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
id_fix_diam = new char[n];
strcpy(id_fix_diam,id);
strcat(id_fix_diam,"_FIX_STORE_DIAM");
newarg[0] = id_fix_diam;
modify->add_fix(5,newarg);
fix_diam = (FixStore *) modify->fix[modify->nfix-1];
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = radius[i];
else vec[i] = 0.0;
}
}
}
if (chgflag) {
int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
id_fix_chg = new char[n];
strcpy(id_fix_chg,id);
strcat(id_fix_chg,"_FIX_STORE_CHG");
newarg[0] = id_fix_chg;
modify->add_fix(5,newarg);
fix_chg = (FixStore *) modify->fix[modify->nfix-1];
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = q[i];
else vec[i] = 0.0;
}
}
}
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::init()
{
int i,j;
// allow a dynamic group only if ATOM attribute not used
if (group->dynamic[igroup])
for (int i = 0; i < nadapt; i++)
if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt/fep atom");
// when using kspace, we need to recompute some additional parameters in kspace->setup()
if (force->kspace) force->kspace->qsum_update_flag = 1;
// setup and error checks
anypair = 0;
@ -217,9 +307,18 @@ void FixAdaptFEP::init()
if (ad->which == PAIR) {
anypair = 1;
Pair *pair = NULL;
Pair *pair = force->pair_match(ad->pstyle,1);
if (pair == NULL) error->all(FLERR,"Fix adapt/fep pair style does not exist");
if (lmp->suffix_enable) {
char psuffix[128];
strcpy(psuffix,ad->pstyle);
strcat(psuffix,"/");
strcat(psuffix,lmp->suffix);
pair = force->pair_match(psuffix,1);
}
if (pair == NULL) pair = force->pair_match(ad->pstyle,1);
if (pair == NULL)
error->all(FLERR, "Fix adapt/fep pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL)
error->all(FLERR,"Fix adapt/fep pair style param not supported");
@ -268,22 +367,18 @@ void FixAdaptFEP::init()
}
}
#ifdef ADAPT_DEBUG
if (comm->me == 0 && screen) {
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
fprintf(screen, "###ADAPT original %s %s\n", ad->pstyle, ad->pparam);
fprintf(screen, "###ADAPT I J old_param\n");
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
fprintf(screen, "###ADAPT %2d %2d %9.5f\n", i, j,
ad->array_orig[i][j]);
}
}
// fixes that store initial per-atom values
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_diam = (FixStore *) modify->fix[ifix];
}
if (id_fix_chg) {
int ifix = modify->find_fix(id_fix_chg);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_chg = (FixStore *) modify->fix[ifix];
}
#endif
}
/* ---------------------------------------------------------------------- */
@ -349,17 +444,6 @@ void FixAdaptFEP::change_settings()
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
#ifdef ADAPT_DEBUG
if (comm->me == 0 && screen) {
fprintf(screen, "###ADAPT change %s %s\n", ad->pstyle, ad->pparam);
fprintf(screen, "###ADAPT I J param\n");
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
fprintf(screen, "###ADAPT %2d %2d %9.5f\n", i, j, ad->array[i][j]);
}
#endif
}
// set kspace scale factor
@ -369,7 +453,7 @@ void FixAdaptFEP::change_settings()
} else if (ad->which == ATOM) {
// set radius from diameter
// reset radius from diameter
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
@ -381,15 +465,16 @@ void FixAdaptFEP::change_settings()
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int natom = atom->nlocal + atom->nghost;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (mflag == 0) {
for (i = 0; i < natom; i++)
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < natom; i++)
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
@ -403,22 +488,12 @@ void FixAdaptFEP::change_settings()
int *atype = atom->type;
double *q = atom->q;
int *mask = atom->mask;
int natom = atom->nlocal + atom->nghost;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < natom; i++)
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit) q[i] = value;
#ifdef ADAPT_DEBUG
if (comm->me == 0 && screen) {
fprintf(screen, "###ADAPT change charge\n");
fprintf(screen, "###ADAPT atom I q\n");
for (i = 0; i < atom->nlocal; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit)
fprintf(screen, "###ADAPT %5d %2d %9.5f\n", i, atype[i], q[i]);
}
#endif
}
}
}
@ -430,6 +505,10 @@ void FixAdaptFEP::change_settings()
// and also offset and tail corrections
if (anypair) force->pair->reinit();
if (force->kspace)
force->kspace->setup();
}
/* ----------------------------------------------------------------------
@ -452,9 +531,36 @@ void FixAdaptFEP::restore_settings()
*kspace_scale = 1.0;
} else if (ad->which == ATOM) {
if (diamflag) {
double density;
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = vec[i];
rmass[i] = 4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i] * density;
}
}
if (chgflag) {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) q[i] = vec[i];
}
}
}
if (anypair) force->pair->reinit();
if (force->kspace) force->kspace->setup();
}

3
src/USER-FEP/fix_adapt_fep.h
View File

@ -32,6 +32,7 @@ class FixAdaptFEP : public Fix {
FixAdaptFEP(class LAMMPS *, int, char **);
~FixAdaptFEP();
int setmask();
void post_constructor();
void init();
void setup_pre_force(int);
void pre_force(int);
@ -40,6 +41,8 @@ class FixAdaptFEP : public Fix {
private:
int nadapt,resetflag,scaleflag,afterflag;
int anypair;
char *id_fix_diam,*id_fix_chg;
class FixStore *fix_diam,*fix_chg;
struct Adapt {
int which,ivar;

9
src/kspace.cpp
View File

@ -68,6 +68,8 @@ KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
suffix_flag = Suffix::NONE;
adjust_cutoff_flag = 1;
scalar_pressure_flag = 0;
qsum_update_flag = 0;
warn_neutral = 1;
accuracy_absolute = -1.0;
accuracy_real_6 = -1.0;
@ -284,8 +286,11 @@ void KSpace::qsum_qsq(int flag)
if (fabs(qsum) > SMALL) {
char str[128];
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
if (flag) error->all(FLERR,str);
else if (comm->me == 0) error->warning(FLERR,str);
if (warn_neutral && (comm->me == 0)) {
if (flag) error->all(FLERR,str);
else error->warning(FLERR,str);
}
warn_neutral = 0;
}
}

2
src/kspace.h
View File

@ -51,6 +51,7 @@ class KSpace : protected Pointers {
// for LJ coefficients
int slabflag;
int scalar_pressure_flag; // 1 if using MSM fast scalar pressure
int qsum_update_flag; // 1 if setup() needs to call qsum_qsq()
double slab_volfactor;
@ -168,6 +169,7 @@ class KSpace : protected Pointers {
int minorder,overlap_allowed;
int adjust_cutoff_flag;
int suffix_flag; // suffix compatibility flag
int warn_neutral; // warn about non-neutral system if 1
bigint natoms_original;
double scale,qqrd2e;
double qsum,qsqsum,q2;