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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7262 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-12-01 15:47:17 +00:00
parent 8f728e4823
commit ba728e5e07
17 changed files with 115 additions and 85 deletions
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20
src/KSPACE/ewald.cpp
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@ -95,7 +95,6 @@ void Ewald::init()
// extract short-range Coulombic cutoff from pair style
qqrd2e = force->qqrd2e;
scale = 1.0;
if (force->pair == NULL)
@ -270,10 +269,12 @@ void Ewald::compute(int eflag, int vflag)
// convert E-field to force
const double qscale = force->qqrd2e * scale;
for (i = 0; i < nlocal; i++) {
f[i][0] += qqrd2e*scale * q[i]*ek[i][0];
f[i][1] += qqrd2e*scale * q[i]*ek[i][1];
f[i][2] += qqrd2e*scale * q[i]*ek[i][2];
f[i][0] += qscale * q[i]*ek[i][0];
f[i][1] += qscale * q[i]*ek[i][1];
f[i][2] += qscale * q[i]*ek[i][2];
}
// energy if requested
@ -284,7 +285,7 @@ void Ewald::compute(int eflag, int vflag)
sfacim_all[k]*sfacim_all[k]);
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qqrd2e*scale;
energy *= qscale;
}
// virial if requested
@ -295,7 +296,7 @@ void Ewald::compute(int eflag, int vflag)
uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
for (n = 0; n < 6; n++) virial[n] += uk*vg[k][n];
}
for (n = 0; n < 6; n++) virial[n] *= qqrd2e*scale;
for (n = 0; n < 6; n++) virial[n] *= qscale;
}
if (slabflag) slabcorr(eflag);
@ -817,16 +818,17 @@ void Ewald::slabcorr(int eflag)
// compute corrections
double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
if (eflag) energy += qqrd2e*scale * e_slabcorr;
if (eflag) energy += qscale * e_slabcorr;
// add on force corrections
double ffact = -4.0*MY_PI*dipole_all/volume;
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += qqrd2e*scale * q[i]*ffact;
for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
}
/* ----------------------------------------------------------------------

1
src/KSPACE/ewald.h
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@ -36,7 +36,6 @@ class Ewald : public KSpace {
protected:
double precision;
int kcount,kmax,kmax3d,kmax_created;
double qqrd2e;
double gsqmx,qsum,qsqsum,volume;
int nmax;

16
src/KSPACE/pppm.cpp
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@ -139,7 +139,6 @@ void PPPM::init()
// extract short-range Coulombic cutoff from pair style
qqrd2e = force->qqrd2e;
scale = 1.0;
if (force->pair == NULL)
@ -714,6 +713,8 @@ void PPPM::compute(int eflag, int vflag)
// sum energy across procs and add in volume-dependent term
const double qscale = force->qqrd2e * scale;
if (eflag) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
@ -722,7 +723,7 @@ void PPPM::compute(int eflag, int vflag)
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qqrd2e*scale;
energy *= qscale;
}
// sum virial across procs
@ -730,7 +731,7 @@ void PPPM::compute(int eflag, int vflag)
if (vflag) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qqrd2e*scale*volume*virial_all[i];
for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
}
// 2d slab correction
@ -1734,7 +1735,7 @@ void PPPM::fieldforce()
}
// convert E-field to force
const double qfactor = qqrd2e*scale*q[i];
const double qfactor = force->qqrd2e * scale * q[i];
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
f[i][2] += qfactor*ekz;
@ -1887,16 +1888,17 @@ void PPPM::slabcorr(int eflag)
// compute corrections
double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
if (eflag) energy += qqrd2e*scale * e_slabcorr;
if (eflag) energy += qscale * e_slabcorr;
// add on force corrections
double ffact = -4.0*MY_PI*dipole_all/volume;
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += qqrd2e*scale * q[i]*ffact;
for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
}
/* ----------------------------------------------------------------------

1
src/KSPACE/pppm.h
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@ -51,7 +51,6 @@ class PPPM : public KSpace {
int nfactors;
int *factors;
double qsum,qsqsum;
double qqrd2e;
double cutoff;
double volume;
double delxinv,delyinv,delzinv,delvolinv;

16
src/KSPACE/pppm_cg.cpp
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@ -23,6 +23,7 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "pppm_cg.h"
@ -172,6 +173,8 @@ void PPPMCG::compute(int eflag, int vflag)
// sum energy across procs and add in volume-dependent term
const double qscale = force->qqrd2e * scale;
if (eflag) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
@ -180,7 +183,7 @@ void PPPMCG::compute(int eflag, int vflag)
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qqrd2e*scale;
energy *= qscale;
}
// sum virial across procs
@ -188,7 +191,7 @@ void PPPMCG::compute(int eflag, int vflag)
if (vflag) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qqrd2e*scale*volume*virial_all[i];
for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
}
// 2d slab correction
@ -341,7 +344,7 @@ void PPPMCG::fieldforce()
}
// convert E-field to force
const double qfactor = qqrd2e*scale*q[i];
const double qfactor = force->qqrd2e * scale * q[i];
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
f[i][2] += qfactor*ekz;
@ -375,13 +378,14 @@ void PPPMCG::slabcorr(int eflag)
// compute corrections
double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
if (eflag) energy += qqrd2e*scale * e_slabcorr;
if (eflag) energy += qscale * e_slabcorr;
// add on force corrections
double ffact = -4.0*MY_PI*dipole_all/volume * qqrd2e * scale;
const double ffact = -4.0*MY_PI*dipole_all/volume * qscale;
double **f = atom->f;
for (int j = 0; j < num_charged; j++) {

3
src/KSPACE/pppm_tip4p.cpp
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@ -19,6 +19,7 @@
#include "pppm_tip4p.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "memory.h"
#include "error.h"
@ -205,7 +206,7 @@ void PPPMTIP4P::fieldforce()
}
// convert E-field to force
const double qfactor = qqrd2e*scale*q[i];
const double qfactor = force->qqrd2e * scale * q[i];
if (type[i] != typeO) {
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;

4
src/MANYBODY/pair_airebo.cpp
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@ -3283,10 +3283,10 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
add pages to REBO neighbor list
------------------------------------------------------------------------- */
void PairAIREBO::add_pages()
void PairAIREBO::add_pages(int howmany)
{
int toppage = maxpage;
maxpage += PGDELTA;
maxpage += howmany*PGDELTA;
pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"AIREBO:pages");

2
src/MANYBODY/pair_airebo.h
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@ -101,7 +101,7 @@ class PairAIREBO : public Pair {
double piRCSpline(double, double, double, int, int, double *);
double TijSpline(double, double, double, double *);
void add_pages();
void add_pages(int howmany=1);
void read_file(char *);
double Sp5th(double, double *, double *);

33
src/MANYBODY/pair_comb.cpp
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@ -1243,27 +1243,6 @@ double PairComb::comb_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
double PairComb::comb_gijk(double costheta, Param *param)
{
double comb_c = param->c;
double comb_d = param->d;
return (1.0 + pow(comb_c/comb_d,2.0) -
pow(comb_c,2.0) / (pow(comb_d,2.0) + pow(param->h - costheta,2.0)));
}
/* ---------------------------------------------------------------------- */
double PairComb::comb_gijk_d(double costheta, Param *param)
{
double numerator = -2.0 * pow(param->c,2) * (param->h - costheta);
double denominator = pow(pow(param->d,2.0) +
pow(param->h - costheta,2.0),2.0);
return numerator/denominator;
}
/*------------------------------------------------------------------------- */
void PairComb::attractive(Param *param, double prefactor,
double rsqij, double rsqik,
double *delrij, double *delrik,
@ -1649,10 +1628,10 @@ void PairComb::field(Param *param, double rsq, double iq,double jq,
double PairComb::yasu_char(double *qf_fix, int &igroup)
{
int i,j,k,ii,jj,kk,jnum,itag,jtag;
int itype,jtype,ktype,iparam_i,iparam_ij,iparam_ijk;
int i,j,ii,jj,jnum,itag,jtag;
int itype,jtype,iparam_i,iparam_ij;
double xtmp,ytmp,ztmp;
double rsq1,rsq2,delr1[3],delr2[3],zeta_ij;
double rsq1,delr1[3];
int *ilist,*jlist,*numneigh,**firstneigh;
double iq,jq,fqi,fqj,fqij,fqjj;
double potal,fac11,fac11e,sr1,sr2,sr3;
@ -2147,15 +2126,13 @@ void PairComb::Short_neigh()
/* ---------------------------------------------------------------------- */
void PairComb::add_pages()
void PairComb::add_pages(int howmany)
{
int toppage = maxpage;
maxpage += PGDELTA;
maxpage += howmany*PGDELTA;
pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages");
for (int i = toppage; i < maxpage; i++)
memory->create(pages[i],pgsize,"pair:pages[i]");
}
/* ---------------------------------------------------------------------- */

46
src/MANYBODY/pair_comb.h
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@ -28,16 +28,16 @@ class PairComb : public Pair {
public:
PairComb(class LAMMPS *);
virtual ~PairComb();
void compute(int, int);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
double memory_usage();
double yasu_char(double *, int &);
virtual double yasu_char(double *, int &);
private:
protected:
struct Param {
double lam11,lam12,lam21,lam22;
double c,d,h;
@ -100,8 +100,24 @@ class PairComb : public Pair {
virtual double comb_fa_d(double, Param *, double,double);
double comb_bij(double, Param *);
double comb_bij_d(double, Param *);
double comb_gijk(double, Param *);
double comb_gijk_d(double, Param *);
inline double comb_gijk(const double costheta, const Param * const param) const {
const double comb_c = param->c * param->c;
const double comb_d = param->d * param->d;
const double hcth = param->h - costheta;
return param->gamma*(1.0 + comb_c/comb_d - comb_c / (comb_d + hcth*hcth));
}
inline double comb_gijk_d(const double costheta, const Param * const param) const {
const double comb_c = param->c * param->c;
const double comb_d = param->d * param->d;
const double hcth = param->h - costheta;
const double numerator = -2.0 * comb_c * hcth;
const double denominator = 1.0/(comb_d + hcth*hcth);
return param->gamma*numerator*denominator*denominator;
}
void comb_zetaterm_d(double, double *, double, double *, double,
double *, double *, double *, Param *);
void costheta_d(double *, double, double *, double,
@ -129,7 +145,7 @@ class PairComb : public Pair {
// Short range neighbor list
void add_pages();
void add_pages(int howmany=1);
void Short_neigh();
int maxpage, pgsize, oneatom, **pages;
int *sht_num, **sht_first; // short-range neighbor list
@ -137,17 +153,25 @@ class PairComb : public Pair {
// vector functions, inline for efficiency
inline double vec3_dot(double *x, double *y) {
inline double vec3_dot(const double x[3], const double y[3]) const {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
inline void vec3_add(double *x, double *y, double *z) {
inline void vec3_add(const double x[3], const double y[3],
double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(double k, double *x, double *y) {
inline void vec3_scale(const double k, const double x[3],
double y[3]) const {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
inline void vec3_scaleadd(double k, double *x, double *y, double *z) {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
inline void vec3_scaleadd(const double k, const double x[3],
const double y[3], double * const z) const {
z[0] = k*x[0]+y[0];
z[1] = k*x[1]+y[1];
z[2] = k*x[2]+y[2];
}
};

10
src/MOLECULE/angle_hybrid.cpp
View File

@ -282,6 +282,16 @@ void AngleHybrid::coeff(int narg, char **arg)
}
}
/* ----------------------------------------------------------------------
run angle style specific initialization
------------------------------------------------------------------------- */
void AngleHybrid::init_style()
{
for (int m = 0; m < nstyles; m++)
if (styles[m]) styles[m]->init_style();
}
/* ----------------------------------------------------------------------
return an equilbrium angle length
------------------------------------------------------------------------- */

8
src/MOLECULE/angle_hybrid.h
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@ -27,11 +27,16 @@ namespace LAMMPS_NS {
class AngleHybrid : public Angle {
public:
int nstyles; // # of different angle styles
Angle **styles; // class list for each Angle style
char **keywords; // keyword for each Angle style
AngleHybrid(class LAMMPS *);
~AngleHybrid();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
@ -39,9 +44,6 @@ class AngleHybrid : public Angle {
double memory_usage();
private:
int nstyles; // # of different angle styles
Angle **styles; // class list for each Angle style
char **keywords; // keyword for each Angle style
int *map; // which style each angle type points to
int *nanglelist; // # of angles in sub-style anglelists

7
src/MOLECULE/dihedral_hybrid.h
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@ -27,6 +27,10 @@ namespace LAMMPS_NS {
class DihedralHybrid : public Dihedral {
public:
int nstyles; // # of different dihedral styles
Dihedral **styles; // class list for each Dihedral style
char **keywords; // keyword for each dihedral style
DihedralHybrid(class LAMMPS *);
~DihedralHybrid();
void compute(int, int);
@ -38,9 +42,6 @@ class DihedralHybrid : public Dihedral {
double memory_usage();
private:
int nstyles; // # of different dihedral styles
Dihedral **styles; // class list for each Dihedral style
char **keywords; // keyword for each dihedral style
int *map; // which style each dihedral type points to
int *ndihedrallist; // # of dihedrals in sub-style dihedrallists

7
src/MOLECULE/improper_hybrid.h
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@ -27,6 +27,10 @@ namespace LAMMPS_NS {
class ImproperHybrid : public Improper {
public:
int nstyles; // # of different improper styles
Improper **styles; // class list for each Improper style
char **keywords; // keyword for each improper style
ImproperHybrid(class LAMMPS *);
~ImproperHybrid();
void compute(int, int);
@ -37,9 +41,6 @@ class ImproperHybrid : public Improper {
double memory_usage();
private:
int nstyles; // # of different improper styles
Improper **styles; // class list for each Improper style
char **keywords; // keyword for each improper style
int *map; // which style each improper type points to
int *nimproperlist; // # of impropers in sub-style improperlists

22
src/USER-EWALDN/ewald_n.cpp
View File

@ -87,7 +87,6 @@ void EwaldN::init()
error->all(FLERR,"Incorrect boundaries with slab EwaldN");
}
qqrd2e = force->qqrd2e; // check pair_style
scale = 1.0;
//mumurd2e = force->mumurd2e;
//dielectric = force->dielectric;
@ -368,9 +367,11 @@ void EwaldN::init_self()
memset(energy_self, 0, EWALD_NFUNCS*sizeof(double)); // self energy
memset(virial_self, 0, EWALD_NFUNCS*sizeof(double));
const double qscale = force->qqrd2e * scale;
if (function[0]) { // 1/r
virial_self[0] = -0.5*M_PI*qqrd2e*scale/(g2*volume)*sum[0].x*sum[0].x;
energy_self[0] = sum[0].x2*qqrd2e*scale*g1/sqrt(M_PI)-virial_self[0];
virial_self[0] = -0.5*M_PI*qscale/(g2*volume)*sum[0].x*sum[0].x;
energy_self[0] = sum[0].x2*qscale*g1/sqrt(M_PI)-virial_self[0];
}
if (function[1]) { // geometric 1/r^6
virial_self[1] = M_PI*sqrt(M_PI)*g3/(6.0*volume)*sum[1].x*sum[1].x;
@ -484,8 +485,9 @@ void EwaldN::compute_force()
complex *cek, zc, zx, zxy;
double *f = atom->f[0], *fn = f+3*atom->nlocal, *q = atom->q, *t = NULL;
double *mu = atom->mu ? atom->mu[0] : NULL;
const double qscale = force->qqrd2e * scale;
double *ke, c[EWALD_NFUNCS] = {
8.0*M_PI*qqrd2e*scale/volume, 2.0*M_PI*sqrt(M_PI)/(12.0*volume),
8.0*M_PI*qscale/volume, 2.0*M_PI*sqrt(M_PI)/(12.0*volume),
2.0*M_PI*sqrt(M_PI)/(192.0*volume), 8.0*M_PI*mumurd2e/volume};
double kt = 4.0*pow(g_ewald, 3.0)/3.0/sqrt(M_PI)/c[3];
int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type;
@ -587,8 +589,9 @@ void EwaldN::compute_energy(int eflag)
complex *cek = cek_global;
double *ke = kenergy;
const double qscale = force->qqrd2e * scale;
double c[EWALD_NFUNCS] = {
4.0*M_PI*qqrd2e*scale/volume, 2.0*M_PI*sqrt(M_PI)/(24.0*volume),
4.0*M_PI*qscale/volume, 2.0*M_PI*sqrt(M_PI)/(24.0*volume),
2.0*M_PI*sqrt(M_PI)/(192.0*volume), 4.0*M_PI*mumurd2e/volume};
double sum[EWALD_NFUNCS];
int func[EWALD_NFUNCS];
@ -625,8 +628,9 @@ void EwaldN::compute_virial(int vflag)
complex *cek = cek_global;
double *kv = kvirial;
const double qscale = force->qqrd2e * scale;
double c[EWALD_NFUNCS] = {
4.0*M_PI*qqrd2e*scale/volume, 2.0*M_PI*sqrt(M_PI)/(24.0*volume),
4.0*M_PI*qscale/volume, 2.0*M_PI*sqrt(M_PI)/(24.0*volume),
2.0*M_PI*sqrt(M_PI)/(192.0*volume), 4.0*M_PI*mumurd2e/volume};
shape sum[EWALD_NFUNCS];
int func[EWALD_NFUNCS];
@ -685,14 +689,16 @@ void EwaldN::compute_slabcorr(int eflag)
while ((x+=3)<xn) dipole += *x * *(q++);
MPI_Allreduce(&dipole, &dipole_all, 1, MPI_DOUBLE, MPI_SUM, world);
const double qscale = force->qqrd2e * scale;
double ffact = -4.0*M_PI*qqrd2e*scale*dipole_all/volume;
double ffact = -4.0*M_PI*qscale*dipole_all/volume;
double *f = atom->f[0]-1, *fn = f+3*atom->nlocal-3;
q = atom->q;
while ((f+=3)<fn) *f += ffact* *(q++);
if (eflag) // energy correction
energy += qqrd2e*scale*(2.0*M_PI*dipole_all*dipole_all/volume);
energy += qscale*(2.0*M_PI*dipole_all*dipole_all/volume);
}

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

@ -57,7 +57,7 @@ class EwaldN : public KSpace {
hvector *hvec;
kvector *kvec;
double qqrd2e, mumurd2e, dielectric, *B, volume;
double mumurd2e, dielectric, *B, volume;
struct Sum { double x, x2; } sum[EWALD_MAX_NSUMS];
complex *cek_local, *cek_global;

2
src/pair.h
View File

@ -19,6 +19,8 @@
namespace LAMMPS_NS {
class Pair : protected Pointers {
friend class AngleSDK;
friend class AngleSDKOMP;
friend class BondQuartic;
friend class BondQuarticOMP;
friend class DihedralCharmm;