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

src/KSPACE/ewald.cpp

@@ -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][0] += qscale * q[i]*ek[i][0];
-    f[i][1] += qqrd2e*scale * q[i]*ek[i][1];
+    f[i][1] += qscale * q[i]*ek[i][1];
-    f[i][2] += qqrd2e*scale * q[i]*ek[i][2];
+    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;
 }
 
 /* ----------------------------------------------------------------------

src/KSPACE/ewald.h

@@ -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;
 

src/KSPACE/pppm.cpp

@@ -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;
 }
 
 /* ----------------------------------------------------------------------

src/KSPACE/pppm.h

@@ -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;

src/KSPACE/pppm_cg.cpp

@@ -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++) {

src/KSPACE/pppm_tip4p.cpp

@@ -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;

src/MANYBODY/pair_airebo.cpp

@@ -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");

src/MANYBODY/pair_airebo.h

@@ -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 *);

src/MANYBODY/pair_comb.cpp

@@ -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 i,j,ii,jj,jnum,itag,jtag;
-  int itype,jtype,ktype,iparam_i,iparam_ij,iparam_ijk;
+  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]");
 }
-
-/* ---------------------------------------------------------------------- */

src/MANYBODY/pair_comb.h

@@ -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];
   }
 };
 

src/MOLECULE/angle_hybrid.cpp

@@ -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 
 ------------------------------------------------------------------------- */

src/MOLECULE/angle_hybrid.h

@@ -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

src/MOLECULE/dihedral_hybrid.h

@@ -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

src/MOLECULE/improper_hybrid.h

@@ -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

src/USER-EWALDN/ewald_n.cpp

@@ -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;
+    virial_self[0] = -0.5*M_PI*qscale/(g2*volume)*sum[0].x*sum[0].x;
-    energy_self[0] = sum[0].x2*qqrd2e*scale*g1/sqrt(M_PI)-virial_self[0];
+    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];
@@ -686,13 +690,15 @@ void EwaldN::compute_slabcorr(int eflag)
   while ((x+=3)<xn) dipole += *x * *(q++);
   MPI_Allreduce(&dipole, &dipole_all, 1, MPI_DOUBLE, MPI_SUM, world);
 
-  double ffact = -4.0*M_PI*qqrd2e*scale*dipole_all/volume;
+  const double qscale = force->qqrd2e * scale;
+  
+  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);
 }
 

src/USER-EWALDN/ewald_n.h

@@ -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;
  

src/pair.h

@@ -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;