forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7262 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
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8f728e4823
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ba728e5e07
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@ -95,7 +95,6 @@ void Ewald::init()
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// extract short-range Coulombic cutoff from pair style
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qqrd2e = force->qqrd2e;
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scale = 1.0;
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if (force->pair == NULL)
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@ -270,10 +269,12 @@ void Ewald::compute(int eflag, int vflag)
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// convert E-field to force
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const double qscale = force->qqrd2e * scale;
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for (i = 0; i < nlocal; i++) {
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f[i][0] += qqrd2e*scale * q[i]*ek[i][0];
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f[i][1] += qqrd2e*scale * q[i]*ek[i][1];
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f[i][2] += qqrd2e*scale * q[i]*ek[i][2];
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f[i][0] += qscale * q[i]*ek[i][0];
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f[i][1] += qscale * q[i]*ek[i][1];
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f[i][2] += qscale * q[i]*ek[i][2];
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}
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// energy if requested
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@ -284,7 +285,7 @@ void Ewald::compute(int eflag, int vflag)
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sfacim_all[k]*sfacim_all[k]);
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energy -= g_ewald*qsqsum/MY_PIS +
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MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
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energy *= qqrd2e*scale;
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energy *= qscale;
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}
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// virial if requested
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@ -295,7 +296,7 @@ void Ewald::compute(int eflag, int vflag)
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uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
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for (n = 0; n < 6; n++) virial[n] += uk*vg[k][n];
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}
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for (n = 0; n < 6; n++) virial[n] *= qqrd2e*scale;
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for (n = 0; n < 6; n++) virial[n] *= qscale;
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}
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if (slabflag) slabcorr(eflag);
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@ -817,16 +818,17 @@ void Ewald::slabcorr(int eflag)
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// compute corrections
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double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double qscale = force->qqrd2e * scale;
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if (eflag) energy += qqrd2e*scale * e_slabcorr;
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if (eflag) energy += qscale * e_slabcorr;
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// add on force corrections
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double ffact = -4.0*MY_PI*dipole_all/volume;
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double **f = atom->f;
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for (int i = 0; i < nlocal; i++) f[i][2] += qqrd2e*scale * q[i]*ffact;
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for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
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}
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/* ----------------------------------------------------------------------
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@ -36,7 +36,6 @@ class Ewald : public KSpace {
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protected:
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double precision;
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int kcount,kmax,kmax3d,kmax_created;
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double qqrd2e;
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double gsqmx,qsum,qsqsum,volume;
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int nmax;
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@ -139,7 +139,6 @@ void PPPM::init()
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// extract short-range Coulombic cutoff from pair style
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qqrd2e = force->qqrd2e;
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scale = 1.0;
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if (force->pair == NULL)
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@ -714,6 +713,8 @@ void PPPM::compute(int eflag, int vflag)
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// sum energy across procs and add in volume-dependent term
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const double qscale = force->qqrd2e * scale;
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if (eflag) {
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double energy_all;
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MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
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@ -722,7 +723,7 @@ void PPPM::compute(int eflag, int vflag)
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energy *= 0.5*volume;
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energy -= g_ewald*qsqsum/MY_PIS +
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MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
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energy *= qqrd2e*scale;
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energy *= qscale;
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}
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// sum virial across procs
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@ -730,7 +731,7 @@ void PPPM::compute(int eflag, int vflag)
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if (vflag) {
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double virial_all[6];
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MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) virial[i] = 0.5*qqrd2e*scale*volume*virial_all[i];
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for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
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}
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// 2d slab correction
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@ -1734,7 +1735,7 @@ void PPPM::fieldforce()
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}
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// convert E-field to force
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const double qfactor = qqrd2e*scale*q[i];
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const double qfactor = force->qqrd2e * scale * q[i];
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f[i][0] += qfactor*ekx;
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f[i][1] += qfactor*eky;
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f[i][2] += qfactor*ekz;
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@ -1887,16 +1888,17 @@ void PPPM::slabcorr(int eflag)
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// compute corrections
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double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double qscale = force->qqrd2e * scale;
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if (eflag) energy += qqrd2e*scale * e_slabcorr;
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if (eflag) energy += qscale * e_slabcorr;
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// add on force corrections
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double ffact = -4.0*MY_PI*dipole_all/volume;
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double **f = atom->f;
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for (int i = 0; i < nlocal; i++) f[i][2] += qqrd2e*scale * q[i]*ffact;
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for (int i = 0; i < nlocal; i++) f[i][2] += qscale * q[i]*ffact;
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}
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/* ----------------------------------------------------------------------
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@ -51,7 +51,6 @@ class PPPM : public KSpace {
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int nfactors;
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int *factors;
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double qsum,qsqsum;
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double qqrd2e;
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double cutoff;
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double volume;
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double delxinv,delyinv,delzinv,delvolinv;
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@ -23,6 +23,7 @@
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "memory.h"
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#include "pppm_cg.h"
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@ -172,6 +173,8 @@ void PPPMCG::compute(int eflag, int vflag)
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// sum energy across procs and add in volume-dependent term
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const double qscale = force->qqrd2e * scale;
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if (eflag) {
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double energy_all;
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MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
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@ -180,7 +183,7 @@ void PPPMCG::compute(int eflag, int vflag)
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energy *= 0.5*volume;
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energy -= g_ewald*qsqsum/MY_PIS +
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MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
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energy *= qqrd2e*scale;
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energy *= qscale;
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}
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// sum virial across procs
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@ -188,7 +191,7 @@ void PPPMCG::compute(int eflag, int vflag)
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if (vflag) {
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double virial_all[6];
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MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) virial[i] = 0.5*qqrd2e*scale*volume*virial_all[i];
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for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
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}
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// 2d slab correction
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@ -341,7 +344,7 @@ void PPPMCG::fieldforce()
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}
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// convert E-field to force
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const double qfactor = qqrd2e*scale*q[i];
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const double qfactor = force->qqrd2e * scale * q[i];
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f[i][0] += qfactor*ekx;
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f[i][1] += qfactor*eky;
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f[i][2] += qfactor*ekz;
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@ -375,13 +378,14 @@ void PPPMCG::slabcorr(int eflag)
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// compute corrections
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double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
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const double qscale = force->qqrd2e * scale;
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if (eflag) energy += qqrd2e*scale * e_slabcorr;
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if (eflag) energy += qscale * e_slabcorr;
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// add on force corrections
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double ffact = -4.0*MY_PI*dipole_all/volume * qqrd2e * scale;
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const double ffact = -4.0*MY_PI*dipole_all/volume * qscale;
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double **f = atom->f;
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for (int j = 0; j < num_charged; j++) {
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@ -19,6 +19,7 @@
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#include "pppm_tip4p.h"
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#include "atom.h"
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#include "domain.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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@ -205,7 +206,7 @@ void PPPMTIP4P::fieldforce()
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}
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// convert E-field to force
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const double qfactor = qqrd2e*scale*q[i];
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const double qfactor = force->qqrd2e * scale * q[i];
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if (type[i] != typeO) {
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f[i][0] += qfactor*ekx;
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f[i][1] += qfactor*eky;
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@ -3283,10 +3283,10 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
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add pages to REBO neighbor list
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------------------------------------------------------------------------- */
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void PairAIREBO::add_pages()
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void PairAIREBO::add_pages(int howmany)
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{
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int toppage = maxpage;
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maxpage += PGDELTA;
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maxpage += howmany*PGDELTA;
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pages = (int **)
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memory->srealloc(pages,maxpage*sizeof(int *),"AIREBO:pages");
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@ -101,7 +101,7 @@ class PairAIREBO : public Pair {
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double piRCSpline(double, double, double, int, int, double *);
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double TijSpline(double, double, double, double *);
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void add_pages();
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void add_pages(int howmany=1);
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void read_file(char *);
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double Sp5th(double, double *, double *);
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@ -1243,27 +1243,6 @@ double PairComb::comb_bij_d(double zeta, Param *param)
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/* ---------------------------------------------------------------------- */
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double PairComb::comb_gijk(double costheta, Param *param)
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{
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double comb_c = param->c;
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double comb_d = param->d;
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return (1.0 + pow(comb_c/comb_d,2.0) -
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pow(comb_c,2.0) / (pow(comb_d,2.0) + pow(param->h - costheta,2.0)));
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}
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/* ---------------------------------------------------------------------- */
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double PairComb::comb_gijk_d(double costheta, Param *param)
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{
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double numerator = -2.0 * pow(param->c,2) * (param->h - costheta);
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double denominator = pow(pow(param->d,2.0) +
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pow(param->h - costheta,2.0),2.0);
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return numerator/denominator;
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}
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/*------------------------------------------------------------------------- */
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void PairComb::attractive(Param *param, double prefactor,
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double rsqij, double rsqik,
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double *delrij, double *delrik,
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@ -1649,10 +1628,10 @@ void PairComb::field(Param *param, double rsq, double iq,double jq,
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double PairComb::yasu_char(double *qf_fix, int &igroup)
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{
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int i,j,k,ii,jj,kk,jnum,itag,jtag;
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int itype,jtype,ktype,iparam_i,iparam_ij,iparam_ijk;
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int i,j,ii,jj,jnum,itag,jtag;
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int itype,jtype,iparam_i,iparam_ij;
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double xtmp,ytmp,ztmp;
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double rsq1,rsq2,delr1[3],delr2[3],zeta_ij;
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double rsq1,delr1[3];
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int *ilist,*jlist,*numneigh,**firstneigh;
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double iq,jq,fqi,fqj,fqij,fqjj;
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double potal,fac11,fac11e,sr1,sr2,sr3;
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@ -2147,15 +2126,13 @@ void PairComb::Short_neigh()
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/* ---------------------------------------------------------------------- */
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void PairComb::add_pages()
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void PairComb::add_pages(int howmany)
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{
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int toppage = maxpage;
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maxpage += PGDELTA;
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maxpage += howmany*PGDELTA;
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pages = (int **)
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memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages");
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for (int i = toppage; i < maxpage; i++)
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memory->create(pages[i],pgsize,"pair:pages[i]");
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}
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/* ---------------------------------------------------------------------- */
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@ -28,16 +28,16 @@ class PairComb : public Pair {
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public:
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PairComb(class LAMMPS *);
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virtual ~PairComb();
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void compute(int, int);
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void init_style();
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double init_one(int, int);
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double memory_usage();
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double yasu_char(double *, int &);
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virtual double yasu_char(double *, int &);
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private:
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protected:
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struct Param {
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double lam11,lam12,lam21,lam22;
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double c,d,h;
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@ -100,8 +100,24 @@ class PairComb : public Pair {
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virtual double comb_fa_d(double, Param *, double,double);
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double comb_bij(double, Param *);
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double comb_bij_d(double, Param *);
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double comb_gijk(double, Param *);
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double comb_gijk_d(double, Param *);
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inline double comb_gijk(const double costheta, const Param * const param) const {
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const double comb_c = param->c * param->c;
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const double comb_d = param->d * param->d;
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const double hcth = param->h - costheta;
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return param->gamma*(1.0 + comb_c/comb_d - comb_c / (comb_d + hcth*hcth));
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}
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inline double comb_gijk_d(const double costheta, const Param * const param) const {
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const double comb_c = param->c * param->c;
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const double comb_d = param->d * param->d;
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const double hcth = param->h - costheta;
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const double numerator = -2.0 * comb_c * hcth;
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const double denominator = 1.0/(comb_d + hcth*hcth);
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return param->gamma*numerator*denominator*denominator;
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}
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void comb_zetaterm_d(double, double *, double, double *, double,
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double *, double *, double *, Param *);
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void costheta_d(double *, double, double *, double,
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// Short range neighbor list
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void add_pages();
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void add_pages(int howmany=1);
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void Short_neigh();
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int maxpage, pgsize, oneatom, **pages;
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int *sht_num, **sht_first; // short-range neighbor list
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@ -137,17 +153,25 @@ class PairComb : public Pair {
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// vector functions, inline for efficiency
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inline double vec3_dot(double *x, double *y) {
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inline double vec3_dot(const double x[3], const double y[3]) const {
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return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
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}
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inline void vec3_add(double *x, double *y, double *z) {
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inline void vec3_add(const double x[3], const double y[3],
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double * const z) const {
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z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
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}
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inline void vec3_scale(double k, double *x, double *y) {
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inline void vec3_scale(const double k, const double x[3],
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double y[3]) const {
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y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
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}
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inline void vec3_scaleadd(double k, double *x, double *y, double *z) {
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z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
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inline void vec3_scaleadd(const double k, const double x[3],
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const double y[3], double * const z) const {
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z[0] = k*x[0]+y[0];
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z[1] = k*x[1]+y[1];
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z[2] = k*x[2]+y[2];
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}
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};
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@ -282,6 +282,16 @@ void AngleHybrid::coeff(int narg, char **arg)
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}
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}
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/* ----------------------------------------------------------------------
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run angle style specific initialization
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------------------------------------------------------------------------- */
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void AngleHybrid::init_style()
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{
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) styles[m]->init_style();
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}
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/* ----------------------------------------------------------------------
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return an equilbrium angle length
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------------------------------------------------------------------------- */
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@ -27,11 +27,16 @@ namespace LAMMPS_NS {
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class AngleHybrid : public Angle {
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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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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);
|
||||
}
|
||||
|
||||
|
|
|
@ -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;
|
||||
|
||||
|
|
|
@ -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;
|
||||
|
|
Loading…
Reference in New Issue