Bug fix for gay-berne potential when mu != 1.0. (a0d74ca2) · Commits · 郑智淋 / lammps

doc/src/PDF/pair_gayberne_extra.pdf

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doc/src/PDF/pair_gayberne_extra.tex

+1 −1

Original line number	Diff line number	Diff line
		@@ -131,7 +131,7 @@ and

		$$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
		r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
		\times \mathbf{\iota} ). $$
		\times \mathbf{\iota} ) \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu}. $$

		For the derivative of the $\eta$ term, we were unable to find a matrix
		expression due to the determinant. Let $a_{mi}$ be the mth row of the

lib/gpu/lal_gayberne.cu

+3 −4

Original line number	Diff line number	Diff line
		@@ -316,10 +316,9 @@ __kernel void k_gayberne(const __global numtyp4 *restrict x_,
		numtyp tempv[3];
		gpu_row_times3(iota,b1,tempv);
		gpu_cross3(tempv,iota,tchi);
		temp1 = (numtyp)-4.0irir;
		tchi[0] *= temp1;
		tchi[1] *= temp1;
		tchi[2] *= temp1;
		tchi[0] *= temp2;
		tchi[1] *= temp2;
		tchi[2] *= temp2;
		}

		numtyp temp2 = factor_ljetachi;

src/ASPHERE/pair_gayberne.cpp

+22 −24

Original line number	Diff line number	Diff line
		@@ -28,7 +28,6 @@
		#include "citeme.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;

		@@ -461,20 +460,20 @@ void PairGayBerne::read_restart(FILE *fp)
		int i,j;
		int me = comm->me;
		for (i = 1; i <= atom->ntypes; i++) {
		if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
		if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
		MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
		if (setwell[i]) {
		if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
		if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
		MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
		}
		for (j = i; j <= atom->ntypes; j++) {
		if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
		if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
		MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
		if (setflag[i][j]) {
		if (me == 0) {
		utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
		fread(&epsilon[i][j],sizeof(double),1,fp);
		fread(&sigma[i][j],sizeof(double),1,fp);
		fread(&cut[i][j],sizeof(double),1,fp);
		}
		MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
		MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
		@@ -506,12 +505,12 @@ void PairGayBerne::read_restart_settings(FILE *fp)
		{
		int me = comm->me;
		if (me == 0) {
		utils::sfread(FLERR,&gamma,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&upsilon,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
		utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
		utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
		fread(&gamma,sizeof(double),1,fp);
		fread(&upsilon,sizeof(double),1,fp);
		fread(&mu,sizeof(double),1,fp);
		fread(&cut_global,sizeof(double),1,fp);
		fread(&offset_flag,sizeof(int),1,fp);
		fread(&mix_flag,sizeof(int),1,fp);
		}
		MPI_Bcast(&gamma,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&upsilon,1,MPI_DOUBLE,0,world);
		@@ -644,10 +643,10 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
		dchi[2] = temp2(iota[2]-temp1r12hat[2]);

		temp1 = -eta*u_r;
		temp2 = eta*chi;
		fforce[0] = temp1dchi[0]-temp2dUr[0];
		fforce[1] = temp1dchi[1]-temp2dUr[1];
		fforce[2] = temp1dchi[2]-temp2dUr[2];
		temp3 = eta*chi;
		fforce[0] = temp1dchi[0]-temp3dUr[0];
		fforce[1] = temp1dchi[1]-temp3dUr[1];
		fforce[2] = temp1dchi[2]-temp3dUr[2];

		// torque for particle 1 and 2
		// compute dUr
		@@ -668,18 +667,17 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],

		MathExtra::vecmat(iota,b1,tempv);
		MathExtra::cross3(tempv,iota,dchi);
		temp1 = -4.0/rsq;
		dchi[0] *= temp1;
		dchi[1] *= temp1;
		dchi[2] *= temp1;
		dchi[0] *= temp2;
		dchi[1] *= temp2;
		dchi[2] *= temp2;
		double dchi2[3];

		if (newton_pair \|\| j < nlocal) {
		MathExtra::vecmat(iota,b2,tempv);
		MathExtra::cross3(tempv,iota,dchi2);
		dchi2[0] *= temp1;
		dchi2[1] *= temp1;
		dchi2[2] *= temp1;
		dchi2[0] *= temp2;
		dchi2[1] *= temp2;
		dchi2[2] *= temp2;
		}

		// compute d_eta

src/USER-INTEL/pair_gayberne_intel.cpp

+10 −11

Original line number	Diff line number	Diff line
		@@ -555,10 +555,10 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
		dchi_2 = temp2 * (iota_2 - temp1 * r12hat_2);

		temp1 = -eta * u_r;
		temp2 = eta * chi;
		fforce_0 = temp1 * dchi_0 - temp2 * dUr_0;
		fforce_1 = temp1 * dchi_1 - temp2 * dUr_1;
		fforce_2 = temp1 * dchi_2 - temp2 * dUr_2;
		temp3 = eta * chi;
		fforce_0 = temp1 * dchi_0 - temp3 * dUr_0;
		fforce_1 = temp1 * dchi_1 - temp3 * dUr_1;
		fforce_2 = temp1 * dchi_2 - temp3 * dUr_2;

		// torque for particle 1 and 2
		// compute dUr
		@@ -579,18 +579,17 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,

		ME_vecmat(iota, b1, tempv);
		ME_cross3(tempv, iota, dchi);
		temp1 = (flt_t)-4.0 / rsq_form[jj];
		dchi_0 *= temp1;
		dchi_1 *= temp1;
		dchi_2 *= temp1;
		dchi_0 *= temp2;
		dchi_1 *= temp2;
		dchi_2 *= temp2;
		flt_t dchi2_0, dchi2_1, dchi2_2;

		if (NEWTON_PAIR) {
		ME_vecmat(iota, b2, tempv);
		ME_cross3(tempv, iota, dchi2);
		dchi2_0 *= temp1;
		dchi2_1 *= temp1;
		dchi2_2 *= temp1;
		dchi2_0 *= temp2;
		dchi2_1 *= temp2;
		dchi2_2 *= temp2;
		}

		// compute d_eta

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