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[求助]
碳酸根C-O/O/O离平面能力场编写
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C原子离O平面距离为rn,离平面能为E=K2*rn^2+K4*rn^4,然后控温就会有问题,具体表现是温度一直升高,源文件如下: /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "mpi.h" #include "math.h" #include "stdlib.h" #include "improper_usr.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 /* ---------------------------------------------------------------------- */ ImproperUsr::ImproperUsr(LAMMPS *lmp) : Improper(lmp) { writedata = 1; } /* ---------------------------------------------------------------------- */ ImproperUsr::~ImproperUsr() { if (allocated) { memory->destroy(setflag); memory->destroy(k2); memory->destroy(k4); } } /* ---------------------------------------------------------------------- */ void ImproperUsr::compute(int eflag, int vflag) { int i1,i2,i3,i4,n,type; double b12x,b12y,b12z,b13x,b13y,b13z,b14x,b14y,b14z,b134a,b134b,b134c; double eimproper,f1[3],f2[3],f3[3],f4[3]; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z; double dr1ax,dr1ay,dr1az,dr1bx,dr1by,dr1bz,dr1cx,dr1cy,dr1cz; double dr3ax,dr3ay,dr3az,dr3bx,dr3by,dr3bz,dr3cx,dr3cy,dr3cz; double dr4ax,dr4ay,dr4az,dr4bx,dr4by,dr4bz,dr4cx,dr4cy,dr4cz; double rsqb134,rb134,rn; double drsqb1341a,drsqb1341b,drsqb1341c,drsqb1343a,drsqb1343b,drsqb1343c; double drsqb1344a,drsqb1344b,drsqb1344c; eimproper = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = 0; double **x = atom->x; double **f = atom->f; int **improperlist = neighbor->improperlist; int nimproperlist = neighbor->nimproperlist; int nlocal = atom->nlocal; int newton_bond = force->newton_bond; for (n = 0; n < nimproperlist; n++) { i1 = improperlist[n][0]; i2 = improperlist[n][1]; i3 = improperlist[n][2]; i4 = improperlist[n][3]; type = improperlist[n][4]; // geometry of 4-body b12x = x[i2][0] - x[i1][0]; b12y = x[i2][1] - x[i1][1]; b12z = x[i2][2] - x[i1][2]; b13x = x[i3][0] - x[i1][0]; b13y = x[i3][1] - x[i1][1]; b13z = x[i3][2] - x[i1][2]; b14x = x[i4][0] - x[i1][0]; b14y = x[i4][1] - x[i1][1]; b14z = x[i4][2] - x[i1][2]; //Virial Calculation vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2]; vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2]; vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; //Virial cal end //b134=b13xb14 b134a=b13y*b14z-b13z*b14y; b134b=b13z*b14x-b13x*b14z; b134c=b13x*b14y-b13y*b14x; //Derivative of b13xb14 dr1ax=0; dr1ay=-b13z+b14z; dr1az=-b14y+b13y; dr1bx=-b14z+b13z; dr1by=0; dr1bz=-b13x+b14x; dr1cx=-b13y+b14y; dr1cy=-b14x+b13x; dr1cz=0; dr3ax=0; dr3ay=-b14z; dr3az=b14y; dr3bx=b14z; dr3by=0; dr3bz=-b14x; dr3cx=-b14y; dr3cy=b14x; dr3cz=0; dr4ax=0; dr4ay=b13z; dr4az=-b13y; dr4bx=-b13z; dr4by=0; dr4bz=b13x; dr4cx=b13y; dr4cy=-b13x; dr4cz=0; rsqb134 = b134a*b134a + b134b*b134b+b134c*b134c; if (rsqb134 < SMALL) rsqb134 = SMALL*100; rb134 = sqrt(rsqb134); rn=(b134a*b12x+b134b*b12y+b134c*b12z)/rb134; // if (screen) { // fprintf(screen,"User Style Success\n"  ; // } //Derivative of (b13xb14)^2 drsqb1341a=-(b134a*0+b134b*(-b13z+b14z)+b134c*(-b14y+b13y))/pow(rsqb134,-1.5); drsqb1341b=-(b134a*(-b14z+b13z)+b134b*0+b134c*(-b13x+b14x))/pow(rsqb134,-1.5); drsqb1341c=-(b134a*(-b13y+b14y)+b134b*(-b14x+b13x)+b134c*0)/pow(rsqb134,-1.5); drsqb1343a=-(b134a*0+b134b*(-b14z)+b134c*(b14y))/pow(rsqb134,-1.5); drsqb1343b=-(b134a*(b14z)+b134b*0+b134c*(-b14x))/pow(rsqb134,-1.5); drsqb1343c=-(b134a*(-b14y)+b134b*(b14x)+b134c*0)/pow(rsqb134,-1.5); drsqb1344a=-(b134a*0+b134b*(b13z)+b134c*(-b13y))/pow(rsqb134,-1.5); drsqb1344b=-(b134a*(-b13z)+b134b*0+b134c*(b13x))/pow(rsqb134,-1.5); drsqb1344c=-(b134a*(b13y)+b134b*(-b13x)+b134c*0)/pow(rsqb134,-1.5); //Forces on each atoms f1[0]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr1ax*b12x+dr1ay*b12y+dr1az*b12z-b134a)/rb134+rn*(-0.5)*drsqb1341a/pow(rsqb134,2)); f1[1]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr1bx*b12x+dr1by*b12y+dr1bz*b12z-b134b)/rb134+rn*(-0.5)*drsqb1341b/pow(rsqb134,2)); f1[2]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr1cx*b12x+dr1cy*b12y+dr1cz*b12z-b134c)/rb134+rn*(-0.5)*drsqb1341c/pow(rsqb134,2)); f3[0]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr3ax*b12x+dr3ay*b12y+dr3az*b12z)/rb134+rn*(-0.5)*drsqb1343a/pow(rsqb134,2)); f3[1]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr3bx*b12x+dr3by*b12y+dr3bz*b12z)/rb134+rn*(-0.5)*drsqb1343b/pow(rsqb134,2)); f3[2]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr3cx*b12x+dr3cy*b12y+dr3cz*b12z)/rb134+rn*(-0.5)*drsqb1343c/pow(rsqb134,2)); f2[0]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((b134a)/rb134); f2[1]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((b134b)/rb134); f2[2]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((b134c)/rb134); f4[0]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr4ax*b12x+dr4ay*b12y+dr4az*b12z)/rb134+rn*(-0.5)*drsqb1344a/pow(rsqb134,2)); f4[1]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr4bx*b12x+dr4by*b12y+dr4bz*b12z)/rb134+rn*(-0.5)*drsqb1344b/pow(rsqb134,2)); f4[2]=-(2*k2[type]+4*k4[type]*pow(rn,2))*rn*((dr4cx*b12x+dr4cy*b12y+dr4cz*b12z)/rb134+rn*(-0.5)*drsqb1344c/pow(rsqb134,2)); if (eflag) eimproper = k2[type]*rn*rn+k4[type]*pow(rn,4); if (eflag && screen && n==100) { fprintf(screen,"******compute:::K2: %g K4: %g\n",k2[type],k4[type]); fprintf(screen,"******compute:::energy: %g\n",eimproper); fprintf(screen,"******compute:::rn: %g rsqb134: %g rb134: %g\n",rn,rsqb134,rb134); fprintf(screen,"******compute:::rn: %g %g %g\n",f1[0],f1[1],f1[2]); fprintf(screen,"******compute:::f1: %g %g %g\n",f1[0],f1[1],f1[2]); fprintf(screen,"******compute:::f2: %g %g %g\n",f2[0],f2[1],f2[2]); fprintf(screen,"******compute:::f3: %g %g %g\n",f3[0],f3[1],f3[2]); fprintf(screen,"******compute:::f4: %g %g %g\n",f4[0],f4[1],f4[2]); } // apply force to each of 4 atoms if (newton_bond || i1 < nlocal) { f[i1][0] += f1[0]; f[i1][1] += f1[1]; f[i1][2] += f1[2]; } if (newton_bond || i2 < nlocal) { f[i2][0] += f2[0]; f[i2][1] += f2[1]; f[i2][2] += f2[2]; } if (newton_bond || i3 < nlocal) { f[i3][0] += f3[0]; f[i3][1] += f3[1]; f[i3][2] += f3[2]; } if (newton_bond || i4 < nlocal) { f[i4][0] += f4[0]; f[i4][1] += f4[1]; f[i4][2] += f4[2]; } if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); } } /* ---------------------------------------------------------------------- */ void ImproperUsr::allocate() { allocated = 1; int n = atom->nimpropertypes; fprintf(screen,"*************allocate:::: n: %g\n",n); memory->create(k2,n+1,"improper:k2" ;memory->create(k4,n+1,"improper:k4" ;memory->create(setflag,n+1,"improper:setflag" ;for (int i = 1; i <= n; i++) setflag = 0; } /* ---------------------------------------------------------------------- set coeffs for one type ------------------------------------------------------------------------- */ void ImproperUsr::coeff(int narg, char **arg) { if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" ;if (!allocated) allocate(); int ilo,ihi; force->bounds(arg[0],atom->nimpropertypes,ilo,ihi); fprintf(screen,"*************coeff:::ilo: %d ihi: %d\n",ilo,ihi); double k2_one = force->numeric(FLERR,arg[1]); double k4_one = force->numeric(FLERR,arg[2]); fprintf(screen,"*************coeff k2: %g k4: %g\n",k2_one,k4_one); // convert chi from degrees to radians int count = 0; for (int i = ilo; i <= ihi; i++) { fprintf(screen,"*************coeff k2_one: %g k4_one: %g\n",k2_one,k4_one); k2 = k2_one; k4 = k4_one; fprintf(screen,"*************coeff count=%g i= %d k2: %g k4: %g\n",count,i,k2,k4); setflag = 1; count++; } if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" ;} /* ---------------------------------------------------------------------- proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ void ImproperUsr::write_restart(FILE *fp) { fwrite(&k2[1],sizeof(double),atom->nimpropertypes,fp); fwrite(&k4[1],sizeof(double),atom->nimpropertypes,fp); } /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ void ImproperUsr::read_restart(FILE *fp) { allocate(); if (comm->me == 0) { fread(&k2[1],sizeof(double),atom->nimpropertypes,fp); fread(&k4[1],sizeof(double),atom->nimpropertypes,fp); } MPI_Bcast(&k2[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&k4[1],atom->nimpropertypes,MPI_DOUBLE,0,world); for (int i = 1; i <= atom->nimpropertypes; i++) setflag = 1; } /* ---------------------------------------------------------------------- proc 0 writes to data file ------------------------------------------------------------------------- */ void ImproperUsr::write_data(FILE *fp) { for (int i = 1; i <= atom->nimpropertypes; i++) fprintf(fp,"%d %g %g\n",i,k2,k4); } |
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2015-10-25 16:44:46, 10.15 K
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