forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10946 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
ed9d5b6dc4
commit
5e6680916b
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@ -12,7 +12,8 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Tzu-Ray Shan (U Florida, rayshan@ufl.edu)
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Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
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------------------------------------------------------------------------- */
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#include "lmptype.h"
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@ -21,6 +22,7 @@
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#include "stdlib.h"
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#include "string.h"
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#include "pair_comb.h"
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#include "pair_comb3.h"
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#include "fix_qeq_comb.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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@ -88,6 +90,7 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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for (int i = 0; i < nlocal; i++) qf[i] = 0.0;
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comb = NULL;
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comb3 = NULL;
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comm_forward = 1;
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}
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@ -121,8 +124,9 @@ void FixQEQComb::init()
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error->all(FLERR,"Fix qeq/comb requires atom attribute q");
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comb = (PairComb *) force->pair_match("comb",1);
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if (comb == NULL)
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error->all(FLERR,"Must use pair_style comb with fix qeq/comb");
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comb3 = (PairComb3 *) force->pair_match("comb3",1);
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if (comb == NULL && comb3 == NULL)
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error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb");
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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@ -188,8 +192,8 @@ void FixQEQComb::post_force(int vflag)
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// more loops for first-time charge equilibrium
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iloop = 0;
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if (firstflag) loopmax = 500;
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else loopmax = 200;
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if (firstflag) loopmax = 200;
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else loopmax = 100;
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// charge-equilibration loop
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@ -211,9 +215,14 @@ void FixQEQComb::post_force(int vflag)
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int *tag = atom->tag;
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int nlocal = atom->nlocal;
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inum = comb->list->inum;
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ilist = comb->list->ilist;
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if (comb) {
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inum = comb->list->inum;
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ilist = comb->list->ilist;
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}
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if (comb3) {
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inum = comb3->list->inum;
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ilist = comb3->list->ilist;
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}
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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q1[i] = q2[i] = qf[i] = 0.0;
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@ -227,9 +236,11 @@ void FixQEQComb::post_force(int vflag)
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q[i] += q1[i];
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}
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}
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comm->forward_comm_fix(this);
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comm->forward_comm_fix(this);
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if(comb) enegtot = comb->yasu_char(qf,igroup);
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if(comb3) enegtot = comb3->combqeq(qf,igroup);
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enegtot /= ngroup;
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enegchk = enegmax = 0.0;
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@ -48,6 +48,7 @@ class FixQEQComb : public Fix {
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FILE *fp;
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class PairComb *comb;
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class PairComb3 *comb3;
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int nmax;
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double *qf,*q1,*q2;
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};
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,333 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(comb3,PairComb3)
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#else
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#ifndef LMP_PAIR_COMB3_H
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#define LMP_PAIR_COMB3_H
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#include "pair.h"
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#include "my_page.h"
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namespace LAMMPS_NS {
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class PairComb3 : public Pair {
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public:
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PairComb3(class LAMMPS *);
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virtual ~PairComb3();
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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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virtual double combqeq(double *, int &);
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// general potential parameters
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protected:
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struct Param {
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int ielement,jelement,kelement,powermint;
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int ielementgp,jelementgp,kelementgp; //element group
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int ang_flag,pcn_flag,rad_flag,tor_flag; //angle, coordination,radical, torsion flag
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double lami,lambda,alfi,alpha1,alpha2,alpha3,beta;
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double pcos6,pcos5,pcos4,pcos3,pcos2,pcos1,pcos0;
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double gamma,powerm,powern,bigA,bigB1,bigB2,bigB3;
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double bigd,bigr,cut,cutsq,c1,c2,c3,c4;
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double plp1,plp2,plp3,plp4,plp5,plp6;
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double pbb1,pbb2,ptork1,ptork2;
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double addrep, vdwflag;
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double QU,QL,DU,DL,Qo,dQ,aB,bB,nD,bD,qmin,qmax;
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double chi,dj,dk,dl,dm,esm,cmn1,cmn2,pcmn1,pcmn2;
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double coulcut, lcut, lcutsq;
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double veps, vsig, pcna, pcnb, pcnc, pcnd, polz, curl, pcross;
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double paaa, pbbb;
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double curlcut1, curlcut2, curl0;
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};
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// general setups
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int nelements; // # of unique elements
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int ***elem2param; // mapping from element triplets to parameters
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int *map; // mapping from atom types to elements
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int nparams; // # of stored parameter sets
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int maxparam; // max # of parameter sets
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double PI,PI2,PI4,PIsq; // PIs
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double cutmin; // min cutoff for all elements
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double cutmax; // max cutoff for all elements
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double precision; // tolerance for QEq convergence
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char **elements; // names of unique elements
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Param *params; // parameter set for an I-J-K interaction
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int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs
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int pack_flag;
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// Short range neighbor list
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void Short_neigh();
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int pgsize, oneatom;
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int *sht_num, **sht_first;
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MyPage<int> *ipage;
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// loop up tables and flags
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int nmax, **intype;
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int pol_flag, polar;
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double *qf, **bbij, *charge, *NCo;
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double *esm, **fafb, **dfafb, **ddfafb, **phin, **dphin, **erpaw;
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double **vvdw, **vdvdw;
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double **afb, **dafb;
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double **dpl, bytes;
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double *xcctmp, *xchtmp, *xcotmp;
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// additional carbon parameters
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int cflag;
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int nsplpcn,nsplrad,nspltor;
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int maxx,maxy,maxz,maxxc,maxyc,maxconj;
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int maxxcn[4];
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double vmaxxcn[4],dvmaxxcn[4];
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int ntab;
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double iin2[16][2],iin3[64][3];
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double brad[4], btor[4], bbtor, ptorr;
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double fi_tor[3], fj_tor[3], fk_tor[3], fl_tor[3];
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double radtmp, fi_rad[3], fj_rad[3], fk_rad[3];
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double ccutoff[6],ch_a[7];
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//COMB3-v18 arrays for CHO
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// We wanna dynamic arrays
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// C angle arrays, size = ntab+1
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double pang[20001];
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double dpang[20001];
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double ddpang[20001];
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//coordination spline arrays
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double pcn_grid[4][5][5][5];
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double pcn_gridx[4][5][5][5];
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double pcn_gridy[4][5][5][5];
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double pcn_gridz[4][5][5][5];
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double pcn_cubs[4][4][4][4][64];
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//coordination spline arrays
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double rad_grid[3][5][5][11];
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double rad_gridx[3][5][5][11];
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double rad_gridy[3][5][5][11];
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double rad_gridz[3][5][5][11];
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double rad_spl[3][4][4][10][64];
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//torsion spline arrays
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double tor_grid[1][5][5][11];
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double tor_gridx[1][5][5][11];
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double tor_gridy[1][5][5][11];
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double tor_gridz[1][5][5][11];
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double tor_spl[1][4][4][10][64];
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// initialization functions
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void allocate();
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void read_lib();
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void setup();
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virtual void read_file(char *);
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// cutoff functions
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double comb_fc(double, Param *);
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double comb_fc_d(double, Param *);
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double comb_fc_curl(double, Param *);
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double comb_fc_curl_d(double, Param *);
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double comb_fccc(double);
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double comb_fccc_d(double);
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double comb_fcch(double);
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double comb_fcch_d(double);
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double comb_fccch(double);
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double comb_fccch_d(double);
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double comb_fcsw(double);
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// short range terms
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void attractive(Param *, Param *, Param *, double, double, double, double,
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double, double, double, double *, double *, double *,
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double *, double *, int, double);
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virtual void comb_fa(double, Param *, Param *, double, double,
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double &, double &);
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virtual void repulsive(Param *, Param *,double, double &, int,
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double &, double, double);
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// bond order terms
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double comb_bij(double, Param *, double, int, double);
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double comb_gijk(double, Param *, double);
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void comb_gijk_d(double, Param *, double, double &, double &);
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double zeta(Param *, Param *, double, double, double *, double *, int, double);
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void comb_bij_d(double, Param *, double, int, double &,
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double &, double &, double &, double &, double &, double);
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void coord(Param *, double, int, double &, double &,
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double &, double &, double &, double);
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void comb_zetaterm_d(double, double, double, double, double,
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double *, double, double *, double, double *, double *,
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double *, Param *, Param *, Param *, double);
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void costheta_d(double *, double, double *, double,
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double *, double *, double *);
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void force_zeta(Param *, Param *, double, double, double, double &,
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double &, double &, double &, double &, double &, double &,
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double &, double &, double &, double &, double &, double &,
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int, double &, double,double, int, int, int,
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double , double , double);
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void cntri_int(int, double, double, double, int, int, int,
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double &, double &, double &, double &, Param *);
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// Legendre polynomials
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void selflp(Param *, Param *, double, double &, double &);
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double elp(Param *, Param *, double, double, double *, double * ,double &);
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void flp(Param *, Param *, double, double, double *, double *, double *,
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double *, double *);
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// long range q-dependent terms
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double self(Param *, double);
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void tables();
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void potal_calc(double &, double &, double &);
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void tri_point(double, int &, int &, int &, double &, double &,
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double &);
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void vdwaals(int,int,int,int,double,double,double,double,
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double &, double &);
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void direct(Param *, Param *, int,int,int,double,double,
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double,double,double,double, double,double,double &,double &,
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int, int);
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void field(Param *, Param *,double,double,double,double &,double &);
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int heaviside(double);
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double switching(double);
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double switching_d(double);
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double chicut1, chicut2;
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// radical terms
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double rad_init(double, Param *, int, double &, double);
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void rad_calc(double, Param *, Param *, double, double, int,
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int, double, double);
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void rad_int(int , double, double, double, int, int, int,
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double &, double &, double &, double &);
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void rad_forceik(Param *, double, double *, double, double);
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void rad_force(Param *, double, double *, double);
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// torsion terms
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double bbtor1(int, Param *, Param *, double, double, double,
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double *, double *, double *, double); //modified by TAO
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void tor_calc(double, Param *, Param *, double, double, int,
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int, double, double);
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void tor_int(int , double, double, double, int, int, int,
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double &, double &, double &, double &);
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void tor_force(int, Param *, Param *, double, double, double,
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double, double *, double *, double *); //modified by TAO
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// charge force terms
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double qfo_self(Param *, double);
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void qfo_short(Param *, Param *, double, double, double,
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double &, double &, int, int, int);
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void qfo_direct(Param *, Param *, int, int, int, double,
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double, double, double, double, double &, double &,
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double, double, int, int);
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void qfo_field(Param *, Param *,double,double ,double ,double &, double &);
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void qfo_dipole(double, int, int, int, int, double, double *, double,
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double, double, double &, double &, int, int);
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void qsolve(double *);
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// dipole - polarization terms
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double dipole_self(Param *, int);
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void dipole_init(Param *, Param *, double, double *, double,
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int, int, int, double, double, double, double, double, int , int);
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void dipole_calc(Param *, Param *, double, double, double, double, double,
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int, int, int, double, double, double, double, double, int , int,
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double &, double &, double *);
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// communication functions
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int pack_reverse_comm(int, int, double *);
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void unpack_reverse_comm(int, int *, double *);
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int pack_comm(int , int *, double *, int, int *);
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void unpack_comm(int , int , double *);
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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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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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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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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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}
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Incorrect args for pair coefficients
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Self-explanatory. Check the input script or data file.
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E: Pair style COMB requires atom IDs
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This is a requirement to use the AIREBO potential.
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E: Pair style COMB requires newton pair on
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See the newton command. This is a restriction to use the COMB
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potential.
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E: Pair style COMB requires atom attribute q
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Self-explanatory.
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E: All pair coeffs are not set
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All pair coefficients must be set in the data file or by the
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pair_coeff command before running a simulation.
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E: Cannot open COMB potential file %s
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The specified COMB potential file cannot be opened. Check that the
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path and name are correct.
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E: Incorrect format in COMB potential file
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Incorrect number of words per line in the potential file.
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E: Illegal COMB parameter
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One or more of the coefficients defined in the potential file is
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invalid.
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E: Potential file has duplicate entry
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The potential file for a SW or Tersoff potential has more than
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one entry for the same 3 ordered elements.
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E: Potential file is missing an entry
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The potential file for a SW or Tersoff potential does not have a
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needed entry.
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W: Pair COMB charge %.10f with force %.10f hit min barrier
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Something is possibly wrong with your model.
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W: Pair COMB charge %.10f with force %.10f hit max barrier
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Something is possibly wrong with your model.
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*/
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