Unverified Commit cf8bee9b authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

remove unused and redundant data elements. no write_data support for tables.

parent 2558509b

src/USER-MISC/dihedral_table_cut.cpp

+4 −78
Original line number Diff line number Diff line
@@ -425,17 +425,6 @@ DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : Dihedral(lmp) 
DihedralTableCut::~DihedralTableCut()

{

  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(setflag_d);

    memory->destroy(setflag_aat);



    memory->destroy(k1);

    memory->destroy(k2);

    memory->destroy(k3);

    memory->destroy(phi1);

    memory->destroy(phi2);

    memory->destroy(phi3);



    memory->destroy(aat_k);

    memory->destroy(aat_theta0_1);

    memory->destroy(aat_theta0_2);
@@ -761,27 +750,15 @@ void DihedralTableCut::allocate() 
  allocated = 1;

  int n = atom->ndihedraltypes;



  memory->create(k1,n+1,"dihedral:k1");

  memory->create(k2,n+1,"dihedral:k2");

  memory->create(k3,n+1,"dihedral:k3");

  memory->create(phi1,n+1,"dihedral:phi1");

  memory->create(phi2,n+1,"dihedral:phi2");

  memory->create(phi3,n+1,"dihedral:phi3");



  memory->create(aat_k,n+1,"dihedral:aat_k");

  memory->create(aat_theta0_1,n+1,"dihedral:aat_theta0_1");

  memory->create(aat_theta0_2,n+1,"dihedral:aat_theta0_2");



  memory->create(setflag,n+1,"dihedral:setflag");

  memory->create(setflag_d,n+1,"dihedral:setflag_d");

  memory->create(setflag_aat,n+1,"dihedral:setflag_aat");



  memory->create(tabindex,n+1,"dihedral:tabindex");

  //memory->create(phi0,n+1,"dihedral:phi0"); <-equilibrium angles not supported

  memory->create(setflag,n+1,"dihedral:setflag");



  for (int i = 1; i <= n; i++)

    setflag[i] = setflag_d[i] = setflag_aat[i] = 0;

    setflag[i] = 0;

}



void DihedralTableCut::settings(int narg, char **arg)
@@ -824,9 +801,6 @@ void DihedralTableCut::coeff(int narg, char **arg) 
  int ilo,ihi;

  force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi);



  int count = 0;





  double k_one = force->numeric(FLERR,arg[2]);

  double theta0_1_one = force->numeric(FLERR,arg[3]);

  double theta0_2_one = force->numeric(FLERR,arg[4]);
@@ -837,8 +811,6 @@ void DihedralTableCut::coeff(int narg, char **arg) 
    aat_k[i] = k_one;

    aat_theta0_1[i] = theta0_1_one/180.0 * MY_PI;

    aat_theta0_2[i] = theta0_2_one/180.0 * MY_PI;

    setflag_aat[i] = 1;

    count++;

  }



  int me;
@@ -998,8 +970,7 @@ void DihedralTableCut::coeff(int narg, char **arg) 
            //  To be nice and report something, I do the same thing here.)

            cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi);

          f = -dU_dphi;

        }

        else

        } else

          // Otherwise we calculated the tb->f[] array.  Report its contents.

          f = tb->f[i];

        if (tb->use_degrees) {
@@ -1015,9 +986,8 @@ void DihedralTableCut::coeff(int narg, char **arg) 
  } // if (me == 0)



  // store ptr to table in tabindex

  count = 0;

  for (int i = ilo; i <= ihi; i++)

  {

  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    tabindex[i] = ntables;

    //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported

    setflag[i] = 1;
@@ -1025,12 +995,7 @@ void DihedralTableCut::coeff(int narg, char **arg) 
  }

  ntables++;





  if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");



  for (int i = ilo; i <= ihi; i++)

    if (setflag_d[i] == 1 && setflag_aat[i] == 1 )

      setflag[i] = 1;

}



/* ----------------------------------------------------------------------
@@ -1041,12 +1006,6 @@ void DihedralTableCut::write_restart(FILE *fp) 
{

  fwrite(&tabstyle,sizeof(int),1,fp);

  fwrite(&tablength,sizeof(int),1,fp);

  fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);



  fwrite(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);

  fwrite(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
@@ -1064,32 +1023,18 @@ void DihedralTableCut::read_restart(FILE *fp) 
  if (comm->me == 0) {

    fread(&tabstyle,sizeof(int),1,fp);

    fread(&tablength,sizeof(int),1,fp);

    fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);



    fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);

    fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);

  }



  MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&phi1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&phi2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&phi3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);



  MPI_Bcast(&aat_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&aat_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&aat_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&tabstyle,1,MPI_INT,0,world);

  MPI_Bcast(&tablength,1,MPI_INT,0,world);



  allocate();

  for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;

}
@@ -1474,22 +1419,3 @@ void DihedralTableCut::bcast_table(Table *tb) 
}





/* ----------------------------------------------------------------------

   proc 0 writes to data file

------------------------------------------------------------------------- */



void DihedralTableCut::write_data(FILE *fp)

{

  for (int i = 1; i <= atom->ndihedraltypes; i++)

    fprintf(fp,"%d %g %g %g %g %g %g\n",i,

            k1[i],phi1[i]*180.0/MY_PI,

            k2[i],phi2[i]*180.0/MY_PI,

            k3[i],phi3[i]*180.0/MY_PI);



  fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n");

  for (int i = 1; i <= atom->ndihedraltypes; i++)

    fprintf(fp,"%d %g %g %g\n",i,aat_k[i],

            aat_theta0_1[i]*180.0/MY_PI,aat_theta0_2[i]*180.0/MY_PI);



}

src/USER-MISC/dihedral_table_cut.h

+0 −8
Original line number Diff line number Diff line
@@ -20,7 +20,6 @@ DihedralStyle(table/cut,DihedralTableCut) 
#ifndef LMP_DIHEDRAL_TABLE_CUT_H

#define LMP_DIHEDRAL_TABLE_CUT_H



#include <stdio.h>

#include "dihedral.h"



namespace LAMMPS_NS {
@@ -34,26 +33,19 @@ class DihedralTableCut : public Dihedral { 
  void coeff(int, char **);

  void write_restart(FILE *);

  void read_restart(FILE *);

  void write_data(FILE *);

  double single(int type, int i1, int i2, int i3, int i4);



 protected:

  double *k1,*k2,*k3;

  double *phi1,*phi2,*phi3;

  double *aat_k,*aat_theta0_1,*aat_theta0_2;

  int *setflag_d;

  int *setflag_aat;



  void allocate();



  int tabstyle,tablength;

  // double *phi0;       <- equilibrium angles not supported

  char *checkU_fname;

  char *checkF_fname;



  struct Table {

    int ninput;

    //double phi0;      <-equilibrium angles not supported

    int f_unspecified; // boolean (but MPI does not like type "bool")

    int use_degrees;   // boolean (but MPI does not like type "bool")

    double *phifile,*efile,*ffile;

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