Commit 71fbecea authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2286 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 269d3adc

src/force.cpp

+36 −13
Original line number Diff line number Diff line
@@ -55,6 +55,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp) 


  special_lj[1] = special_lj[2] = special_lj[3] = 0.0;

  special_coul[1] = special_coul[2] = special_coul[3] = 0.0;

  special_dihedral = 0;



  dielectric = 1.0;
@@ -352,31 +353,53 @@ void Force::set_special(int narg, char **arg) 
{

  if (narg == 0) error->all("Illegal special_bonds command");



  if (narg == 1 && strcmp(arg[0],"charmm") == 0) {

  if (strcmp(arg[0],"charmm") == 0) {

    if (narg != 1) error->all("Illegal special_bonds command");

    special_lj[1] = 0.0;

    special_lj[2] = 0.0;

    special_lj[3] = 0.0;

    special_coul[1] = 0.0;

    special_coul[2] = 0.0;

    special_coul[3] = 0.0;

  } else if (narg == 1 && strcmp(arg[0],"amber") == 0) {

    special_dihedral = 0;

    return;

  }



  if (strcmp(arg[0],"amber") == 0) {

    if (narg != 1) error->all("Illegal special_bonds command");

    special_lj[1] = 0.0;

    special_lj[2] = 0.0;

    special_lj[3] = 0.5;

    special_coul[1] = 0.0;

    special_coul[2] = 0.0;

    special_coul[3] = 5.0/6.0;

  } else if (narg == 3) {

    special_lj[1] = special_coul[1] = atof(arg[0]);

    special_lj[2] = special_coul[2] = atof(arg[1]);

    special_lj[3] = special_coul[3] = atof(arg[2]);

  } else if (narg == 6) {

    special_lj[1] = atof(arg[0]);

    special_lj[2] = atof(arg[1]);

    special_lj[3] = atof(arg[2]);

    special_coul[1] = atof(arg[3]);

    special_coul[2] = atof(arg[4]);

    special_coul[3] = atof(arg[5]);

    special_dihedral = 0;

    return;

  }



  int iarg;

  if (strcmp(arg[0],"dihedral") == 0) {

    special_dihedral = 1;

    iarg = 1;

  } else if (strcmp(arg[0],"explicit") == 0) {

    special_dihedral = 0;

    iarg = 1;

  } else {

    special_dihedral = 0;

    iarg = 0;

  }



  if (narg-iarg == 3) {

    special_lj[1] = special_coul[1] = atof(arg[iarg+0]);

    special_lj[2] = special_coul[2] = atof(arg[iarg+1]);

    special_lj[3] = special_coul[3] = atof(arg[iarg+2]);

  } else if (narg-iarg == 6) {

    special_lj[1] = atof(arg[iarg+0]);

    special_lj[2] = atof(arg[iarg+1]);

    special_lj[3] = atof(arg[iarg+2]);

    special_coul[1] = atof(arg[iarg+3]);

    special_coul[2] = atof(arg[iarg+4]);

    special_coul[3] = atof(arg[iarg+5]);

  } else error->all("Illegal special_bonds command");

}

src/force.h

+2 −0
Original line number Diff line number Diff line
@@ -52,6 +52,8 @@ class Force : protected Pointers { 
                             // index [0] is not used in these arrays

  double special_lj[4];      // 1-2, 1-3, 1-4 prefactors for LJ

  double special_coul[4];    // 1-2, 1-3, 1-4 prefactors for Coulombics

  int special_dihedral;      // 0 if defined dihedrals are ignored

                             // 1 if only weight 1,4 atoms if in a dihedral



  Force(class LAMMPS *);

  ~Force();

src/input.cpp

+5 −3
Original line number Diff line number Diff line
@@ -1080,20 +1080,22 @@ void Input::shape() 


void Input::special_bonds()

{

  // store 1-3,1-4 values before change

  // store 1-3,1-4 and dihedral flag values before change



  double lj2 = force->special_lj[2];

  double lj3 = force->special_lj[3];

  double coul2 = force->special_coul[2];

  double coul3 = force->special_coul[3];

  int dihedral = force->special_dihedral;



  force->set_special(narg,arg);



  // if simulation box defined and 1-3,1-4 values changed, redo special list

  // if simulation box defined and saved values changed, redo special list



  if (domain->box_exist && atom->molecular) {

    if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||

	coul2 != force->special_coul[2] || coul3 != force->special_coul[3]) {

	coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||

	dihedral != force->special_dihedral) {

      Special special(lmp);

      special.build();

    }

src/special.cpp

+163 −0
Original line number Diff line number Diff line
@@ -546,6 +546,7 @@ void Special::build() 
  delete [] bufcopy;



  combine();

  if (force->special_dihedral) dihedral_trim();

}



/* ----------------------------------------------------------------------
@@ -690,3 +691,165 @@ void Special::combine() 
  atom->nghost = 0;

  atom->map_set();

}



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

   trim list of 1-4 neighbors by checking defined dihedrals

   delete a 1-4 neigh if those atoms are not end points of a defined dihedral

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



void Special::dihedral_trim()

{

  int i,j,m,n,iglobal,jglobal,ilocal,jlocal;

  MPI_Request request;

  MPI_Status status;



  int *tag = atom->tag;

  int *num_dihedral = atom->num_dihedral;

  int **dihedral_atom1 = atom->dihedral_atom1;

  int **dihedral_atom4 = atom->dihedral_atom4;

  int **nspecial = atom->nspecial;

  int **special = atom->special;

  int nlocal = atom->nlocal;



  // stats on old 1-4 neighbor counts



  double onefourcount = 0.0;

  for (i = 0; i < nlocal; i++)

    onefourcount += nspecial[i][2] - nspecial[i][1];



  double allcount;

  MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);



  if (me == 0) {

    if (screen)

      fprintf(screen,

	      "  %g = # of 1-4 neighbors before dihedral trim\n",allcount);

    if (logfile)

      fprintf(logfile,

	      "  %g = # of 1-4 neighbors before dihedral trim\n",allcount);

  }



  // if dihedrals are defined, flag each 1-4 neigh if it appears in a dihedral



  if (num_dihedral && atom->ndihedrals) {



    // dflag = flag for 1-4 neighs of all owned atoms



    int maxcount = 0;

    for (i = 0; i < nlocal; i++)

      maxcount = MAX(maxcount,nspecial[i][2]-nspecial[i][1]);

    int **dflag =

      memory->create_2d_int_array(nlocal,maxcount,"special::dflag");



    for (i = 0; i < nlocal; i++) {

      n = nspecial[i][2] - nspecial[i][1];

      for (j = 0; j < n; j++) dflag[i][j] = 0;

    }



    // nbufmax = largest buffer needed to hold info from any proc

    // info for each atom = list of 1,4 atoms in each dihedral stored by atom



    int nbuf = 0;

    for (i = 0; i < nlocal; i++) nbuf += 2*num_dihedral[i];



    int nbufmax;

    MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);



    int *buf = new int[nbufmax];

    int *bufcopy = new int[nbufmax];



    // fill buffer with list of 1,4 atoms in each dihedral



    int size = 0;

    for (i = 0; i < nlocal; i++)

      for (j = 0; j < num_dihedral[i]; j++) {

	buf[size++] = dihedral_atom1[i][j];

	buf[size++] = dihedral_atom4[i][j];

      }



    // cycle buffer around ring of procs back to self

    // when receive buffer, scan list of 1,4 atoms looking for atoms I own

    // when find one, scan its 1-4 neigh list and mark I,J as in a dihedral



    int next = me + 1;

    int prev = me -1; 

    if (next == nprocs) next = 0;

    if (prev < 0) prev = nprocs - 1;



    int messtag = 7;

    for (int loop = 0; loop < nprocs; loop++) {

      i = 0;

      while (i < size) {

	iglobal = buf[i];

	jglobal = buf[i+1];

	ilocal = atom->map(iglobal);

	jlocal = atom->map(jglobal);

	if (ilocal >= 0 && ilocal < nlocal)

	  for (m = nspecial[ilocal][1]; m < nspecial[ilocal][2]; m++)

	    if (jglobal == special[ilocal][m]) {

	      dflag[ilocal][m-nspecial[ilocal][1]] = 1;

	      break;

	    }

	if (jlocal >= 0 && jlocal < nlocal)

	  for (m = nspecial[jlocal][1]; m < nspecial[jlocal][2]; m++)

	    if (iglobal == special[jlocal][m]) {

	      dflag[jlocal][m-nspecial[jlocal][1]] = 1;

	      break;

	    }

	i += 2;

      }

      if (me != next) {

	MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);

	MPI_Send(buf,size,MPI_INT,next,messtag,world);

	MPI_Wait(&request,&status);

	MPI_Get_count(&status,MPI_INT,&size);

	for (j = 0; j < size; j++) buf[j] = bufcopy[j];

      }

    }



    // delete 1-4 neighbors if they are not flagged in dflag

    

    int offset;

    for (i = 0; i < nlocal; i++) {

      offset = m = nspecial[i][1];

      for (j = nspecial[i][1]; j < nspecial[i][2]; j++)

	if (dflag[i][j-offset]) special[i][m++] = special[i][j];

      nspecial[i][2] = m;

    }

    

    // clean up



    memory->destroy_2d_int_array(dflag);

    delete [] buf;

    delete [] bufcopy;



  // if no dihedrals are defined, delete all 1-4 neighs



  } else for (i = 0; i < nlocal; i++) nspecial[i][2] = nspecial[i][1];



  // reset atom->maxspecial



  int maxspecial = 0;

  for (i = 0; i < nlocal; i++)

    maxspecial = MAX(maxspecial,nspecial[i][2]);



  MPI_Allreduce(&maxspecial,&atom->maxspecial,1,MPI_INT,MPI_MAX,world);

  atom->maxspecial = MAX(atom->maxspecial,1);



  // stats on new 1-4 neighbor counts



  onefourcount = 0.0;

  for (i = 0; i < nlocal; i++)

    onefourcount += nspecial[i][2] - nspecial[i][1];



  MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);



  if (me == 0) {

    if (screen)

      fprintf(screen,

	      "  %g = # of 1-4 neighbors after dihedral trim\n",allcount);

    if (logfile)

      fprintf(logfile,

	      "  %g = # of 1-4 neighbors after dihedral trim\n",allcount);

  }

}

src/special.h

+2 −0
Original line number Diff line number Diff line
@@ -27,8 +27,10 @@ class Special : protected Pointers { 
 private:

  int me,nprocs;

  int **onetwo,**onethree,**onefour;

  int dihedral_flag;



  void combine();

  void dihedral_trim();

};



}

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