mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14661 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
d2d5b0cb75
commit
dc0dc5a7d9
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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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/* ----------------------------------------------------------------------
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Contributing author: Carsten Svaneborg (SDU)
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdlib.h>
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#include "angle_zero.h"
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#include "atom.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AngleZero::AngleZero(LAMMPS *lmp) : Angle(lmp) {}
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/* ---------------------------------------------------------------------- */
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AngleZero::~AngleZero()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleZero::compute(int eflag, int vflag)
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{
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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}
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/* ---------------------------------------------------------------------- */
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void AngleZero::allocate()
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{
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allocated = 1;
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int n = atom->nangletypes;
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memory->create(setflag,n+1,"angle:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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void AngleZero::coeff(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Incorrect args for angle coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nangletypes,ilo,ihi);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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setflag[i] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleZero::equilibrium_angle(int i)
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{
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return 0;
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void AngleZero::write_restart(FILE *fp) {}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void AngleZero::read_restart(FILE *fp)
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{
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allocate();
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for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
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}
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/* ---------------------------------------------------------------------- */
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double AngleZero::single(int type, int i1, int i2, int i3)
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{
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return 0;
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}
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/* -*- c++ -*- ----------------------------------------------------------
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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 ANGLE_CLASS
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AngleStyle(zero,AngleZero)
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#else
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#ifndef LMP_ANGLE_ZERO_H
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#define LMP_ANGLE_ZERO_H
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#include <stdio.h>
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#include "angle.h"
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namespace LAMMPS_NS {
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class AngleZero : public Angle {
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public:
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AngleZero(class LAMMPS *);
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virtual ~AngleZero();
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virtual void compute(int, int);
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virtual void coeff(int, char **);
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double equilibrium_angle(int);
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void write_restart(FILE *);
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void read_restart(FILE *);
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double single(int, int, int, int);
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protected:
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void allocate();
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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: Incorrect args for angle coefficients
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Self-explanatory. Check the input script or data file.
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*/
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@ -0,0 +1,97 @@
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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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/* ----------------------------------------------------------------------
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Contributing author: Carsten Svaneborg (SDU)
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <math.h>
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#include <stdlib.h>
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#include "dihedral_zero.h"
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#include "atom.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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DihedralZero::DihedralZero(LAMMPS *lmp) : Dihedral(lmp) {}
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/* ---------------------------------------------------------------------- */
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DihedralZero::~DihedralZero()
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{
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if (allocated) {
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memory->destroy(setflag);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralZero::compute(int eflag, int vflag)
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{
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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}
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/* ---------------------------------------------------------------------- */
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void DihedralZero::allocate()
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{
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allocated = 1;
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int n = atom->ndihedraltypes;
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memory->create(setflag,n+1,"dihedral:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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------------------------------------------------------------------------- */
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void DihedralZero::coeff(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Incorrect args for dihedral coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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setflag[i] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void DihedralZero::write_restart(FILE *fp) {}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void DihedralZero::read_restart(FILE *fp)
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{
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allocate();
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for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
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}
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/* -*- c++ -*- ----------------------------------------------------------
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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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||||
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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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Identical to dihedral harmonic, except if all k's are zero the
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force loop is skipped.
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------------------------------------------------------------------------- */
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#ifdef DIHEDRAL_CLASS
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DihedralStyle(zero,DihedralZero)
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#else
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#ifndef LMP_DIHEDRAL_ZERO_H
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#define LMP_DIHEDRAL_ZERO_H
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#include "stdio.h"
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#include "dihedral.h"
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namespace LAMMPS_NS {
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class DihedralZero : public Dihedral {
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public:
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DihedralZero(class LAMMPS *);
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virtual ~DihedralZero();
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virtual void compute(int, int);
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void coeff(int, char **);
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void write_restart(FILE *);
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void read_restart(FILE *);
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protected:
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void allocate();
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};
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}
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#endif
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#endif
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@ -0,0 +1,197 @@
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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
|
||||
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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/* ----------------------------------------------------------------------
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Contributing author: Carsten Svaneborg (SDU)
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "pair_zero.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairZero::PairZero(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairZero::~PairZero()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(cut);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairZero::compute(int eflag, int vflag)
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{
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairZero::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 1;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(cut,n+1,n+1,"pair:cut");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairZero::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(FLERR,arg[0]);
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// reset cutoffs that have been explicitly set
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allocate();
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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cut[i][j] = cut_global;
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}
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|
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairZero::coeff(int narg, char **arg)
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{
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if (narg < 2 || narg > 3)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double cut_one = cut_global;
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if (narg == 3) cut_one = force->numeric(FLERR,arg[2]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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cut[i][j] = cut_one;
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count++;
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||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
|
||||
|
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double PairZero::init_one(int i, int j)
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{
|
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if (setflag[i][j] == 0) {
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
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}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::write_restart(FILE *fp)
|
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{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
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allocate();
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|
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int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
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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) {
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::write_restart_settings(FILE *fp)
|
||||
{
|
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fwrite(&cut_global,sizeof(double),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
|
||||
Pair zero is a dummy pair interaction useful for requiring a
|
||||
force cutoff distance in the absense of pair-interactions or
|
||||
with hybrid/overlay if a larger force cutoff distance is required.
|
||||
|
||||
This can be used in conjunction with bond/create to create bonds
|
||||
that are longer than the cutoff of a given force field, or to
|
||||
calculate radial distribution functions for models without
|
||||
pair interactions.
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(zero,PairZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_ZERO_H
|
||||
#define LMP_PAIR_ZERO_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairZero : public Pair {
|
||||
public:
|
||||
PairZero(class LAMMPS *);
|
||||
virtual ~PairZero();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair cutoff < Respa interior cutoff
|
||||
|
||||
One or more pairwise cutoffs are too short to use with the specified
|
||||
rRESPA cutoffs.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue