forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6643 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
81965223f1
commit
74abb3cd0c
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@ -2,21 +2,41 @@
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if (test $1 = 1) then
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cp angle_cosineshift.cpp ..
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cp angle_cosineshiftexp.cpp ..
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cp bond_harmonic_shift.cpp ..
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cp bond_harmonic_shift_cut.cpp ..
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cp compute_temp_rotate.cpp ..
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cp dihedral_cosineshiftexp.cpp ..
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cp fix_addtorque.cpp ..
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cp pair_dipole_sf.cpp ..
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cp angle_cosineshift.h ..
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cp angle_cosineshiftexp.h ..
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cp bond_harmonic_shift.h ..
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cp bond_harmonic_shift_cut.h ..
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cp compute_temp_rotate.h ..
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cp dihedral_cosineshiftexp.h ..
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cp fix_addtorque.h ..
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cp pair_dipole_sf.h ..
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elif (test $1 = 0) then
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rm -f ../angle_cosineshift.cpp
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rm -f ../angle_cosineshiftexp.cpp
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rm -f ../bond_harmonic_shift.cpp
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rm -f ../bond_harmonic_shift_cut.cpp
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rm -f ../compute_temp_rotate.cpp
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rm -f ../dihedral_cosineshiftexp.cpp
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rm -f ../fix_addtorque.cpp
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rm -f ../pair_dipole_sf.cpp
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rm -f ../angle_cosineshift.h
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rm -f ../angle_cosineshiftexp.h
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rm -f ../bond_harmonic_shift.h
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rm -f ../bond_harmonic_shift_cut.h
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rm -f ../compute_temp_rotate.h
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rm -f ../dihedral_cosineshiftexp.h
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rm -f ../fix_addtorque.h
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rm -f ../pair_dipole_sf.h
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@ -16,6 +16,11 @@ feature or its code.
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------------------------------------------------------------
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compute temp/rotate, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8Aug11
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fix addtorque, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8Aug11
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pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8Aug11
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angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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compute temp/rotate, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11
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dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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fix addtorque, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11
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pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
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@ -0,0 +1,263 @@
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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, science@zqex.dk
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "angle_cosineshift.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "domain.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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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {}
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/* ---------------------------------------------------------------------- */
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AngleCosineShift::~AngleCosineShift()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(kcost);
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memory->destroy(ksint);
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memory->destroy(theta);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCosineShift::compute(int eflag, int vflag)
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{
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int i1,i2,i3,n,type;
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double delx1,dely1,delz1,delx2,dely2,delz2;
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double eangle,f1[3],f3[3];
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double rsq1,rsq2,r1,r2,c,s,cps,kcos,ksin,a11,a12,a22;
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eangle = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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double **x = atom->x;
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double **f = atom->f;
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int **anglelist = neighbor->anglelist;
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int nanglelist = neighbor->nanglelist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nanglelist; n++) {
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i1 = anglelist[n][0];
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i2 = anglelist[n][1];
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i3 = anglelist[n][2];
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type = anglelist[n][3];
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// 1st bond
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delx1 = x[i1][0] - x[i2][0];
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dely1 = x[i1][1] - x[i2][1];
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delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1,dely1,delz1);
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rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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r1 = sqrt(rsq1);
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// 2nd bond
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delx2 = x[i3][0] - x[i2][0];
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dely2 = x[i3][1] - x[i2][1];
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delz2 = x[i3][2] - x[i2][2];
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domain->minimum_image(delx2,dely2,delz2);
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rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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r2 = sqrt(rsq2);
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// c = cosine of angle
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c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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// C= sine of angle
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s = sqrt(1.0 - c*c);
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if (s < SMALL) s = SMALL;
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// force & energy
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if (eflag) eangle = -k[type]-kcos*c-ksin*s;
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kcos=kcost[type];
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ksin=ksint[type];
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cps = c/s; // NOTE absorbed one c
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a11 = (-kcos +ksin*cps )*c/ rsq1;
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a12 = ( kcos -ksin*cps ) / (r1*r2);
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a22 = (-kcos +ksin*cps )*c/ rsq2;
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f1[0] = a11*delx1 + a12*delx2;
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f1[1] = a11*dely1 + a12*dely2;
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f1[2] = a11*delz1 + a12*delz2;
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f3[0] = a22*delx2 + a12*delx1;
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f3[1] = a22*dely2 + a12*dely1;
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f3[2] = a22*delz2 + a12*delz1;
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// apply force to each of 3 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= f1[0] + f3[0];
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f[i2][1] -= f1[1] + f3[1];
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f[i2][2] -= f1[2] + f3[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
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delx1,dely1,delz1,delx2,dely2,delz2);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCosineShift::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(k ,n+1,"Angle:k");
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memory->create(ksint ,n+1,"Angle:ksint");
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memory->create(kcost ,n+1,"Angle:kcost");
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memory->create(theta ,n+1,"Angle:theta");
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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 type
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------------------------------------------------------------------------- */
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void AngleCosineShift::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all("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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double umin = force->numeric(arg[1]);
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double theta0 = force->numeric(arg[2]);
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// k=Umin/2
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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k[i] = umin/2;
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kcost[i] = umin/2*cos(theta0*3.14159265/180);
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ksint[i] = umin/2*sin(theta0*3.14159265/180);
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theta[i] = theta0*3.14159265/180;
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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("Incorrect args for angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleCosineShift::equilibrium_angle(int i)
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{
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return theta[i];
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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 AngleCosineShift::write_restart(FILE *fp)
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{
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fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&kcost[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&ksint[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&theta[1],sizeof(double),atom->nangletypes,fp);
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}
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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 AngleCosineShift::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0)
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{
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fread(&k[1],sizeof(double),atom->nangletypes,fp);
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fread(&kcost[1],sizeof(double),atom->nangletypes,fp);
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fread(&ksint[1],sizeof(double),atom->nangletypes,fp);
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fread(&theta[1],sizeof(double),atom->nangletypes,fp);
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}
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MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&kcost[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&ksint[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&theta[1],atom->nangletypes,MPI_DOUBLE,0,world);
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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 AngleCosineShift::single(int type, int i1, int i2, int i3)
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{
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double **x = atom->x;
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double delx1 = x[i1][0] - x[i2][0];
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double dely1 = x[i1][1] - x[i2][1];
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double delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1,dely1,delz1);
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double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
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double delx2 = x[i3][0] - x[i2][0];
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double dely2 = x[i3][1] - x[i2][1];
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double delz2 = x[i3][2] - x[i2][2];
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domain->minimum_image(delx2,dely2,delz2);
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double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
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double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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double s=sqrt(1.0-c*c);
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return -k[type]-kcost[type]*c-ksint[type]*s;
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}
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@ -0,0 +1,67 @@
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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
|
||||
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.
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------------------------------------------------------------------------- */
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/*
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The angle is defined from (R1-R2) . (R3-R2) hence a straight
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bond has costheta=180.
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U(theta,theta0,umin)= -Umin (1+cos[theta-theta0])/2
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potential has minimum at theta=theta0 where U() = -Umin
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potential has maximum at theta=theta0+180 where U() = 0
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At the minimum U(theta,theta0,umin)=-Umin+Umin/4 (theta-theta0)^2+O( ()^4)
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hence the effective spring constant is k=umin/2.
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to match U(theta,theta0,K)=K(theta-theta0)^2 at the minimum Umin=4*K
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*/
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|
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#ifdef ANGLE_CLASS
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AngleStyle(cosineshift,AngleCosineShift)
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|
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#else
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|
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#ifndef LMP_ANGLE_COSINESHIFT_H
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#define LMP_ANGLE_COSINESHIFT_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 AngleCosineShift : public Angle {
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public:
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AngleCosineShift(class LAMMPS *);
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~AngleCosineShift();
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virtual void compute(int, int);
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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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|
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private:
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double *k;
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double *a;
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double *theta;
|
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double *ksint;
|
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double *kcost;
|
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|
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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 +1,306 @@
|
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/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg, science@zqex.dk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
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#include "stdlib.h"
|
||||
#include "angle_cosineshiftexp.h"
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#include "atom.h"
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#include "neighbor.h"
|
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#include "domain.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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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
|
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AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) {}
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|
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/* ---------------------------------------------------------------------- */
|
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||||
AngleCosineShiftExp::~AngleCosineShiftExp()
|
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{
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if (allocated) {
|
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memory->destroy(setflag);
|
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memory->destroy(umin);
|
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memory->destroy(a);
|
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memory->destroy(opt1);
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memory->destroy(cost);
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memory->destroy(sint);
|
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memory->destroy(theta0);
|
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memory->destroy(doExpansion);
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}
|
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}
|
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/* ---------------------------------------------------------------------- */
|
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|
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void AngleCosineShiftExp::compute(int eflag, int vflag)
|
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{
|
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int i1,i2,i3,n,type;
|
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double delx1,dely1,delz1,delx2,dely2,delz2;
|
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double eangle,f1[3],f3[3],ff;
|
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double rsq1,rsq2,r1,r2,c,s,cc,ss,a11,a12,a22;
|
||||
double exp2,aa,uumin,cccpsss,cssmscc;
|
||||
|
||||
eangle = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int **anglelist = neighbor->anglelist;
|
||||
int nanglelist = neighbor->nanglelist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
for (n = 0; n < nanglelist; n++) {
|
||||
i1 = anglelist[n][0];
|
||||
i2 = anglelist[n][1];
|
||||
i3 = anglelist[n][2];
|
||||
type = anglelist[n][3];
|
||||
|
||||
// 1st bond
|
||||
|
||||
delx1 = x[i1][0] - x[i2][0];
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
|
||||
delx2 = x[i3][0] - x[i2][0];
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// c = cosine of angle
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
// C= sine of angle
|
||||
s = sqrt(1.0 - c*c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
|
||||
// force & energy
|
||||
|
||||
aa=a[type];
|
||||
uumin=umin[type];
|
||||
|
||||
cccpsss = c*cost[type]+s*sint[type];
|
||||
cssmscc = c*sint[type]-s*cost[type];
|
||||
|
||||
if (doExpansion[type])
|
||||
{ // |a|<0.01 so use expansions relative precision <1e-5
|
||||
// std::cout << "Using expansion\n";
|
||||
if (eflag) eangle = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
|
||||
ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
|
||||
}
|
||||
else
|
||||
{
|
||||
// std::cout << "Not using expansion\n";
|
||||
exp2=exp(0.5*aa*(1+cccpsss));
|
||||
if (eflag) eangle = opt1[type]*(1-exp2);
|
||||
ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
|
||||
}
|
||||
|
||||
a11 = ff*c/ rsq1;
|
||||
a12 = -ff / (r1*r2);
|
||||
a22 = ff*c/ rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2;
|
||||
f1[1] = a11*dely1 + a12*dely2;
|
||||
f1[2] = a11*delz1 + a12*delz2;
|
||||
f3[0] = a22*delx2 + a12*delx1;
|
||||
f3[1] = a22*dely2 + a12*dely1;
|
||||
f3[2] = a22*delz2 + a12*delz1;
|
||||
|
||||
// apply force to each of 3 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] -= f1[0] + f3[0];
|
||||
f[i2][1] -= f1[1] + f3[1];
|
||||
f[i2][2] -= f1[2] + f3[2];
|
||||
}
|
||||
|
||||
if (newton_bond || i3 < nlocal) {
|
||||
f[i3][0] += f3[0];
|
||||
f[i3][1] += f3[1];
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AngleCosineShiftExp::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
|
||||
memory->create(doExpansion, n+1, "angle:doExpansion");
|
||||
memory->create(umin , n+1, "angle:umin");
|
||||
memory->create(a , n+1, "angle:a");
|
||||
memory->create(sint , n+1, "angle:sint");
|
||||
memory->create(cost , n+1, "angle:cost");
|
||||
memory->create(opt1 , n+1, "angle:opt1");
|
||||
memory->create(theta0 , n+1, "angle:theta0");
|
||||
memory->create(setflag , n+1, "angle:setflag");
|
||||
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleCosineShiftExp::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all("Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
|
||||
|
||||
double umin_ = force->numeric(arg[1]);
|
||||
double theta0_ = force->numeric(arg[2]);
|
||||
double a_ = force->numeric(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
doExpansion[i]=(fabs(a_)<0.001);
|
||||
umin[i] = umin_;
|
||||
a[i] = a_;
|
||||
cost[i] = cos(theta0_*3.14159265/180);
|
||||
sint[i] = sin(theta0_*3.14159265/180);
|
||||
theta0[i]= theta0_*3.14159265/180;
|
||||
|
||||
if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
|
||||
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double AngleCosineShiftExp::equilibrium_angle(int i)
|
||||
{
|
||||
return theta0[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleCosineShiftExp::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&umin[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&a[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&cost[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&sint[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleCosineShiftExp::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0)
|
||||
{
|
||||
fread(&umin[1],sizeof(double),atom->nangletypes,fp);
|
||||
fread(&a[1],sizeof(double),atom->nangletypes,fp);
|
||||
fread(&cost[1],sizeof(double),atom->nangletypes,fp);
|
||||
fread(&sint[1],sizeof(double),atom->nangletypes,fp);
|
||||
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
|
||||
}
|
||||
MPI_Bcast(&umin[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cost[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sint[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
|
||||
for (int i = 1; i <= atom->nangletypes; i++)
|
||||
{
|
||||
setflag[i] = 1;
|
||||
doExpansion[i]=(fabs(a[i])<0.01);
|
||||
if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double AngleCosineShiftExp::single(int type, int i1, int i2, int i3)
|
||||
{
|
||||
double **x = atom->x;
|
||||
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
double s=sqrt(1.0-c*c);
|
||||
|
||||
double cccpsss=c*cost[type]+s*sint[type];
|
||||
double cssmscc=c*sint[type]-s*cost[type];
|
||||
|
||||
if (doExpansion[type])
|
||||
{
|
||||
return -0.125*(1+cccpsss)*(4+a[type]*(cccpsss-1))*umin[type];
|
||||
}
|
||||
else
|
||||
{
|
||||
return opt1[type]*(1-exp(0.5*a[type]*(1+cccpsss)));
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/*
|
||||
The angle is defined from Cos(theta)= b1.b2 / |b1||b2| where b1=(R1-R2) and
|
||||
b2=(R3-R2) a straight bond has costheta=180.
|
||||
|
||||
U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]]
|
||||
with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2
|
||||
|
||||
potential has minimum at theta=theta0 where U() = -Umin
|
||||
potential has maximum at theta=theta0+180 where U() = 0
|
||||
|
||||
The spring constant around the minimum is controlled by a and
|
||||
is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0
|
||||
the spring constant is k=Umin/2 and the potential reduces to
|
||||
the cosineshifted potential.
|
||||
|
||||
The potential is implemented such that for a<0.001 a series
|
||||
expansion to linear order is used instead of the expression
|
||||
above. This ensures a precision of about 1e-5 or better for
|
||||
energies and forces, and ensures the potential is well
|
||||
behaved for a=0
|
||||
*/
|
||||
|
||||
#ifdef ANGLE_CLASS
|
||||
AngleStyle(cosineshiftexp,AngleCosineShiftExp)
|
||||
#else
|
||||
|
||||
#ifndef LMP_ANGLE_COSINESHIFTEXP_H
|
||||
#define LMP_ANGLE_COSINESHIFTEXP_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "angle.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AngleCosineShiftExp : public Angle {
|
||||
public:
|
||||
AngleCosineShiftExp(class LAMMPS *);
|
||||
~AngleCosineShiftExp();
|
||||
void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
double equilibrium_angle(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, int, int, int);
|
||||
|
||||
private:
|
||||
bool *doExpansion;
|
||||
double *umin,*a,*opt1;
|
||||
double *theta0;
|
||||
double *sint;
|
||||
double *cost;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg, science@zqex.dk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "bond_harmonic_shift.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondHarmonicShift::BondHarmonicShift(LAMMPS *lmp) : Bond(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondHarmonicShift::~BondHarmonicShift()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(k);
|
||||
memory->destroy(r0);
|
||||
memory->destroy(r1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShift::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r,dr,rk;
|
||||
|
||||
ebond = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
for (n = 0; n < nbondlist; n++) {
|
||||
i1 = bondlist[n][0];
|
||||
i2 = bondlist[n][1];
|
||||
type = bondlist[n][2];
|
||||
|
||||
delx = x[i1][0] - x[i2][0];
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx,dely,delz);
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
r = sqrt(rsq);
|
||||
|
||||
dr = r - r0[type];
|
||||
rk = k[type] * dr;
|
||||
|
||||
// force & energy
|
||||
|
||||
if (r > 0.0) fbond = -2.0*rk/r;
|
||||
else fbond = 0.0;
|
||||
|
||||
if (eflag) ebond = k[type]*(dr*dr -(r0[type]-r1[type])*(r0[type]-r1[type]) );
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShift::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
|
||||
memory->create(k , n+1,"bond:k");
|
||||
memory->create(r0, n+1,"bond:r0");
|
||||
memory->create(r1, n+1,"bond:r1");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShift::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all("Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
|
||||
|
||||
double Umin = force->numeric(arg[1]); // energy at minimum
|
||||
double r0_one = force->numeric(arg[2]); // position of minimum
|
||||
double r1_one = force->numeric(arg[3]); // position where energy = 0
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = Umin/((r0_one-r1_one)*(r0_one-r1_one));
|
||||
r0[i] = r0_one;
|
||||
r1[i] = r1_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return an equilbrium bond length
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondHarmonicShift::equilibrium_distance(int i)
|
||||
{
|
||||
return r0[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShift::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShift::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fread(&r1[1],sizeof(double),atom->nbondtypes,fp);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondHarmonicShift::single(int type, double rsq, int i, int j)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
double dr = r - r0[type];
|
||||
double dr2=r0[type]-r1[type];
|
||||
|
||||
return k[type]*(dr*dr - dr2*dr2);
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
|
||||
BondStyle(harmonicshift,BondHarmonicShift)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_HARMONICSHIFT_H
|
||||
#define LMP_BOND_HARMONICSHIFT_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "bond.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondHarmonicShift : public Bond {
|
||||
public:
|
||||
BondHarmonicShift(class LAMMPS *);
|
||||
~BondHarmonicShift();
|
||||
void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
double equilibrium_distance(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, double, int, int);
|
||||
|
||||
private:
|
||||
double *k,*r0,*r1;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,202 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg, science@zqex.dk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "bond_harmonic_shift_cut.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondHarmonicShiftCut::BondHarmonicShiftCut(LAMMPS *lmp) : Bond(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondHarmonicShiftCut::~BondHarmonicShiftCut()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(k);
|
||||
memory->destroy(r0);
|
||||
memory->destroy(r1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShiftCut::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r,dr,rk;
|
||||
|
||||
ebond = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
for (n = 0; n < nbondlist; n++) {
|
||||
i1 = bondlist[n][0];
|
||||
i2 = bondlist[n][1];
|
||||
type = bondlist[n][2];
|
||||
|
||||
delx = x[i1][0] - x[i2][0];
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx,dely,delz);
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
r = sqrt(rsq);
|
||||
|
||||
if (r>r1[type]) continue;
|
||||
|
||||
dr = r - r0[type];
|
||||
rk = k[type] * dr;
|
||||
|
||||
// force & energy
|
||||
|
||||
if (r > 0.0) fbond = -2.0*rk/r;
|
||||
else fbond = 0.0;
|
||||
|
||||
if (eflag) ebond = k[type]*(dr*dr -(r0[type]-r1[type])*(r0[type]-r1[type]) );
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShiftCut::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
|
||||
memory->create(k , n+1,"bond:k");
|
||||
memory->create(r0, n+1,"bond:r0");
|
||||
memory->create(r1, n+1,"bond:r1");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShiftCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all("Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
|
||||
|
||||
double Umin = force->numeric(arg[1]); // energy at minimum
|
||||
double r0_one = force->numeric(arg[2]); // position of minimum
|
||||
double r1_one = force->numeric(arg[3]); // position where energy = 0 = cutoff
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = Umin/((r0_one-r1_one)*(r0_one-r1_one));
|
||||
r0[i] = r0_one;
|
||||
r1[i] = r1_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return an equilbrium bond length
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondHarmonicShiftCut::equilibrium_distance(int i)
|
||||
{
|
||||
return r0[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShiftCut::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondHarmonicShiftCut::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fread(&r1[1],sizeof(double),atom->nbondtypes,fp);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondHarmonicShiftCut::single(int type, double rsq, int i, int j)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
|
||||
if (r>r1[type]) return 0;
|
||||
|
||||
double dr = r - r0[type];
|
||||
double dr2=r0[type]-r1[type];
|
||||
return k[type]*(dr*dr - dr2*dr2);
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
|
||||
BondStyle(harmonicshiftcut,BondHarmonicShiftCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_HARMONICSHIFTCUT_H
|
||||
#define LMP_BOND_HARMONICSHIFTCUT_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "bond.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondHarmonicShiftCut : public Bond {
|
||||
public:
|
||||
BondHarmonicShiftCut(class LAMMPS *);
|
||||
~BondHarmonicShiftCut();
|
||||
void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
double equilibrium_distance(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, double, int, int);
|
||||
|
||||
private:
|
||||
double *k,*r0,*r1;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,343 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg, science@zqex.dk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "lmptype.h"
|
||||
#include "mpi.h"
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "dihedral_cosineshiftexp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
#define SMALL 0.001
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralCosShiftExp::DihedralCosShiftExp(LAMMPS *lmp) : Dihedral(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralCosShiftExp::~DihedralCosShiftExp()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(umin);
|
||||
memory->destroy(a);
|
||||
memory->destroy(opt1);
|
||||
memory->destroy(cost);
|
||||
memory->destroy(sint);
|
||||
memory->destroy(theta);
|
||||
memory->destroy(doExpansion);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralCosShiftExp::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,i,m,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
|
||||
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
|
||||
double c,s,p,sx2,sy2,sz2;
|
||||
double cccpsss,cssmscc,exp2;
|
||||
|
||||
edihedral = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int **dihedrallist = neighbor->dihedrallist;
|
||||
int ndihedrallist = neighbor->ndihedrallist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
for (n = 0; n < ndihedrallist; n++) {
|
||||
i1 = dihedrallist[n][0];
|
||||
i2 = dihedrallist[n][1];
|
||||
i3 = dihedrallist[n][2];
|
||||
i4 = dihedrallist[n][3];
|
||||
type = dihedrallist[n][4];
|
||||
|
||||
// 1st bond
|
||||
|
||||
vb1x = x[i1][0] - x[i2][0];
|
||||
vb1y = x[i1][1] - x[i2][1];
|
||||
vb1z = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(vb1x,vb1y,vb1z);
|
||||
|
||||
// 2nd bond
|
||||
|
||||
vb2x = x[i3][0] - x[i2][0];
|
||||
vb2y = x[i3][1] - x[i2][1];
|
||||
vb2z = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(vb2x,vb2y,vb2z);
|
||||
|
||||
vb2xm = -vb2x;
|
||||
vb2ym = -vb2y;
|
||||
vb2zm = -vb2z;
|
||||
domain->minimum_image(vb2xm,vb2ym,vb2zm);
|
||||
|
||||
// 3rd bond
|
||||
|
||||
vb3x = x[i4][0] - x[i3][0];
|
||||
vb3y = x[i4][1] - x[i3][1];
|
||||
vb3z = x[i4][2] - x[i3][2];
|
||||
domain->minimum_image(vb3x,vb3y,vb3z);
|
||||
|
||||
// c,s calculation
|
||||
|
||||
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||
|
||||
rasq = ax*ax + ay*ay + az*az;
|
||||
rbsq = bx*bx + by*by + bz*bz;
|
||||
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||||
rg = sqrt(rgsq);
|
||||
|
||||
rginv = ra2inv = rb2inv = 0.0;
|
||||
if (rg > 0) rginv = 1.0/rg;
|
||||
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||
rabinv = sqrt(ra2inv*rb2inv);
|
||||
|
||||
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
|
||||
int me;
|
||||
MPI_Comm_rank(world,&me);
|
||||
if (screen) {
|
||||
char str[128];
|
||||
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
|
||||
me,update->ntimestep,
|
||||
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
|
||||
error->warning(str,0);
|
||||
fprintf(screen," 1st atom: %d %g %g %g\n",
|
||||
me,x[i1][0],x[i1][1],x[i1][2]);
|
||||
fprintf(screen," 2nd atom: %d %g %g %g\n",
|
||||
me,x[i2][0],x[i2][1],x[i2][2]);
|
||||
fprintf(screen," 3rd atom: %d %g %g %g\n",
|
||||
me,x[i3][0],x[i3][1],x[i3][2]);
|
||||
fprintf(screen," 4th atom: %d %g %g %g\n",
|
||||
me,x[i4][0],x[i4][1],x[i4][2]);
|
||||
}
|
||||
}
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
double aa=a[type];
|
||||
double uumin=umin[type];
|
||||
|
||||
cccpsss = c*cost[type]+s*sint[type];
|
||||
cssmscc = c*sint[type]-s*cost[type];
|
||||
|
||||
// eflag=1;
|
||||
|
||||
if (doExpansion[type])
|
||||
{ // |a|<0.001 so use expansions relative precision <1e-5
|
||||
if (eflag) edihedral = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
|
||||
df=0.5*uumin*( cssmscc + 0.5*aa*cccpsss);
|
||||
}
|
||||
else
|
||||
{
|
||||
exp2=exp(0.5*aa*(1+cccpsss));
|
||||
if (eflag) edihedral = opt1[type]*(1-exp2);
|
||||
df= 0.5*opt1[type]*aa* ( exp2*cssmscc );
|
||||
}
|
||||
|
||||
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
|
||||
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
|
||||
fga = fg*ra2inv*rginv;
|
||||
hgb = hg*rb2inv*rginv;
|
||||
gaa = -ra2inv*rg;
|
||||
gbb = rb2inv*rg;
|
||||
|
||||
dtfx = gaa*ax;
|
||||
dtfy = gaa*ay;
|
||||
dtfz = gaa*az;
|
||||
dtgx = fga*ax - hgb*bx;
|
||||
dtgy = fga*ay - hgb*by;
|
||||
dtgz = fga*az - hgb*bz;
|
||||
dthx = gbb*bx;
|
||||
dthy = gbb*by;
|
||||
dthz = gbb*bz;
|
||||
|
||||
sx2 = df*dtgx;
|
||||
sy2 = df*dtgy;
|
||||
sz2 = df*dtgz;
|
||||
|
||||
f1[0] = df*dtfx;
|
||||
f1[1] = df*dtfy;
|
||||
f1[2] = df*dtfz;
|
||||
|
||||
f2[0] = sx2 - f1[0];
|
||||
f2[1] = sy2 - f1[1];
|
||||
f2[2] = sz2 - f1[2];
|
||||
|
||||
f4[0] = df*dthx;
|
||||
f4[1] = df*dthy;
|
||||
f4[2] = df*dthz;
|
||||
|
||||
f3[0] = -sx2 - f4[0];
|
||||
f3[1] = -sy2 - f4[1];
|
||||
f3[2] = -sz2 - 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,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralCosShiftExp::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
|
||||
memory->create(doExpansion, n+1, "dihedral:doExpansion");
|
||||
memory->create(umin,n+1,"dihedral:umin");
|
||||
memory->create(a,n+1,"dihedral:a");
|
||||
memory->create(sint,n+1,"dihedral:sind");
|
||||
memory->create(cost,n+1,"dihedral:cosd");
|
||||
memory->create(opt1,n+1,"dihedral:opt1");
|
||||
memory->create(theta,n+1,"dihedral:opt1");
|
||||
memory->create(setflag, n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralCosShiftExp::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
|
||||
|
||||
double umin_ = force->numeric(arg[1]);
|
||||
double theta0_ = force->numeric(arg[2]);
|
||||
double a_ = force->numeric(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
doExpansion[i]=(fabs(a_)<0.001);
|
||||
umin[i] = umin_;
|
||||
a[i] = a_;
|
||||
cost[i] = cos(theta0_*3.14159265/180);
|
||||
sint[i] = sin(theta0_*3.14159265/180);
|
||||
theta[i] = theta0_*3.14159265/180;
|
||||
|
||||
if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
|
||||
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralCosShiftExp::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&sint[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&theta[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralCosShiftExp::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fread(&a[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fread(&sint[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fread(&theta[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
}
|
||||
MPI_Bcast(&umin[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cost[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sint[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&theta[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) {
|
||||
setflag[i] = 1;
|
||||
doExpansion[i]=(fabs(a[i])<0.01);
|
||||
if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/*
|
||||
The torsion angle is defined such that a straight bond has costheta=180.
|
||||
|
||||
U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]]
|
||||
with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2
|
||||
|
||||
potential has minimum at theta=theta0 where U() = -Umin
|
||||
potential has maximum at theta=theta0+180 where U() = 0
|
||||
|
||||
The spring constant around the minimum is controlled by a and
|
||||
is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0
|
||||
the spring constant is k=Umin/2 and the potential reduces to
|
||||
the cosineshifted potential.
|
||||
|
||||
The potential is implemented such that for a<0.001 a series
|
||||
expansion to linear order is used instead of the expression
|
||||
above. This ensures a precision of about 1e-5 or better for
|
||||
energies and forces, and ensures the potential is well
|
||||
behaved for a=0
|
||||
*/
|
||||
|
||||
#ifdef DIHEDRAL_CLASS
|
||||
|
||||
DihedralStyle(cosineshiftexp,DihedralCosShiftExp)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DIHEDRAL_COSINESHIFTEDEXP_H
|
||||
#define LMP_DIHEDRAL_COSINESHIFTEDEXP_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "dihedral.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DihedralCosShiftExp : public Dihedral {
|
||||
public:
|
||||
DihedralCosShiftExp(class LAMMPS *);
|
||||
~DihedralCosShiftExp();
|
||||
void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
|
||||
private:
|
||||
bool *doExpansion;
|
||||
double *umin,*a,*opt1;
|
||||
double *sint;
|
||||
double *cost;
|
||||
double *theta;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue