105 lines
3.5 KiB
C++
105 lines
3.5 KiB
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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Contributing author: David Nicholson (MIT)
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------------------------------------------------------------------------- */
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#include "compute_temp_uef.h"
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#include <cstring>
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#include "fix_nh_uef.h"
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#include "modify.h"
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#include "fix.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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* Base constructor initialized to use rotation matrix
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* ----------------------------------------------------------------------*/
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ComputeTempUef::ComputeTempUef(LAMMPS *lmp, int narg, char **arg) :
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ComputeTemp(lmp, narg, arg)
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{
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rot_flag=true;
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}
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/* ----------------------------------------------------------------------
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* Check for the uef fix
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* ----------------------------------------------------------------------*/
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void ComputeTempUef::init()
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{
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ComputeTemp::init();
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// check to make sure the other uef fix is on
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// borrowed from Pieter's nvt/sllod code
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int i=0;
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for (i=0; i<modify->nfix; i++) {
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if (strcmp(modify->fix[i]->style,"nvt/uef")==0)
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break;
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if (strcmp(modify->fix[i]->style,"npt/uef")==0)
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break;
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}
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if (i==modify->nfix)
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error->all(FLERR,"Can't use compute temp/uef without defining a fix nvt/npt/uef");
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ifix_uef=i;
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}
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/* ----------------------------------------------------------------------
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Compute the ke tensor in the proper coordinate system
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------------------------------------------------------------------------- */
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void ComputeTempUef::compute_vector()
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{
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ComputeTemp::compute_vector();
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if (rot_flag) {
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double rot[3][3];
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( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot);
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virial_rot(vector,rot);
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}
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}
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/* ----------------------------------------------------------------------
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* turn the rotation matrix on or off to properly account for the
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* coordinate system of the velocities
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------------------------------------------------------------------------- */
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void ComputeTempUef::yes_rot()
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{
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rot_flag =true;
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}
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void ComputeTempUef::no_rot()
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{
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rot_flag =false;
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}
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/* ----------------------------------------------------------------------
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Transform the pressure tensor to the rotated coordinate system
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[P]rot = Q.[P].Q^t
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------------------------------------------------------------------------- */
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void ComputeTempUef::virial_rot(double *x, const double r[3][3])
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{
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double t[3][3];
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// [00 10 20 ] [ 0 3 4 ] [00 01 02 ]
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// [01 11 21 ] [ 3 1 5 ] [10 11 12 ]
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// [02 12 22 ] [ 4 5 2 ] [20 21 22 ]
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for (int k = 0; k<3; ++k) {
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t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k];
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t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k];
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t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k];
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}
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x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0];
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x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1];
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x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2];
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x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1];
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x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2];
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x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2];
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}
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