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lammps/src/USER-PHONON/fix_phonon.h
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fix_phonon.h
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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 authors:
Ling-Ti Kong
Contact:
School of Materials Science and Engineering,
Shanghai Jiao Tong University,
800 Dongchuan Road, Minhang,
Shanghai 200240, CHINA
konglt@sjtu.edu.cn; konglt@gmail.com
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(phonon,FixPhonon)
#else
#ifndef FIX_PHONON_H
#define FIX_PHONON_H
#include <complex>
#include "fix.h"
#include <map>
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
namespace LAMMPS_NS {
class FixPhonon : public Fix {
public:
FixPhonon(class LAMMPS *, int, char **);
~FixPhonon();
int setmask();
void init();
void setup(int);
void end_of_step();
void post_run();
double memory_usage();
int modify_param(int, char **);
private:
int me,nprocs;
bigint waitsteps; // wait these number of timesteps before recording atom positions
bigint prev_nstep; // number of steps from previous run(s); to judge if waitsteps is reached.
int nfreq, ifreq; // after this number of measurement (nfreq), the result will be output once
int nx,ny,nz,nucell,ntotal; // surface dimensions in x- and y-direction, number of atom per unit surface cell
int neval; // # of evaluations
int sysdim; // system dimension
int ngroup, nfind; // total number of atoms in group; total number of atoms on this proc
char *prefix, *logfile; // prefix of output file names
FILE *flog;
double *M_inv_sqrt;
class FFT3d *fft; // to do fft via the fft3d wraper
int nxlo,nxhi,mysize; // size info for local MPI_FFTW
int mynpt,mynq,fft_nsend;
int *fft_cnts, *fft_disp;
int fft_dim, fft_dim2;
double *fft_data;
int itag, idx, idq; // index variables
std::map<int,int> tag2surf, surf2tag; // Mapping info
double **RIloc; // R(r) and index on local proc
double **RIall; // gathered R(r) and index
double **Rsort; // sorted R(r)
double **Rnow; // Current R(r) on local proc
double **Rsum; // Accumulated R(r) on local proc
int *recvcnts, *displs; // MPI related variables
std::complex<double> **Rqnow; // Current R(q) on local proc
std::complex<double> **Rqsum; // Accumulator for conj(R(q)_alpha)*R(q)_beta
std::complex<double> **Phi_q; // Phi's on local proc
std::complex<double> **Phi_all; // Phi for all
void readmap(); // to read the mapping of gf atoms
char *mapfile; // file name of the map file
void getmass(); // to get the mass of each atom in a unit cell
int nasr;
void postprocess(); // to post process the data
void EnforceASR(); // to apply acoustic sum rule to gamma point force constant matrix
char *id_temp; // compute id for temperature
double *TempSum; // to get the average temperature vector
double inv_nTemp; // inverse of number of atoms in temperature group
class Compute *temperature; // compute that computes the temperature
double hsum[6], **basis;
int *basetype;
// private methods to do matrix inversion
void GaussJordan(int, std::complex<double>*);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal fix phonon 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: No atom found for fix phonon!
Self-explanatory. Number of atoms in the group that was passed to
fix-phonon is less than 1.
E: Can not open output file %s"
Self-explanatory.
E: Illegal fix_modify command
Self-explanatory.
E: Could not find fix_modify temp ID
Self-explanatory.
E: Fix_modify temp ID does not compute temperature
Self-explanatory.
E: Cannot open input map file %s
Self-explanatory.
E: Error while reading header of mapping file!
Self-explanatory. The first line of the map file is expected to
contain 4 positive integer numbers.
E: FFT mesh and number of atoms in group mismatch!
Self-explanatory. The product of the 4 numbers should be exactly the
total number of atoms in the group that was passed to fix-phonon.
E: Error while reading comment of mapping file!
Self-explanatory. The second line of the map file should be a comment line.
E: The mapping is incomplete!
Self-explanatory.
E: Error while reading mapping file!
Self-explanatory.
E: The mapping info read is incorrect!
Self-explanatory.
E: Singular matrix in complex GaussJordan!
Self-explanatory.
W: More than one fix phonon defined
Self-explanatory. Just to warn that more than one fix-phonon is defined, but allowed.
*/
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