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/* If passed a non-null pointer, assume is pointer to three integers
* Shift everything by these numbers of FFT grid cells
*
* If pointer is null, attempt to work out what shift would be required
* in x,y and z independently.
*
* Assumes all 3D data are on same FFT grid
*
* Revised 2019 so that automatic mode tries to centre molecule in cell,
* and does so precisely if there is no grid data to worry about
*/
/* Copyright (c) 2007,2019 MJ Rutter
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3
* of the Licence, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, see http://www.gnu.org/licenses/
*/
#include<stdio.h>
#include<stdlib.h>
#include<math.h>
#include "c2xsf.h"
void molecule_fix(int m_abc[3], double m_rel[3], struct unit_cell *c,
struct contents *m, struct symmetry *s,
struct grid *gptr){
int i,j,k,ii,jj,kk,off1,off2,npts,ic;
int fft[3],shift[3];
double amin,amax,ashift[3],*grid3;
if (gptr->data){
fft[0]=gptr->size[0];
fft[1]=gptr->size[1];
fft[2]=gptr->size[2];
}
else fft[0]=fft[1]=fft[2]=1000;
if(!m_abc){ /* We are expected to determine the shift automatically */
if (m_rel){
for(i=0;i<3;i++) ashift[i]=m_rel[i];
}
else{
/* Have we one data grid with an offset origin? */
if ((gptr)&&(gptr->origin_abs)&&((!gptr->next)||(!gptr->next->data))){
if (debug) fprintf(stderr,"Shifting atoms by (%f,%f,%f) A\n",
-gptr->origin_abs[0],-gptr->origin_abs[1],
-gptr->origin_abs[2]);
for(i=0;i<m->n;i++)
for(k=0;k<3;k++)
m->atoms[i].abs[k]-=gptr->origin_abs[k];
addfrac(m->atoms,m->n,c->recip);
free(gptr->origin_abs);
gptr->origin_abs=NULL;
return;
} /* General case */
else{
for(k=0;k<3;k++){
amin=1000;
amax=-1000;
for(i=0;i<m->n;i++){
if (m->atoms[i].frac[k]>amax)
amax=m->atoms[i].frac[k];
if (m->atoms[i].frac[k]<amin)
amin=m->atoms[i].frac[k];
}
ashift[k]=0.5-0.5*(amax+amin);
}
}
}
if (!gptr->data){
if ((!m_rel)||(debug))
fprintf(stderr,"Shifting by (%.6f,%.6f,%.6f)\n",ashift[0],
ashift[1],ashift[2]);
for(i=0;i<m->n;i++)
for(k=0;k<3;k++)
m->atoms[i].frac[k]+=ashift[k];
addabs(m->atoms,m->n,c->basis);
sym_shift(s,ashift,c);
return;
}
else{
m_abc=malloc(3*sizeof(int));
if (!m_abc) error_exit("Malloc error in molecule_fix");
for(k=0;k<3;k++) m_abc[k]=floor(ashift[k]*fft[k]+0.5);
}
}
if (debug)
fprintf(stderr,"Will translate grid by (%d,%d,%d) gridpoints\n"
" which is (%f,%f,%f)\n",
m_abc[0],m_abc[1],m_abc[2],(double)m_abc[0]/fft[0],
(double)m_abc[1]/fft[1],(double)m_abc[2]/fft[2]);
/* Ions are easy */
for(i=0;i<m->n;i++)
for(k=0;k<3;k++)
m->atoms[i].frac[k]+=(double)m_abc[k]/fft[k];
addabs(m->atoms,m->n,c->basis);
/* Symmetry operations */
for(i=0;i<3;i++)
ashift[i]=(double)m_abc[i]/fft[i];
sym_shift(s,ashift,c);
/* Grids are harder */
while((gptr)&&(gptr->data)){
npts=gptr->size[0]*gptr->size[1]*gptr->size[2];
grid3=malloc(sizeof(double)*npts*gptr->comps);
if (!grid3) error_exit("Memory allocation error in grid shift");
for(k=0;k<3;k++){
shift[k]=(gptr->size[k]-(m_abc[k]*gptr->size[k])/fft[k])%gptr->size[k];
while(shift[k]<0) shift[k]+=gptr->size[k];
}
for(k=0;k<gptr->size[0];k++){
kk=(k+shift[0])%gptr->size[0];
for(j=0;j<gptr->size[1];j++){
jj=(j+shift[1])%gptr->size[1];
off1=(k*gptr->size[1]+j)*gptr->size[2];
off2=(kk*gptr->size[1]+jj)*gptr->size[2];
for(i=0;i<gptr->size[2];i++){
ii=(i+shift[2])%gptr->size[2];
*(grid3+off1+i)=*(gptr->data+off2+ii);
if (gptr->comps>1)
for(ic=1;ic<gptr->comps;ic++)
*(grid3+off1+i+ic*npts)=*(gptr->data+off2+ii+ic*npts);
}
}
}
free(gptr->data);
gptr->data=grid3;
gptr=gptr->next;
}
}
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