From 24a51ac6348c6f53186cf9efbfa486ff842dc79d Mon Sep 17 00:00:00 2001
From: lindahl <lindahl>
Date: Tue, 5 Nov 2002 01:25:47 +0000
Subject: [PATCH] Removed deprecated files.

---
 src/gmxlib/sfac.c | 424 ------------------------------------------------------
 1 file changed, 424 deletions(-)
 delete mode 100644 src/gmxlib/sfac.c

diff --git a/src/gmxlib/sfac.c b/src/gmxlib/sfac.c
deleted file mode 100644
index 9359489b93..0000000000
--- a/src/gmxlib/sfac.c
+++ /dev/null
@@ -1,424 +0,0 @@
-/*
- * $Id$
- * 
- *                This source code is part of
- * 
- *                 G   R   O   M   A   C   S
- * 
- *          GROningen MAchine for Chemical Simulations
- * 
- *                        VERSION 3.1
- * Copyright (c) 1991-2001, University of Groningen, The Netherlands
- * 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 2
- * of the License, or (at your option) any later version.
- * 
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- * 
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- * 
- * For more info, check our website at http://www.gromacs.org
- * 
- * And Hey:
- * Gnomes, ROck Monsters And Chili Sauce
- */
-static char *SRCID_sfac_c = "$Id$";
-#include <stdlib.h>
-#include <math.h>
-#include "assert.h"
-#include "typedefs.h"
-#include "complex.h"
-#include "smalloc.h"
-#include "network.h"
-#include "txtdump.h"
-#include "random.h"
-#include "sfac.h"
-#include "vec.h"
-#include "futil.h"
-#include "matio.h"
-
-void print_hkl(char *hklfn,int nh,int nk,int nl,int l0,real Intensity[],
-	       int nlevels)
-{
-  FILE *out;
-  real *t_x,*t_y,**matrix;
-  real lo,hi,val;
-  t_rgb rlo = { 1.0, 1.0, 0.0 };
-  t_rgb rhi = { 0.0, 0.0, 1.0 };
-  int  n_x,n_y;
-  int  i,j,k,hkl;
-
-  fprintf(stderr,"nh=%d, nk=%d, nl=%d\n",nh,nk,nl);  
-  n_x = (2*nh+1);
-  n_y = (2*nk+1);
-  
-  assert ((l0>= -nl) && (l0<=nl));
-  out=ffopen(hklfn,"w");
-  snew(t_x,n_x);
-  snew(t_y,n_y);
-  for(i=-nh; (i<=nh); i++)
-    t_x[i+nh] = i;
-  for(i=-nk; (i<=nk); i++)
-    t_y[i+nk] = i;
-  lo = 1000;
-  hi = -1000;
-  snew(matrix,n_x);
-  hkl = 0;
-  for(i=-nh; (i<=nh); i++) {
-    snew(matrix[i+nh],n_y);
-    for(j=-nk; (j<=nk); j++) {
-      if ((i == 0) && (j == 0) && (l0 == 0))
-	val = 0.0;
-      else
-	val = Intensity[hkl+nl+l0];
-      lo  = min(lo,val);
-      hi  = max(hi,val);
-      matrix[i+nh][j+nk] =  val;
-      hkl += (2*nl+1);
-    }
-  }
-  write_xpm(out,"HKL l=0","electrons","h","k",n_x,n_y,t_x,t_y,
-	    matrix,lo,hi,rlo,rhi,&nlevels);
-  for(i=0; (i<=n_x); i++)
-    sfree(matrix[i]);
-  sfree(matrix);
-  sfree(t_x);
-  sfree(t_y);
-  fclose(out);
-}
-
-void sum_Fhkl(t_commrec *cr,int nhkl,t_complex Fhkl[])
-{
-  if (PAR(cr))
-    gmx_sum(nhkl*2,(real *)Fhkl,cr);
-}
-
-void calc_Fhkl(FILE *log,int nh,int nk,int nl,
-	       t_complex Fhkl[],int start,int homenr,rvec x[],
-	       real fatom[])
-{
-  /* Calculate the structure factor F(hkl) from the coordinates 
-   * x[start] .. x[start+homenr-1]
-   * Fhkl is a linear array of length (2*nh+1)*(2*nk+1)*(2*nl+1)
-   */
-  int        h,k,l,n,n0,nhkl;
-  real       rh,rk,rl,inproduct,fatomn,F000,F000_1;
-  const real twopi=2.0*M_PI;
-  t_complex  shkl;
-  
-  /* Counter into structure factor array */
-  nhkl       = 0;  
-  
-  for(h=-nh; (h<=nh); h++) {
-    rh = h;
-    for(k=-nk; (k<=nk); k++) {
-      rk = k;
-      for(l=-nl; (l<=nl); l++) {
-	rl = l;
-	shkl = cnul;
-	for(n=0; (n<homenr); n++) {
-	  n0         = n+start;
-	  fatomn     = fatom[n];
-	  inproduct  = twopi*(rh*x[n0][XX] + rk*x[n0][YY] + rl*x[n0][ZZ]);
-	  shkl.re   += fatomn*cos(inproduct);
-	  shkl.im   += fatomn*sin(inproduct);
-	}
-	if ((h==0) && (k==0) && (l==0))
-	  F000 = shkl.re;
-	Fhkl[nhkl++] = shkl;
-      }
-    }
-  }
-  /* Normalize structrue factor */
-  F000_1 = 1.0/F000;
-  /*for(n=0; (n<nhkl); n++) {
-    Fhkl[n].re *= F000_1;
-    Fhkl[n].im *= F000_1;
-  }*/
-  
-}
-
-void calc_I0(int nhkl,t_complex Fhkl[],real I0[])
-{
-  int  i;
-  
-  for(i=0; (i<nhkl); i++) {
-    I0[i] = (sqr(Fhkl[i].re) + sqr(Fhkl[i].im));
-  }
-}
-
-real calc_xray(FILE *log,int nh,int nk,int nl,
-	       t_complex Fhkl[],real I0[],real kI,
-	       int start,int homenr,rvec x[],rvec f_xray[],
-	       real fatom[])
-{
-  int  h,k,l,n,n0,nhkl;
-  real rh,rk,rl,kkk,VVV,DeltaI;
-  real fhkl_re,fhkl_im,fhkl2,FFF;
-  real inproduct,cosrS,sinrS;
-  const real twopi=2.0*M_PI;
-  
-  /* Now compute the potential and forces */
-  nhkl = 0;
-  VVV  = 0;
-  for(h=-nh; (h<=nh); h++) {
-    rh = h;
-    for(k=-nk; (k<=nk); k++) {
-      rk = k;
-      for(l=-nl; (l<=nl); l++) {
-	rl = l;
-
-	fhkl_re  = Fhkl[nhkl].re;
-	fhkl_im  = Fhkl[nhkl].im;
-	fhkl2    = sqr(fhkl_re) + sqr(fhkl_im);
-        DeltaI   = fhkl2-I0[nhkl];
-        VVV     += 0.5*kI*DeltaI*DeltaI;
-	kkk      = kI*DeltaI*2.0*twopi;
-	
-	for(n=0; (n<homenr); n++) {
-	  n0        = n+start;
-	  inproduct = twopi*(rh*x[n0][XX] + rk*x[n0][YY] + rl*x[n0][ZZ]);
-	  cosrS     = cos(inproduct);
-	  sinrS     = sin(inproduct);
-	  FFF       = kkk*fatom[n]*(fhkl_re*sinrS - fhkl_im*cosrS);
-	  
-	  f_xray[n][XX] += rh*FFF;
-	  f_xray[n][YY] += rk*FFF;
-	  f_xray[n][ZZ] += rl*FFF;
-	}
-	nhkl++;
-      }
-    }
-  }
-  return VVV;
-}
-
-void rand_coords(int start,int homenr,rvec x[])
-{
-  int n,m;
-  int seed=1993;
-  
-  for(n=start; (n<start+homenr); n++) {
-    for(m=0; (m<DIM); m++)
-      x[n][m] = 1.0*rando(&seed);
-  }
-}
-
-real *calc_nelectrons(t_atoms *atoms)
-{
-  real *fatom,nel,nel_1;
-  int  i;
-  char c;
-  
-  snew(fatom,atoms->nr);
-  
-  nel = 0;
-  for(i=0; (i<atoms->nr); i++) {
-    c=toupper((*(atoms->atomname[i]))[0]);
-    switch (c) {
-    case 'C':
-      fatom[i] = 6;
-      break;
-    case 'N':
-      fatom[i] = 7;
-      break;
-    case 'O':
-      fatom[i] = 8;
-      break;
-    case 'P':
-      fatom[i] = 15;
-      break;
-    case 'S':
-      fatom[i] = 16;
-      break;
-    case 'D':
-      fatom[i] = 2;
-      break;
-    case 'H':
-      fatom[i] = 1;
-      break;
-    default:
-      fprintf(stderr,"Atom: %s, first char %c\n",*(atoms->atomname[0]),c);
-      fatom[i] = 1;
-    }
-    nel+=fatom[i];
-  }
-  nel_1 = 1.0/nel;
-  for(i=0; (i<atoms->nr); i++)
-    fatom[i] *= nel_1;
-    
-  return fatom;
-}
-
-real lo_calc_sfac(FILE *log,int start,int homenr,rvec x[],
-		  int nh,int nk,int nl,
-		  real kI,real I0[],real *n_elec,
-		  rvec f[],t_commrec *cr)
-{
-  static     bool bFirst = TRUE,bDump=FALSE;
-  static     t_complex *Fhkl=NULL;
-  static     rvec *f_xray=NULL;
-  char       *ptr;
-  rvec       f_xraysum;
-  int        n,nhkl;
-  real       VVV,mass;
-  
-  if (Fhkl == NULL) {
-    fprintf(log,"Initiating data (%s,%d)\n",__FILE__,__LINE__);
-    nhkl  = (2*nh+1)*(2*nk+1)*(2*nl+1);
-    
-    fprintf(log,"Going to malloc %d bytes for F(hkl)\n",
-	    nhkl*sizeof(Fhkl[0]));
-    snew(Fhkl,nhkl);
-    snew(f_xray,homenr);
-    bDump = (getenv("DUMP") != NULL);
-  }
-  
-  /* First calculate the structure factor F(hkl) */
-  calc_Fhkl(log,nh,nk,nl,Fhkl,start,homenr,x,n_elec);
-  
-  /* Now do global summing of F(hkl) if we are in parallel */
-  sum_Fhkl(cr,nhkl,Fhkl);
-
-  if (bFirst) {
-    if (getenv("RANDOM") != NULL)
-      rand_coords(start,homenr,x);
-    bFirst = FALSE;
-  }
-  
-  /* Reset imaginary forces */
-  for(n=0; (n<homenr); n++) {
-    clear_rvec(f_xray[n]);
-  }
-
-  /* Compute potential and forces */
-  VVV = calc_xray(log,nh,nk,nl,Fhkl,I0,kI,
-		  start,homenr,x,f_xray,n_elec);
-  
-  /* Add the forces to f array */
-  clear_rvec(f_xraysum);
-  for(n=0; (n<homenr); n++) {
-    rvec_inc(f[start+n],f_xray[n]);
-    rvec_inc(f_xraysum,f_xray[n]);
-  }
-  
-  /* Dump the forces */
-  if (bDump) {
-    pr_rvecs(log,0,"f_tot",f,homenr);
-    pr_rvecs(log,0,"sum   ",&f_xraysum,1);
-  }
-  return VVV;
-}
-	
-real calc_sfac(FILE *log,int start,int homenr,rvec x[],
-	       rvec f[],t_commrec *cr)
-{
-  static real *I0=NULL,*n_el=NULL,kI;
-  static int  nh,nk,nl;
-  static bool bXray=TRUE;
-  char        *ptr;
-  int         i;
-  
-  if (!bXray)
-    return 0.0;
-    
-  if (I0 == NULL) {
-    if ((ptr = getenv("SFAC")) == NULL) {
-      bXray = FALSE;
-      fprintf(stderr,"No SFAC environment variable: no refinement\n");
-      return 0.0;
-    }
-    read_diffraction(ptr,&nh,&nk,&nl,&I0);
-    if ((ptr = getenv("NELEC")) == NULL) {
-      bXray = FALSE;
-      fprintf(stderr,"No NELEC environment variable: no refinement\n");
-      return 0.0;
-    }
-    read_nelectron(ptr,&i,&n_el);
-    assert(i == homenr);
-
-    fprintf(stderr,"The Intensity grid is %dx%dx%d\n",nh,nk,nl);
-        
-    if ((ptr = getenv("KI")) != NULL)
-      kI = atof(ptr);
-    else
-      kI = 1.0;
-    fprintf(log,"kI = %g\n",kI);
-  }
-  
-  return lo_calc_sfac(log,start,homenr,x,nh,nk,nl,kI,I0,n_el,f,cr);
-}
-
-void write_diffraction(char *fn,int nh,int nk,int nl,real I[])
-{
-  FILE *out;
-  int  hkl,nhkl;
-  
-  out=ffopen(fn,"w");
-  
-  fprintf(out,"%8d%8d%8d\n",nh,nk,nl);
-  nhkl = (2*nh+1)*(2*nk+1)*(2*nl+1);
-  for(hkl = 0; (hkl<nhkl); hkl++)
-    fprintf(out,"%15e\n",I[hkl]);
-    
-  ffclose(out);
-}
-
-void read_diffraction(char *fn,int *nh,int *nk,int *nl,real **I)
-{
-  FILE   *in;
-  int    hkl,nhkl;
-  double d;
-  
-  in=ffopen(fn,"r");
-  
-  fscanf(in,"%8d%8d%8d\n",nh,nk,nl);
-  nhkl = (2* *nh + 1)*(2* *nk + 1)*(2* *nl + 1);
-  snew(*I,nhkl);
-  for(hkl=0; (hkl<nhkl); hkl++) {
-    fscanf(in,"%lf\n",&d);
-    (*I)[hkl] = d;
-  }
-  
-  ffclose(in);
-}
-
-void write_nelectron(char *fn,int natom,real n_el[])
-{
-  FILE *out;
-  int  i;
-  
-  out=ffopen(fn,"w");
-  
-  fprintf(out,"%d\n",natom);
-  for(i = 0; (i<natom); i++)
-    fprintf(out,"%g\n",n_el[i]);
-  
-  ffclose(out);
-}
-
-void read_nelectron(char *fn,int *natom,real **n_el)
-{
-  FILE   *in;
-  int    i;
-  double d;
-  
-  in=ffopen(fn,"r");
-  
-  fscanf(in,"%8d\n",natom);
-  snew(*n_el,*natom);
-  for(i=0; (i<*natom); i++) {
-    fscanf(in,"%lf\n",&d);
-    (*n_el)[i] = d;
-  }
-  
-  ffclose(in);
-}
-
-- 
2.11.4.GIT