Commit JT 042519

- moved examples/SPIN/gneb/interpolate/ toward
tools/spin/interpolate/gneb
- added gneb in the command files in doc/src
- modified the error messages in neb_spin.h/cpp

examples/SPIN/gneb/interpolate/README

@@ -1,31 +0,0 @@
-Interpolate.x tries to perform a cubic polynomial interpolation
-of the MEP.  
-
-Compile the program with:
-gcc interpolate.c -o interpolate.x -lm -lgsl
-
-and then run it as:
-./interpolate.x
-
-Enter N-1 (with N the number of replica).
-The program reads the "neb_init.dat", in which you need to
-replace the current values by your GNEB outputs.
-
-Each line corresponds to a replica, and has to respectively
-contain:
-
-Reac. coords /tab/ pot. energy /tab/ fm dot tangent /tab/
-geodesic dist to next replica
-
-All those information can be provided by the verbose output of
-a neb/spin calculation
-
-The progam outputs the interpolation result, and the
-interpolated MEP in "interpolation_result.dat". 
-
-This code is a courtesy of Aleksei Ivanov, University of
-Iceland.
-For more explanation about this calculation, see Appendix D 
-of the following reference:
-Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015). 
-Computer Physics Communications, 196, 335-347. 

examples/SPIN/gneb/interpolate/interpolate.c

@@ -1,108 +0,0 @@
-/* ------------------------------------------------------------------------
- Provide some explanation here
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-   This program is a courtesy of Aleksei Ivanov (Univ. of Iceland)
-   Contributing authors: Aleksei Ivanov (Univ. of Iceland), 
-   			 Julien Tranchida (SNL)
-------------------------------------------------------------------------- */
-
-#include <stdio.h>
-#include <math.h>
-#include <time.h>
-#include <string.h>
-#include <stdlib.h>
-
-// calculate cubic coefficients
-
-void count_coefficient(double *V, double *F, double *R, double *a, double *b,
-    double *c,double *d,int M){
-  /* R = square of distance between images*/
-  /* V = energy of images */
-  /* F = projection of real real forces along the path? */
-  int i;
-  for(i = 0; i < M ; i++) {
-    a[i] = ( -2.0*(V[i+1]-V[i])/R[i] - F[i] - F[i+1] ) / (R[i]*R[i]);
-    //a[i] = ( -2.0*(V[i+1]-V[i])/sqrt(R[i]) - F[i] - F[i+1] ) / R[i];
-    b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*R[i] ) / (R[i]*R[i]);
-    //b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*sqrt(R[i]) ) / R[i];
-    c[i] = -F[i];
-    d[i] = V[i];
-  }
-}
-
-// cubic spline
-
-double spline(double a,double b,double c,double d,double x) {
-  return (a*x*x*x + b*x*x + c*x + d);
-}
-
-int main() {
-  int M=0; 			// M+1 = number of images
-  double *fmdottan;		// projection of real forces on tangent path
-  double *coords;		// initial value of reaction coords
-  double *V; 			// energy of images
-  double *dist;			// square of the distance between images
-  double *a, *b, *c, *d ;	// coefficients of cubic functions 
-  double x;			// reaction coordinate
-  double A,B; 			// additional variables for rnd
-  double length = 0.0;
-  int i,j;
-  FILE *data;
-  
-  printf("Enter M = number of images - 1 \n");
-  scanf("%d",&M);
-
-  // allocating and initializing tables
-  
-  a = calloc(M,sizeof(double));			// cubic coefficients
-  b = calloc(M,sizeof(double));
-  c = calloc(M,sizeof(double));
-  d = calloc(M,sizeof(double));
-  V = calloc((M+1),sizeof(double)); 		// energies
-  coords = calloc((M+1),sizeof(double));	// reaction coordinates 
-  fmdottan = calloc((M+1),sizeof(double));	// fm dot tangent
-  dist = calloc(M+1,sizeof(double));		// distance between images
-  
-  // reading input file
-
-  if((data=fopen("neb_init.dat","r")) == NULL) {
-    printf("Incorrect input file name.");
-    return 0;
-  }
-
-  for(j=0; j < M+1; j++) {
-    fscanf(data,"%lf\t%lf\t%lf\t%lf\n",&coords[j],&V[j],&fmdottan[j],&dist[j]);
-    length += dist[j];
-    printf("%lf %lf %lf %lf\n",coords[j],V[j],fmdottan[j],dist[j]);
-  }
-
-  if( (fclose(data)) == 0) {
-  	printf("Data stored, input file closed.\n ");
-  }
-
-  // calculate value of coefficients
-  
-  count_coefficient(V,fmdottan,dist,a,b,c,d,M);
- 
-  // plot result of the interpolation
-
-  if( ( data=fopen("interpolation_result.dat","w") )== NULL) {
-    printf("Interpolation file could not be open.");
-    return 0;
-  }
- 
-  A = B = 0.0;
-  for(i = 0; i < M ; i++) {
-    B += dist[i];
-    printf("%13le\n",B);
-    for(j = 0; j <= 1000; j++) {
-      x = dist[i]*1.0e-3*j;
-      fprintf(data,"%13lf\t%13le\n",(x+A)/length,spline(a[i],b[i],c[i],d[i],x));
-    }
-    A += dist[i];
-  }
-
-  return 0;
-}

examples/SPIN/gneb/interpolate/neb_init.dat

@@ -1,8 +0,0 @@
-0.0000000	-3.915271	3.4995081e-17	2.4573077
-0.14285714	-3.9148148	-0.00059075739	2.4573077
-0.28571429	-3.9136926	-0.00072315767	2.4573077
-0.42857143	-3.9127883	-0.0003191228	2.4573265
-0.57142857	-3.9127883	0.0003191228	2.4403341
-0.71428571	-3.9136926	0.00072315767	2.4044093
-0.85714286	-3.9148148	0.00059075739	2.3766041
-1.0000000	-3.915271	-4.1231828e-17	0.0000000