[gmx-users] Normal Mode Analysis

[Berk Hess]

Hi,

But there is a '>' on line 18, at least in my mail.
I tested the patch and it worked for me.
Maybe something went wrong when cut and pasting the patch from the email?
I can mail you the whole file personally tomorrow, if required.

Berk

Date: Tue, 26 May 2009 14:47:52 +0200
Subject: Re: [gmx-users] Normal Mode Analysis
From: f.hoffgaard at gmail.com
To: gmx-users at gromacs.org

Hi

thanks for your reply. I tried patching as you described it, but I got the error message:

patch: **** `>' expected at line 18 of patch

Franzi

---
Franziska Hoffgaard
PhD Student

Bioinformatics & Theo. Biology Group
TU Darmstadt

2009/5/26 Berk Hess <gmx3 at hotmail.com>






Hi,

I just saw that 4.0 uses a new mtx format which can also efficiently store sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix


Berk

61a62,63                                             
> #include "sparsematrix.h"                          
> #include "mtxio.h"                                 
364a367,402                                          

> static void list_mtx(char *fn)                     
> {                                                  
>   int  nrow,ncol,i,j,k;                            
>   real *full=NULL,value;                           

>   gmx_sparsematrix_t * sparse=NULL;                
>                                                    
>   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);    
>                                                    

>   if (full == NULL) {
>     snew(full,nrow*ncol);
>     for(i=0;i<nrow*ncol;i++) {
>       full[i] = 0;
>     }
>
>     for(i=0;i<sparse->nrow;i++) {
>       for(j=0;j<sparse->ndata[i];j++) {

>         k     = sparse->data[i][j].col;
>         value = sparse->data[i][j].value;
>         full[i*ncol+k] = value;
>         full[k*ncol+i] = value;
>       }
>     }
>     gmx_sparsematrix_destroy(sparse);

>   }
>
>   printf("%d %d\n",nrow,ncol);
>   for(i=0; i<nrow; i++) {
>     for(j=0; j<ncol; j++) {
>       printf(" %g",full[i*ncol+j]);
>     }
>     printf("\n");

>   }
>
>   sfree(full);
> }
>
381a420
>     { efMTX, "-mtx", "hessian", ffOPTRD },
409a449,450
>   else if (ftp2bSet(efMTX,NFILE,fnm))
>     list_mtx(ftp2fn(efMTX,NFILE,fnm));



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