[gmx-users] Normal Mode Analysis

[Franzi Hoffgaard]

Hi,

I don't know exactly what went wrong when I tried to patch the file. There
was a > on line 18 in the fix file, actually. I checked it. With the file
you sent me, gmxdump works fine.

Thank you very much for your help.

Best regards, Franzi

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt


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

>  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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