Re: [ESPResSo-devel] Re: gnu autotools

[Yang Ye]

Hi,

I finally found out that the reason. It's my mistake that I have put a 
wrong source filename into the Makefile-am.am.

Running autogen.sh could be omitted if you are confidently changing 
Makefile-am.am and Makefile-am.in following the pattern of other source 
files.

Regards,
Yang Ye

On 11/4/2007 12:30 AM, Yang Ye wrote:
> Hi, Olaf
>
> I have added the two files e.g., foo.c and foo.h to the 
> Espresso_bin_SOURCES in Makefile-am.am and runned ./autogen.
>
> make has then notified me about unable to make target for foo.o 
> because it tries to call
> gcc foo.o -o foo.o
>
> The first foo.o shall be foo.c. Is there anything else that I need to 
> change for it to work?
>
> Regards,
> Yang Ye
>
> On 11/3/2007 4:43 AM, Olaf Lenz wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: RIPEMD160
> >
> > Hello!
> >
> >  
> > > I would like know how the developers have generated the configure and
> > > makefile with GNU autotools.
> > >
> > > I have included additional commands into the program and hope the
> > > makefile could include additional C source file.
> > >     
> >
> > For the future, please use one of ESPResSo's mailing lists for this kind
> > of questions:
> >
> >     https://fias.uni-frankfurt.de/mailman/listinfo/espresso
> >     https://fias.uni-frankfurt.de/mailman/listinfo/espresso-devel
> >
> > The build system is sparsely documented in the developer's guide, which
> > you can find in the subdirectory doc/dg/ of the CVS version or any
> > recent ESPResSo distribution.
> >
> > The short answer is: You will have to add your file to "Makefile-am.am"
> > and run "autogen.sh". Afterwards, you can use configure and make as 
> > usual.
> >
> > Cheers
> >     Olaf
> >
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.2 (GNU/Linux)
> > Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org
> >
> > iD8DBQFHK4uftQ3riQ3oo/oRAxBCAJ4pFDs9Ztw0bmw91mTKZmwbBgVojQCcDy/a
> > ap7li2VwDCF1BPltWPjyxtI=
> > =DHMQ
> > -----END PGP SIGNATURE-----
> >
> >
> >   
>
>
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#include "stdio.h"
#include "stdlib.h"
#ifdef HAVE_CONFIG_H
#undef HAVE_CONFIG_H
#include "xtcio.h"
#define HAVE_CONFIG_H
#else
#include "xtcio.h"
#endif

#include "grid.h"
#include "particle_data.h"
#include "integrate.h"
#include "communication.h"

#include  "xtc_writer.h"

int xfile = -1;
char *xfilename = NULL;
long step = -1;

#define CONV_UNIT_L(x) (x/10.0); /*from A to nm*/

int xtc_init(ClientData data, Tcl_Interp *interp, int argc, char **argv) 
{
   if (argc>1) {
      xfilename=argv[1];
   }
   else {
      xfilename="traj.xtc";
   }

   if (xfile!=-1) {
      close_xtc(xfile);
   }

   xfile = open_xtc(xfilename, "w");
   step = 0;

   Tcl_AppendResult(interp, "XTC: New file opened", (char *)NULL);
   return TCL_OK;
}

int xtc_write(ClientData data, Tcl_Interp *interp, int argc, char **argv) {
   matrix mat;
   int i;
   rvec *x_data;
   double ppos[3];
   int img[3];
   int pnode;
   Particle p_data;
   char buffer[50 + TCL_DOUBLE_SPACE + TCL_INTEGER_SPACE];

   if (xfile==-1) {
      Tcl_AppendResult(interp, "XTC: Did you initialize xtc with a file?", 
(char *)NULL);
      return TCL_ERROR;
   }

   if (n_total_particles<1) {
      Tcl_AppendResult(interp, "XTC: Insufficient particle number", (char 
*)NULL);      
      return TCL_ERROR;
   }

   mat[0][0] = CONV_UNIT_L(box_l[0]);
   mat[0][1] = 0.0;
   mat[0][2] = 0.0;
   mat[1][0] = 0.0;
   mat[1][1] = CONV_UNIT_L(box_l[1]);
   mat[1][2] = 0.0;
   mat[2][0] = 0.0;
   mat[2][1] = 0.0;
   mat[2][2] = CONV_UNIT_L(box_l[2]);

   x_data = (rvec *)malloc(sizeof(rvec)*(max_seen_particle+1));

   if (!particle_node) { 
       build_particle_node();
   }

   Tcl_AppendResult(interp, "XTC: Extracting Data\n", (char *)NULL);

   for (i = 0; i < max_seen_particle+1; i++) {
       pnode = particle_node[i];
       if (pnode == -1) {
          Tcl_PrintDouble(interp, i, buffer);
          Tcl_AppendResult(interp, "XTC: skipping atom #", buffer, "\n", (char 
*)NULL);

          x_data[i][0] = x_data[i][1] = x_data[i][2] = 0.0;
          continue;
       }
     
       mpi_recv_part(pnode, i, &p_data);
       
       memcpy(ppos, p_data.r.p, 3*sizeof(double));
       memcpy(img, p_data.l.i, 3*sizeof(int));
       unfold_position(ppos, img);

       x_data[i][0] = CONV_UNIT_L(ppos[0]);
       x_data[i][1] = CONV_UNIT_L(ppos[1]);
       x_data[i][2] = CONV_UNIT_L(ppos[2]);
   }
   
   write_xtc(xfile, max_seen_particle+1, step, sim_time, mat, x_data, 1000);
   step++;      

   Tcl_PrintDouble(interp, max_seen_particle+1, buffer);
   Tcl_AppendResult(interp, "XTC: Wrote ", buffer, (char *)NULL);
   Tcl_PrintDouble(interp, step, buffer);
   Tcl_AppendResult(interp, " atoms for frame #", buffer, (char *)NULL);
   Tcl_PrintDouble(interp, sim_time, buffer);
   Tcl_AppendResult(interp, " @ time ", buffer, "\n", (char *)NULL);

   free(x_data);

   return TCL_OK;
}

int xtc_close(ClientData data, Tcl_Interp *interp, int argc, char **argv) {
   if (xfile!=-1) {
      close_xtc(xfile);
      xfile = -1;

      Tcl_AppendResult(interp, "XTC: File closed", (char *)NULL);
      return TCL_OK;
   } else {
      Tcl_AppendResult(interp, "XTC: No File is closed", (char *)NULL);
      return TCL_ERROR;
   }
}

#ifndef XTC_WRITER_H
#define XTC_WRITER_H

#include <tcl.h>

int xtc_init(ClientData data, Tcl_Interp *interp, int argc, char **argv);
int xtc_write(ClientData data, Tcl_Interp *interp, int argc, char **argv);
int xtc_close(ClientData data, Tcl_Interp *interp, int argc, char **argv);

#endif