/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- *
- * The make_edi program was generously contributed by Oliver Lange, based
- * on the code from g_anaeig. You can reach him as olange@gwdg.de.
- *
- * 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
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* 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.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
*
- * And Hey:
- * Gromacs Runs One Microsecond At Cannonball Speeds
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/* The make_edi program was generously contributed by Oliver Lange, based
+ * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
+ * probably also holds copyright to the following code.
+ */
+#include "gmxpre.h"
+#include <ctype.h>
#include <math.h>
#include <stdlib.h>
-#include <ctype.h>
#include <string.h>
-#include "readinp.h"
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "pdbio.h"
-#include "confio.h"
-#include "tpxio.h"
-#include "matio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "index.h"
-#include "string2.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
{
static const char *desc[] = {
- "[TT]make_edi[tt] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
- "based on eigenvectors of a covariance matrix ([TT]g_covar[tt]) or from a",
- "normal modes analysis ([TT]g_nmeig[tt]).",
+ "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
+ "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
+ "normal modes analysis ([gmx-nmeig]).",
"ED sampling can be used to manipulate the position along collective coordinates",
"(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
"it may be used to enhance the sampling efficiency of MD simulations by stimulating",
"(collective coordinates etc.), at least on the 'protein' side, ED sampling",
"is not very parallel-friendly from an implementation point of view. Because",
"parallel ED requires some extra communication, expect the performance to be",
- "lower as in a free MD simulation, especially on a large number of nodes and/or",
+ "lower as in a free MD simulation, especially on a large number of ranks and/or",
"when the ED group contains a lot of atoms. [PAR]",
"Please also note that if your ED group contains more than a single protein,",
"then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
static const char* ConstForceStr;
static real * evStepList[evStepNr];
- static real radfix = 0.0;
+ static real radstep = 0.0;
static real deltaF0 = 150;
static real deltaF = 0;
static real tau = .1;
"Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
{ "-accdir", FALSE, etSTR, {&evParams[1]},
"Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
- { "-radstep", FALSE, etREAL, {&radfix},
+ { "-radstep", FALSE, etREAL, {&radstep},
"Stepsize (nm/step) for fixed increment radius expansion"},
{ "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
"Maximum number of steps per cycle" },
};
#define NFILE asize(fnm)
edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
- parse_common_args(&argc, argv, 0,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
EdiFile = ftp2fn(efEDI, NFILE, fnm);
}
}
}
- else if (ev_class == evRADFIX && opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
+ else if (ev_class == evRADFIX)
{
snew(evStepList[ev_class], nvecs);
for (i = 0; i < nvecs; i++)
{
- evStepList[ev_class][i] = radfix;
+ evStepList[ev_class][i] = radstep;
}
}
else if (ev_class == evFLOOD)
printf("\n");
}
- EigvecFile = NULL;
EigvecFile = opt2fn("-f", NFILE, fnm);
/*read eigenvectors from eigvec.trr*/
}
/* Write edi-file */
- write_the_whole_thing(ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);
- thanx(stderr);
+ write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff