/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * 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
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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+ * 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,
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*
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- * the papers on the package - you can find them in the top README file.
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*
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+ * 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:
- * GROwing Monsters And Cloning Shrimps
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_QMMM_GAUSSIAN
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "copyrite.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* TODO: this should be made thread-safe */
/* we read the number of cpus and environment from the environment
* if set.
*/
- buf = getenv("NCPUS");
+ buf = getenv("GMX_QM_GAUSSIAN_NCPUS");
if (buf)
{
sscanf(buf, "%d", &qm->nQMcpus);
qm->nQMcpus = 1;
}
fprintf(stderr, "number of CPUs for gaussian = %d\n", qm->nQMcpus);
- buf = getenv("MEM");
+ buf = getenv("GMX_QM_GAUSSIAN_MEMORY");
if (buf)
{
sscanf(buf, "%d", &qm->QMmem);
qm->QMmem = 50000000;
}
fprintf(stderr, "memory for gaussian = %d\n", qm->QMmem);
- buf = getenv("ACC");
+ buf = getenv("GMX_QM_ACCURACY");
if (buf)
{
sscanf(buf, "%d", &qm->accuracy);
}
fprintf(stderr, "accuracy in l510 = %d\n", qm->accuracy);
- buf = getenv("CPMCSCF");
+ buf = getenv("GMX_QM_CPMCSCF");
if (buf)
{
sscanf(buf, "%d", &i);
{
fprintf(stderr, "NOT using cp-mcscf in l1003\n");
}
- buf = getenv("SASTEP");
+ buf = getenv("GMX_QM_SA_STEP");
if (buf)
{
sscanf(buf, "%d", &qm->SAstep);
fclose(out);
}
/* gaussian settings on the system */
- buf = getenv("GAUSS_DIR");
+ buf = getenv("GMX_QM_GAUSS_DIR");
fprintf(stderr, "%s", buf);
if (buf)
{
- qm->gauss_dir = strdup(buf);
+ qm->gauss_dir = gmx_strdup(buf);
}
else
{
- gmx_fatal(FARGS, "no $GAUSS_DIR, check gaussian manual\n");
+ gmx_fatal(FARGS, "no $GMX_QM_GAUSS_DIR, check gaussian manual\n");
}
- buf = getenv("GAUSS_EXE");
+ buf = getenv("GMX_QM_GAUSS_EXE");
if (buf)
{
- qm->gauss_exe = strdup(buf);
+ qm->gauss_exe = gmx_strdup(buf);
}
else
{
- gmx_fatal(FARGS, "no $GAUSS_EXE, check gaussian manual\n");
+ gmx_fatal(FARGS, "no $GMX_QM_GAUSS_EXE set, check gaussian manual\n");
}
- buf = getenv("DEVEL_DIR");
+ buf = getenv("GMX_QM_MODIFIED_LINKS_DIR");
if (buf)
{
- qm->devel_dir = strdup (buf);
+ qm->devel_dir = gmx_strdup (buf);
}
else
{
- gmx_fatal(FARGS, "no $DEVEL_DIR, this is were the modified links reside.\n");
+ gmx_fatal(FARGS, "no $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside.\n");
}
/* if(fr->bRF){*/
if (!step)
{
snew(buf, 20);
- buf = getenv("STATE");
+ buf = getenv("GMX_QM_GROUND_STATE");
if (buf)
{
sscanf(buf, "%d", &state);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff