* 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
+#include "gmxpre.h"
+
#include <string.h>
#include <math.h>
#include <algorithm>
-#include "macros.h"
-#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "pbc.h"
-#include "bondf.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "txtdump.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/statistics/statistics.h"
#include "gstat.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
#include "gromacs/random/random.h"
-#include "names.h"
-#include "physics.h"
-#include "calcmu.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/calcmu.h"
#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/matio.h"
#include "gmx_ana.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define e2d(x) ENM2DEBYE*(x)
#define EANG2CM E_CHARGE*1.0e-10 /* e Angstrom to Coulomb meter */
snew(gb, 1);
- if ((ptr = getenv("GKRWIDTH")) != NULL)
+ if ((ptr = getenv("GMX_DIPOLE_SPACING")) != NULL)
{
double bw = strtod(ptr, NULL);
gb->spacing = bw;
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix("# ");
- gmx::printBinaryInformation(dip3d, gmx::getProgramContext(),
+ gmx::printBinaryInformation(dip3d, output_env_get_program_context(oenv),
settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
t_filenm fnm[] = {
{ efEDR, "-en", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "Mtot", ffWRITE },
{ efXVG, "-eps", "epsilon", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm), NULL, box,
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
&natoms, NULL, NULL, NULL, top);
snew(gnx, ncos);