########################################################################
# Specify install locations
########################################################################
-set(GMX_LIB_INSTALL_DIR lib CACHE STRING
- "Library installation directory (default: lib)")
+# Use GNUInstallDirst to set paths on multiarch systems
+include(GNUInstallDirs)
+
+set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
+ "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
"Data installation directory under share/ (default: gromacs)")
mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
\end{itemize}
\subsection{CHARMM\index{CHARMM force field}}
+\label{subsec:charmmff}
As of version 4.5, {\gromacs} supports the CHARMM27 force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
Be careful not to use a command which blocks the terminal
({\eg} {\tt vi}), since multiple instances might be run.
\item {\tt GMX_VIRIAL_TEMPERATURE}: print virial temperature energy term
-\item {\tt LOG_BUFS}: the size of the buffer for file I/O. When set
+\item {\tt GMX_LOG_BUFFER}: the size of the buffer for file I/O. When set
to 0, all file I/O will be unbuffered and therefore very slow.
This can be handy for debugging purposes, because it ensures
that all files are always totally up-to-date.
-\item {\tt LOGO}: set display color for logo in {\tt \normindex{ngmx}}.
-\item {\tt LONGFORMAT}: use long float format when printing
+\item {\tt GMX_LOGO_COLOR}: set display color for logo in {\tt \normindex{ngmx}}.
+\item {\tt GMX_PRINT_LONGFORMAT}: use long float format when printing
decimal values.
\item {\tt GMX_COMPELDUMP}: Applies for computational electrophysiology setups
only (see section \ref{sec:compel}). The initial structure gets dumped to
\begin{enumerate}
-\item {\tt DUMPNL}: dump neighbor list.
- If set to a positive number the {\em entire}
- neighbor list is printed in the log file (may be many megabytes).
- Mainly for debugging purposes, but may also be handy for
- porting to other platforms.
-\item {\tt WHERE}: when set, print debugging info on line numbers.
+\item {\tt GMX_PRINT_DEBUG_LINES}: when set, print debugging info on line numbers.
\item {\tt GMX_DD_NST_DUMP}: number of steps that elapse between dumping
the current DD to a PDB file (default 0). This only takes effect
during domain decomposition, so it should typically be
\begin{enumerate}
-\item {\tt DISTGCT}: couple distances between two atoms when doing general coupling
- theory processes. The format is a string containing two integers, separated by a space.
-\item {\tt GALACTIC_DYNAMICS}: planetary simulations are made possible (just for fun) by setting
+\item {\tt GMX_DO_GALACTIC_DYNAMICS}: planetary simulations are made possible (just for fun) by setting
this environment variable, which allows setting {\tt epsilon_r = -1} in the {\tt .mdp}
file. Normally, {\tt epsilon_r} must be greater than zero to prevent a fatal error.
See {\wwwpage} for example input files for a planetary simulation.
\begin{enumerate}
-\item {\tt ACC}: accuracy in Gaussian L510 (MC-SCF) component program.
-\item {\tt BASENAME}: prefix of {\tt .tpr} files, used in Orca calculations
+\item {\tt GMX_QM_ACCURACY}: accuracy in Gaussian L510 (MC-SCF) component program.
+\item {\tt GMX_QM_ORCA_BASENAME}: prefix of {\tt .tpr} files, used in Orca calculations
for input and output file names.
-\item {\tt CPMCSCF}: when set to a nonzero value, Gaussian QM calculations will
+\item {\tt GMX_QM_CPMCSCF}: when set to a nonzero value, Gaussian QM calculations will
iteratively solve the CP-MCSCF equations.
-\item {\tt DEVEL_DIR}: location of modified links in Gaussian.
+\item {\tt GMX_QM_MODIFIED_LINKS_DIR}: location of modified links in Gaussian.
\item {\tt DSSP}: used by {\tt \normindex{do_dssp}} to point to the {\tt dssp}
executable (not just its path).
-\item {\tt GAUSS_DIR}: directory where Gaussian is installed.
-\item {\tt GAUSS_EXE}: name of the Gaussian executable.
-\item {\tt GKRWIDTH}: spacing used by {\tt \normindex{g_dipoles}}.
+\item {\tt GMX_QM_GAUSS_DIR}: directory where Gaussian is installed.
+\item {\tt GMX_QM_GAUSS_EXE}: name of the Gaussian executable.
+\item {\tt GMX_DIPOLE_SPACING}: spacing used by {\tt \normindex{g_dipoles}}.
\item {\tt GMX_MAXRESRENUM}: sets the maximum number of residues to be renumbered by
{\tt \normindex{grompp}}. A value of -1 indicates all residues should be renumbered.
\item {\tt GMX_FFRTP_TER_RENAME}: Some force fields (like AMBER) use specific names for N- and C-
terminal residues (NXXX and CXXX) as {\tt .rtp} entries that are normally renamed. Setting
this environment variable disables this renaming.
\item {\tt GMX_PATH_GZIP}: {\tt gunzip} executable, used by {\tt \normindex{g_wham}}.
-\item {\tt GMXFONT}: name of X11 font used by {\tt \normindex{ngmx}}.
+\item {\tt GMX_FONT}: name of X11 font used by {\tt \normindex{ngmx}}.
\item {\tt GMXTIMEUNIT}: the time unit used in output files, can be
anything in fs, ps, ns, us, ms, s, m or h.
-\item {\tt MEM}: memory used for Gaussian QM calculation.
+\item {\tt GMX_QM_GAUSSIAN_MEMORY}: memory used for Gaussian QM calculation.
\item {\tt MULTIPROT}: name of the {\tt multiprot} executable, used by the
contributed program {\tt \normindex{do_multiprot}}.
\item {\tt NCPUS}: number of CPUs to be used for Gaussian QM calculation
-\item {\tt OPENMM_PLUGIN_DIR}: the location of OpenMM plugins, needed for
- {\tt \normindex{mdrun-gpu}}.
-\item {\tt ORCA_PATH}: directory where Orca is installed.
-\item {\tt SASTEP}: simulated annealing step size for Gaussian QM calculation.
-\item {\tt STATE}: defines state for Gaussian surface hopping calculation.
-\item {\tt TESTMC}: perform 1000 random swaps in Monte Carlo clustering method
- within {\tt \normindex{g_cluster}}.
-\item {\tt TOTAL}: name of the {\tt total} executable used by the contributed
+\item {\tt GMX_ORCA_PATH}: directory where Orca is installed.
+\item {\tt GMX_QM_SA_STEP}: simulated annealing step size for Gaussian QM calculation.
+\item {\tt GMX_QM_GROUND_STATE}: defines state for Gaussian surface hopping calculation.
+\item {\tt GMX_TOTAL}: name of the {\tt total} executable used by the contributed
{\tt \normindex{do_shift}} program.
-\item {\tt VERBOSE}: make {\tt \normindex{g_energy}} and {\tt \normindex{eneconv}}
+\item {\tt GMX_ENER_VERBOSE}: make {\tt \normindex{g_energy}} and {\tt \normindex{eneconv}}
loud and noisy.
\item {\tt VMD_PLUGIN_PATH}: where to find VMD plug-ins. Needed to be
able to read file formats recognized only by a VMD plug-in.
\item {\tt VMDDIR}: base path of VMD installation.
-\item {\tt XMGR}: sets viewer to {\tt xmgr} (deprecated) instead of {\tt xmgrace}.
+\item {\tt GMX_USE_XMGR}: sets viewer to {\tt xmgr} (deprecated) instead of {\tt xmgrace}.
\end{enumerate}
of a supercomputer, you need to configure and compile {\gromacs} with an external
MPI library. All supercomputers are shipped with MPI libraries optimized for
that particular platform, and if you are using a cluster of workstations
-there are several good free MPI implementations;
-Open MPI is usually a good choice. Once you have an MPI library
-installed it's trivial to compile {\gromacs} with MPI support: Just pass
-the option {\tt -DGMX_MPI=on} to {\tt cmake} and (re-)compile. Please see
-{\wwwpage} for more detailed instructions.
-Note that in addition to MPI parallelization, {\gromacs} supports
-thread-parallelization through \normindex{OpenMP}. MPI and OpenMP parallelization
-can be combined, which results in, so called, hybrid parallelization.
-See {\wwwpage} for details on use and performance of the parallelization
-schemes.
-
-For communications over multiple nodes connected by a network,
-there is a program usually called {\tt mpirun} with which you can start
-the parallel processes. A typical command line could look like:
-{\tt mpirun -np 10 mdrun_mpi -s topol -v}
-
-With the implementation of threading available by default in {\gromacs} version 4.5,
-if you have a single machine with multiple processors you don't have to
-use the {\tt mpirun} command, or compile with MPI. Instead, you can
-allow {\gromacs} to determine the number of threads automatically, or use the {\tt mdrun} option {\tt -nt}:
-{\tt mdrun -nt 8 -s topol.tpr}
+there are several good free MPI implementations; OpenMPI is usually a good choice.
+Note that MPI and threaded-MPI support are mutually incompatible.
-Check your local manuals (or online manual) for exact details
-of your MPI implementation.
-
-If you are interested in programming MPI yourself, you can find
-manuals and reference literature on the internet.
+In addition to MPI parallelization, {\gromacs} supports also
+thread-parallelization through \normindex{OpenMP}. MPI and OpenMP parallelization
+can be combined, which results in, so called, hybrid parallelization. It can offer
+better performance and scaling in some cases.
+See {\wwwpage} for details on the use and performance of the different
+parallelization schemes.
\section{Running {\gromacs} on \normindex{GPUs}}
As of version 4.6, {\gromacs} has native GPU support through CUDA.
% LocalWords: MAXRESRENUM grompp FFRTP TER NXXX CXXX rtp GZIP gunzip
% LocalWords: GMXFONT ns MEM MULTIPROT multiprot NCPUS CPUs OPENMM
% LocalWords: PLUGIN OpenMM plugins SASTEP TESTMC eneconv VMD VMDDIR
-% LocalWords: XMGR xmgr parallelization nt online Nvidia nb cpu
+% LocalWords: GMX_USE_XMGR xmgr parallelization nt online Nvidia nb cpu
% LocalWords: testverlet grommp
bond, preferably on heavy atoms. When the {\tt [~dihedrals~]} field is used,
no other dihedrals will be generated for the bonds corresponding to the
specified dihedrals. It is possible to put more than one dihedral
-function on a rotatable bond.
+function on a rotatable bond. In the case of CHARMM27 FF {\tt pdb2gmx}
+can add correction maps to the dihedrals using the default {\tt -cmap} option.
+Please refer to \ssecref{charmmff} for more information.
{\tt pdb2gmx} sets the number of exclusions to 3, which
means that interactions between atoms connected by at most 3 bonds are
#debian/ubuntu needs a : at the end
setenv MANPATH ${GMXMAN}:${MANPATH}
-setenv GMXFONT 10x20
+setenv GMX_FONT 10x20
# Read completions if we understand it (i.e. have tcsh)
# Currently disabled, since the completions don't work with the new
opls_117 HW 1 1.00800 0.410 A 0.00000e+00 0.00000e+00
#endif
opls_118 OW 8 15.99940 0.000 A 3.12000e-01 6.69440e-01
+ opls_118e OW 8 15.99940 0.000 A 3.09700e-01 7.44752e-01 ; J. Chem. Phys. 120 (2004) 6085-6093
opls_119 HW 1 1.00800 0.000 A 0.00000e+00 0.00000e+00
opls_120 OL 0 0.00000 0.000 D 0.00000e+00 0.00000e+00
opls_122 CT 6 12.01100 0.248 A 3.80000e-01 2.09200e-01
--- /dev/null
+[ moleculetype ]
+; molname nrexcl
+SOL 2
+
+[ atoms ]
+; id at type res nr residu name at name cg nr charge
+1 opls_118e 1 SOL OW 1 0
+2 opls_119 1 SOL HW1 1 0.241
+3 opls_119 1 SOL HW2 1 0.241
+4 opls_120 1 SOL LP1 1 -0.241
+5 opls_120 1 SOL LP2 1 -0.241
+
+[ settles ]
+; i funct doh dhh
+1 1 0.09572 0.15139
+
+[ virtual_sites3 ]
+; The position of the virtual site is computed as follows:
+;
+; The distance from OW to L is 0.07 nm, the geometry is tetrahedral
+; (109.47 deg)
+; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
+; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
+;
+; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2)
+; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2)
+; Vsite pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31)
+
+; Vsite from funct a b c
+4 1 2 3 4 -0.344908 -0.344908 -6.4437903493
+5 1 2 3 4 -0.344908 -0.344908 6.4437903493
+
+[ exclusions ]
+1 2 3 4 5
+2 1 3 4 5
+3 1 2 4 5
+4 1 2 3 5
+5 1 2 3 4
tip4p TIP4P TIP 4-point, recommended
tip3p TIP3P TIP 3-point
tip5p TIP5P TIP 5-point
+tip5pe TIP5P TIP 5-point improved for Ewald sums
spc SPC simple point charge
spce SPC/E extended simple point charge
"calling the 'total' program. If you do not have the total program,",
"get it. do_shift assumes that the total executable is in",
"[TT]/home/mdgroup/total/total[tt]. If that is not the case, then you should",
- "set an environment variable [BB]TOTAL[bb] as in: [PAR]",
- "[TT]setenv TOTAL /usr/local/bin/total[tt][PAR]",
+ "set an environment variable [BB]GMX_TOTAL[bb] as in: [PAR]",
+ "[TT]setenv GMX_TOTAL /usr/local/bin/total[tt][PAR]",
"where the right hand side should point to the total executable.[PAR]",
"Output is printed in files [TT]shift.out[tt] where t is the time of the frame.[PAR]",
"The program also needs an input file called [BB]random.dat[bb] which",
gmx_tmpnam(tmpfile);
fprintf(stderr,"pdbfile = %s\ntmpfile = %s\n",pdbfile,tmpfile);
- if ((dptr=getenv("TOTAL")) == NULL)
+ if ((dptr=getenv("GMX_TOTAL")) == NULL)
dptr="/home/mdgroup/total/total";
sprintf(total,"%s > /dev/null",dptr);
fprintf(stderr,"total cmd='%s'\n",total);
cmake_minimum_required(VERSION 2.8)
project(TNG_IO)
+set(PROJECT_VERSION "1.0")
if("${CMAKE_C_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -Wall")
snew(gb, 1);
- if ((ptr = getenv("GKRWIDTH")) != NULL)
+ if ((ptr = getenv("GMX_DIPOLE_SPACING")) != NULL)
{
double bw = strtod(ptr, NULL);
gb->spacing = bw;
int *set;
gmx_bool bVerbose = TRUE;
- if ((getenv("VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != NULL)
{
bVerbose = FALSE;
}
int *set;
gmx_bool bVerbose = TRUE;
- if ((getenv("VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != NULL)
{
bVerbose = FALSE;
}
const char *fm2 = "%3d %-34s";
char **newnm = NULL;
- if ((getenv("VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != NULL)
{
bVerbose = FALSE;
}
if ((p_num == 0) && (n_num == 0))
{
- fprintf(stderr, "No ions to add.\n");
- exit(0);
+ fprintf(stderr, "No ions to add, will just copy input configuration.\n");
}
else
{
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
- }
- if (opt2bSet("-p", NFILE, fnm))
- {
- update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
- }
+ if (opt2bSet("-p", NFILE, fnm))
+ {
+ update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
+ }
- snew(bSet, nw);
- snew(repl, nw);
+ snew(bSet, nw);
+ snew(repl, nw);
- snew(v, atoms.nr);
- snew(atoms.pdbinfo, atoms.nr);
+ snew(v, atoms.nr);
+ snew(atoms.pdbinfo, atoms.nr);
- set_pbc(&pbc, ePBC, box);
+ set_pbc(&pbc, ePBC, box);
- if (seed == 0)
- {
- rng = gmx_rng_init(gmx_rng_make_seed());
- }
- else
- {
- rng = gmx_rng_init(seed);
- }
- /* Now loop over the ions that have to be placed */
- while (p_num-- > 0)
- {
- insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
- 1, p_q, p_name, &atoms, rmin, rng);
- }
- while (n_num-- > 0)
- {
- insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
- -1, n_q, n_name, &atoms, rmin, rng);
- }
- gmx_rng_destroy(rng);
- fprintf(stderr, "\n");
+ if (seed == 0)
+ {
+ rng = gmx_rng_init(gmx_rng_make_seed());
+ }
+ else
+ {
+ rng = gmx_rng_init(seed);
+ }
+ /* Now loop over the ions that have to be placed */
+ while (p_num-- > 0)
+ {
+ insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
+ 1, p_q, p_name, &atoms, rmin, rng);
+ }
+ while (n_num-- > 0)
+ {
+ insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
+ -1, n_q, n_name, &atoms, rmin, rng);
+ }
+ gmx_rng_destroy(rng);
+ fprintf(stderr, "\n");
- if (nw)
- {
- sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
- }
+ if (nw)
+ {
+ sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
+ }
- sfree(atoms.pdbinfo);
- atoms.pdbinfo = NULL;
- write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC,
- box);
+ sfree(atoms.pdbinfo);
+ atoms.pdbinfo = NULL;
+ }
+ write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC, box);
return 0;
}
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#define MAXNAMES 30
-#define NAME_LEN 30
+/* It's not nice to have size limits, but we should not spend more time
+ * on this ancient tool, but instead use the new selection library.
+ */
+#define MAXNAMES 1024
+#define NAME_LEN 1024
gmx_bool bCase = FALSE;
{
const char *desc[] = {
"[THISMODULE] calculates the three principal axes of inertia for a group",
- "of atoms.",
+ "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
+ "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
+ "contains the x/y/z components of the first (major) principal axis for",
+ "each frame, and similarly for the middle and minor axes in paxis2.dat",
+ "and paxis3.dat."
};
static gmx_bool foo = FALSE;
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efDAT, "-a1", "axis1", ffWRITE },
- { efDAT, "-a2", "axis2", ffWRITE },
- { efDAT, "-a3", "axis3", ffWRITE },
+ { efDAT, "-a1", "paxis1", ffWRITE },
+ { efDAT, "-a2", "paxis2", ffWRITE },
+ { efDAT, "-a3", "paxis3", ffWRITE },
{ efDAT, "-om", "moi", ffWRITE }
};
#define NFILE asize(fnm)
calc_principal_axes(&top, x, index, gnx, axes, moi);
- fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[YY][XX], axes[ZZ][XX]);
- fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][YY], axes[YY][YY], axes[ZZ][YY]);
- fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][ZZ], axes[YY][ZZ], axes[ZZ][ZZ]);
+ fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
+ fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
+ fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
fprintf(fmoi, "%15.10f %15.10f %15.10f %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
}
while (read_next_x(oenv, status, &t, x, box));
static void do_sham(const char *fn, const char *ndx,
const char *xpmP, const char *xpm, const char *xpm2,
- const char *xpm3, const char *xpm4, const char *pdb,
+ const char *xpm3, const char *pdb,
const char *logf,
int n, int neig, real **eig,
gmx_bool bGE, int nenerT, real **enerT,
- int nmap, real *mapindex, real **map,
real Tref,
real pmax, real gmax,
real *emin, real *emax, int nlevels, real pmin,
- const char *mname, int *idim, int *ibox,
+ int *idim, int *ibox,
gmx_bool bXmin, real *xmin, gmx_bool bXmax, real *xmax)
{
FILE *fp;
real *min_eig, *max_eig;
real *axis_x, *axis_y, *axis_z, *axis = NULL;
double *P;
- real **PP, *W, *E, **WW, **EE, *S, **SS, *M, **MM, *bE;
+ real **PP, *W, *E, **WW, **EE, *S, **SS, *M, *bE;
rvec xxx;
char *buf;
- double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax, Minf;
+ double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax;
real *delta;
int i, j, k, imin, len, index, d, *nbin, *bindex, bi;
int *nxyz, maxbox;
axis[j] = min_eig[i] + j/bfac[i];
}
}
- if (map)
- {
- snew(M, len);
- snew(MM, maxbox*maxbox);
- for (i = 0; (i < ibox[0]); i++)
- {
- MM[i] = &(M[i*ibox[1]]);
- }
- Mmin = 1e8;
- Mmax = -1e8;
- for (i = 0; (i < nmap); i++)
- {
- Mmin = min(Mmin, map[0][i]);
- Mmax = max(Mmax, map[0][i]);
- }
- Minf = Mmax*1.05;
- for (i = 0; (i < len); i++)
- {
- M[i] = Minf;
- }
- for (i = 0; (i < nmap); i++)
- {
- index = gmx_nint(mapindex[i]);
- if (index >= len)
- {
- gmx_fatal(FARGS, "Number of bins in file from -mdata option does not correspond to current analysis");
- }
- if (P[index] != 0)
- {
- M[index] = map[0][i];
- }
- }
- }
- else
- {
- MM = NULL;
- Minf = NOTSET;
- }
pick_minima(logf, ibox, neig, len, W);
if (gmax <= 0)
{
write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
gmx_ffclose(fp);
- if (map)
- {
- fp = gmx_ffopen(xpm4, "w");
- write_xpm(fp, flags, "Custom Landscape", mname, "PC1", "PC2",
- ibox[0], ibox[1], axis_x, axis_y, MM, 0, Minf, rlo, rhi, &nlevels);
- gmx_ffclose(fp);
- }
}
else if (neig == 3)
{
}
gmx_ffclose(fp);
write_xplor("out.xplor", W, ibox, min_eig, max_eig);
- if (map)
- {
- write_xplor("user.xplor", M, ibox, min_eig, max_eig);
- }
nxyz[XX] = imin/(ibox[1]*ibox[2]);
nxyz[YY] = (imin-nxyz[XX]*ibox[1]*ibox[2])/ibox[2];
nxyz[ZZ] = imin % ibox[2];
gmx_ffclose(fp);
sfree(buf);
}
- if (map)
- {
- sfree(MM);
- sfree(M);
- }
}
static void ehisto(const char *fh, int n, real **enerT, const output_env_t oenv)
static rvec nrbox = {32, 32, 32};
static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1};
static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25;
- static const char *mname = "";
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
"Maximum enthalpy in output, default is calculate" },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels for energy landscape" },
- { "-mname", FALSE, etSTR, {&mname},
- "Legend label for the custom landscape" },
};
#define NPA asize(pa)
FILE *out;
- int n, e_n, d_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
- real **val, **et_val, **dt_val, *t, *e_t, e_dt, d_dt, *d_t, dt, tot, error;
+ int n, e_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
+ real **val, **et_val, *t, *e_t, e_dt, d_dt, dt, tot, error;
real *rmin, *rmax;
double *av, *sig, cum1, cum2, cum3, cum4, db;
const char *fn_ge, *fn_ene;
{ efXPM, "-ls", "gibbs", ffOPTWR },
{ efXPM, "-lsh", "enthalpy", ffOPTWR },
{ efXPM, "-lss", "entropy", ffOPTWR },
- { efXPM, "-map", "map", ffOPTWR },
{ efPDB, "-ls3", "gibbs3", ffOPTWR },
- { efXVG, "-mdata", "mapdata", ffOPTRD },
{ efLOG, "-g", "shamlog", ffOPTWR }
};
#define NFILE asize(fnm)
et_val = NULL;
}
- if (opt2fn_null("-mdata", NFILE, fnm) != NULL)
- {
- dt_val = read_xvg_time(opt2fn("-mdata", NFILE, fnm), bHaveT,
- FALSE, tb, FALSE, te,
- nsets_in, &d_nset, &d_n, &d_dt, &d_t);
- if (d_nset != 1)
- {
- gmx_fatal(FARGS, "Can only handle one mapping data column in %s",
- opt2fn("-mdata", NFILE, fnm));
- }
- }
- else
- {
- dt_val = NULL;
- }
-
if (fn_ene && et_val)
{
ehisto(opt2fn("-histo", NFILE, fnm), e_n, et_val, oenv);
do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm),
opt2fn("-lp", NFILE, fnm),
opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm),
- opt2fn("-lss", NFILE, fnm), opt2fn("-map", NFILE, fnm),
+ opt2fn("-lss", NFILE, fnm),
opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm),
- n, nset, val, fn_ge != NULL, e_nset, et_val, d_n, d_t, dt_val, Tref,
+ n, nset, val, fn_ge != NULL, e_nset, et_val, Tref,
pmax, gmax,
opt2parg_bSet("-emin", NPA, pa) ? &emin : NULL,
opt2parg_bSet("-emax", NPA, pa) ? &emax : NULL,
nlevels, pmin,
- mname, idim, ibox,
+ idim, ibox,
opt2parg_bSet("-xmin", NPA, pa), rmin,
opt2parg_bSet("-xmax", NPA, pa), rmax);
*/
MPI_Comm comm_intra;
- MPI_Comm_split(MPI_COMM_WORLD, gmx_hostname_num(), cr->rank_intranode,
+ MPI_Comm_split(MPI_COMM_WORLD,
+ gmx_physicalnode_id_hash(), cr->rank_intranode,
&comm_intra);
MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
/* MPI_Scan is inclusive, but here we need exclusive */
void gmx_setup_nodecomm(FILE gmx_unused *fplog, t_commrec *cr)
{
gmx_nodecomm_t *nc;
- int n, rank, hostnum, ng, ni;
+ int n, rank, nodehash, ng, ni;
/* Many MPI implementations do not optimize MPI_Allreduce
* (and probably also other global communication calls)
MPI_Comm_size(cr->mpi_comm_mygroup, &n);
MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
- hostnum = gmx_hostname_num();
+ nodehash = gmx_physicalnode_id_hash();
if (debug)
{
/* The intra-node communicator, split on node number */
- MPI_Comm_split(cr->mpi_comm_mygroup, hostnum, rank, &nc->comm_intra);
+ MPI_Comm_split(cr->mpi_comm_mygroup, nodehash, rank, &nc->comm_intra);
MPI_Comm_rank(nc->comm_intra, &nc->rank_intra);
if (debug)
{
/* thread-MPI is not initialized when not running in parallel */
#if defined GMX_MPI && !defined GMX_THREAD_MPI
int nrank_world, rank_world;
- int i, mynum, *num, *num_s, *num_pp, *num_pp_s;
+ int i, myhash, *hash, *hash_s, *hash_pp, *hash_pp_s;
MPI_Comm_size(MPI_COMM_WORLD, &nrank_world);
MPI_Comm_rank(MPI_COMM_WORLD, &rank_world);
- /* Get the node number from the hostname to identify the nodes */
- mynum = gmx_hostname_num();
+ /* Get a (hopefully unique) hash that identifies our physical node */
+ myhash = gmx_physicalnode_id_hash();
/* We can't rely on MPI_IN_PLACE, so we need send and receive buffers */
- snew(num, nrank_world);
- snew(num_s, nrank_world);
- snew(num_pp, nrank_world);
- snew(num_pp_s, nrank_world);
+ snew(hash, nrank_world);
+ snew(hash_s, nrank_world);
+ snew(hash_pp, nrank_world);
+ snew(hash_pp_s, nrank_world);
- num_s[rank_world] = mynum;
- num_pp_s[rank_world] = (cr->duty & DUTY_PP) ? mynum : -1;
+ hash_s[rank_world] = myhash;
+ hash_pp_s[rank_world] = (cr->duty & DUTY_PP) ? myhash : -1;
- MPI_Allreduce(num_s, num, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
- MPI_Allreduce(num_pp_s, num_pp, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(hash_s, hash, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(hash_pp_s, hash_pp, nrank_world, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
nrank_intranode = 0;
rank_intranode = 0;
rank_pp_intranode = 0;
for (i = 0; i < nrank_world; i++)
{
- if (num[i] == mynum)
+ if (hash[i] == myhash)
{
nrank_intranode++;
if (i < rank_world)
rank_intranode++;
}
}
- if (num_pp[i] == mynum)
+ if (hash_pp[i] == myhash)
{
nrank_pp_intranode++;
if ((cr->duty & DUTY_PP) && i < rank_world)
}
}
}
- sfree(num);
- sfree(num_s);
- sfree(num_pp);
- sfree(num_pp_s);
+ sfree(hash);
+ sfree(hash_s);
+ sfree(hash_pp);
+ sfree(hash_pp_s);
#else
/* Serial or thread-MPI code: we run within a single physical node */
nrank_intranode = cr->nnodes;
fprintf(out, " %-32s %16s %15.3f %6.1f\n",
"Total", "", *mflop, tfrac);
fprintf(out, "%s\n\n", myline);
+
+ if (nrnb->n[eNR_NBKERNEL_GENERIC] > 0)
+ {
+ fprintf(out,
+ "WARNING: Using the slow generic C kernel. This is fine if you are\n"
+ "comparing different implementations or MD software. Routine\n"
+ "simulations should use a different non-bonded setup for much better\n"
+ "performance.\n\n");
+ }
}
}
const char *format;
int i, j;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
const char *format;
int i, j;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
const char *flong = "%15.8e";
const char *format;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
case efXVG:
if (!(cmd = getenv(env)) )
{
- if (getenv("XMGR") )
+ if (getenv("GMX_USE_XMGR") )
{
cmd = "xmgr";
}
ir->epsilon_r = 1.0;
}
- if (getenv("GALACTIC_DYNAMICS") == NULL)
+ if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
{
sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
CHECK(ir->epsilon_r < 0);
lookup_nbnxn_kernel_name(*kernel_type),
nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
nbnxn_kernel_to_cj_size(*kernel_type));
+
+ if (nbnxnk4x4_PlainC == *kernel_type ||
+ nbnxnk8x8x8_PlainC == *kernel_type)
+ {
+ md_print_warn(cr, fp,
+ "WARNING: Using the slow %s kernels. This should\n"
+ "not happen during routine usage on supported platforms.\n\n",
+ lookup_nbnxn_kernel_name(*kernel_type));
+ }
}
}
},
'4xn' : {
'Define' : 'GMX_NBNXN_SIMD_4XN',
- 'WidthSetup' : ('#ifdef GMX_NBNXN_HALF_WIDTH_SIMD\n' \
- '#define GMX_USE_HALF_WIDTH_SIMD_HERE\n' \
- '#endif\n'),
+ 'WidthSetup' : (''),
'WidthCheck' : ('#if !(GMX_SIMD_REAL_WIDTH == 2 || GMX_SIMD_REAL_WIDTH == 4 || GMX_SIMD_REAL_WIDTH == 8)\n' \
'#error "unsupported SIMD width"\n' \
'#endif\n'),
#include "typedefs.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+
#ifdef {0}
-{1}
-#include "gromacs/simd/macros.h"
-#include "gromacs/simd/vector_operations.h"
+{1}#include "gromacs/simd/vector_operations.h"
+
{2}
#define GMX_SIMD_J_UNROLL_SIZE {3}
#include "{4}"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * 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.
*/
#include "typedefs.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+
#ifdef __cplusplus
extern "C" {{
#endif
#ifdef GMX_NBNXN_SIMD_4XN
#include "gromacs/simd/vector_operations.h"
+
#if !(GMX_SIMD_REAL_WIDTH == 2 || GMX_SIMD_REAL_WIDTH == 4 || GMX_SIMD_REAL_WIDTH == 8)
#error "unsupported SIMD width"
#endif
/* 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)
}
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);
}
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);
}
else
{
- gmx_fatal(FARGS, "no $DEVEL_DIR, this is were the modified links reside.\n");
+ gmx_fatal(FARGS, "no $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside.\n");
}
/* if(fr->bRF){*/
if (!step)
{
snew(buf, 20);
- buf = getenv("STATE");
+ buf = getenv("GMX_QM_GROUND_STATE");
if (buf)
{
sscanf(buf, "%d", &state);
snew(buf, 200);
/* ORCA settings on the system */
- buf = getenv("BASENAME");
+ buf = getenv("GMX_QM_ORCA_BASENAME");
if (buf)
{
snew(qm->orca_basename, 200);
}
else
{
- gmx_fatal(FARGS, "$BASENAME not set\n");
+ gmx_fatal(FARGS, "$GMX_QM_ORCA_BASENAME is not set\n");
}
/* ORCA directory on the system */
snew(buf, 200);
- buf = getenv("ORCA_PATH");
+ buf = getenv("GMX_ORCA_PATH");
if (buf)
{
}
else
{
- gmx_fatal(FARGS, "$ORCA_PATH not set, check manual\n");
+ gmx_fatal(FARGS, "$GMX_ORCA_PATH not set, check manual\n");
}
fprintf(stderr, "Setting ORCA path to: %s...\n", qm->orca_dir);
{
// Pme correction only needs to be ~1e-6 accuracy single, 1e-10 double
#ifdef GMX_DOUBLE
- setUlpTol((gmx_int64_t)(1e-10/GMX_REAL_EPS));
+ setUlpTol((gmx_int64_t)(5e-10/GMX_REAL_EPS));
#else
- setUlpTol((gmx_int64_t)(1e-6/GMX_REAL_EPS));
+ setUlpTol((gmx_int64_t)(5e-6/GMX_REAL_EPS));
#endif
setRange(0.15, 4);
{
// Pme correction only needs to be ~1e-6 accuracy single, 1e-10 double
#ifdef GMX_DOUBLE
- setUlpTol((gmx_int64_t)(1e-10/GMX_REAL_EPS));
+ setUlpTol((gmx_int64_t)(5e-10/GMX_REAL_EPS));
#else
- setUlpTol((gmx_int64_t)(1e-6/GMX_REAL_EPS));
+ setUlpTol((gmx_int64_t)(5e-6/GMX_REAL_EPS));
#endif
setRange(0.15, 4);
setAbsTol(GMX_REAL_EPS);
#endif
}
-#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
-#include <spi/include/kernel/location.h>
-#endif
-
-int gmx_physicalnode_id_hash(void)
+static int mpi_hostname_hash(void)
{
int hash_int;
return hash_int;
}
-int gmx_hostname_num()
-{
-#ifndef GMX_MPI
- return 0;
-#else
-#ifdef GMX_THREAD_MPI
- /* thread-MPI currently puts the thread number in the process name,
- * we might want to change this, as this is inconsistent with what
- * most MPI implementations would do when running on a single node.
- */
- return 0;
-#else
- int resultlen, hostnum, i, j;
- char mpi_hostname[MPI_MAX_PROCESSOR_NAME], hostnum_str[MPI_MAX_PROCESSOR_NAME];
+#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
+#include <spi/include/kernel/location.h>
- MPI_Get_processor_name(mpi_hostname, &resultlen);
-#ifdef GMX_TARGET_BGQ
+static int bgq_nodenum(void)
+{
+ int hostnum;
Personality_t personality;
Kernel_GetPersonality(&personality, sizeof(personality));
/* Each MPI rank has a unique coordinate in a 6-dimensional space
hostnum += personality.Network_Config.Dcoord;
hostnum *= personality.Network_Config.Enodes;
hostnum += personality.Network_Config.Ecoord;
-#else
- /* This procedure can only differentiate nodes with host names
- * that end on unique numbers.
- */
- i = 0;
- j = 0;
- /* Only parse the host name up to the first dot */
- while (i < resultlen && mpi_hostname[i] != '.')
- {
- if (std::isdigit(mpi_hostname[i]))
- {
- hostnum_str[j++] = mpi_hostname[i];
- }
- i++;
- }
- hostnum_str[j] = '\0';
- if (j == 0)
- {
- hostnum = 0;
- }
- else
- {
- /* Use only the last 9 decimals, so we don't overflow an int */
- hostnum = std::strtol(hostnum_str + std::max(0, j-9), NULL, 10);
- }
-#endif
if (debug)
{
- std::fprintf(debug, "In gmx_hostname_num: hostname '%s', hostnum %d\n",
- mpi_hostname, hostnum);
-#ifdef GMX_TARGET_BGQ
std::fprintf(debug,
"Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\n"
"Node ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
64,
Kernel_ProcessorThreadID(),
4);
-#endif
}
return hostnum;
+}
+#endif
+
+int gmx_physicalnode_id_hash(void)
+{
+ int hash;
+
+#ifndef GMX_MPI
+ hash = 0;
+#else
+#ifdef GMX_THREAD_MPI
+ /* thread-MPI currently puts the thread number in the process name,
+ * we might want to change this, as this is inconsistent with what
+ * most MPI implementations would do when running on a single node.
+ */
+ hash = 0;
+#else
+#ifdef GMX_TARGET_BGQ
+ hash = bgq_nodenum();
+#else
+ hash = mpi_hostname_hash();
#endif
#endif
+#endif
+
+ if (debug)
+ {
+ fprintf(debug, "In gmx_physicalnode_id_hash: hash %d\n", hash);
+ }
+
+ return hash;
}
#ifdef GMX_LIB_MPI
if (bFirst) /* we repeat the check in the locked section because things
might have changed */
{
- if ((temp = getenv("WHERE")) != NULL)
+ if ((temp = getenv("GMX_PRINT_DEBUG_LINES")) != NULL)
{
nskip = strtol(temp, NULL, 10);
}
/* Check whether we should be using buffering (default) or not
* (for debugging)
*/
- if (bUnbuffered || ((bufsize = getenv("LOG_BUFS")) != NULL))
+ if (bUnbuffered || ((bufsize = getenv("GMX_LOG_BUFFER")) != NULL))
{
/* Check whether to use completely unbuffered */
if (bUnbuffered)
#define GMX_UTILITY_REAL_H
/*! \brief Double precision accuracy */
-#define GMX_DOUBLE_EPS 1.11022302E-16
+#define GMX_DOUBLE_EPS 2.2204460492503131e-16
/*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
-#define GMX_DOUBLE_MAX 1.79769312E+308
+#define GMX_DOUBLE_MAX 1.7976931348623157e+308
/*! \brief Minimum double precision value */
-#define GMX_DOUBLE_MIN 2.22507386E-308
+#define GMX_DOUBLE_MIN 2.2250738585072014e-308
/*! \brief Single precision accuracy */
-#define GMX_FLOAT_EPS 5.96046448E-08
+#define GMX_FLOAT_EPS 1.19209290e-07F
/*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
-#define GMX_FLOAT_MAX 3.40282346E+38
+#define GMX_FLOAT_MAX 3.40282346E+38F
/*! \brief Minimum single precision value */
-#define GMX_FLOAT_MIN 1.17549435E-38
+#define GMX_FLOAT_MIN 1.175494351E-38F
/*! \typedef real
gmx_shellfc_t shellfc;
int count, nconverged = 0;
double tcount = 0;
- gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
+ gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
gmx_bool bResetCountersHalfMaxH = FALSE;
gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
gmx_bool bUpdateDoLR;
set_constraints(constr, top, ir, mdatoms, cr);
}
- if (repl_ex_nst > 0)
- {
- /* We need to be sure replica exchange can only occur
- * when the energies are current */
- check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
- "repl_ex_nst", &repl_ex_nst);
- /* This check needs to happen before inter-simulation
- * signals are initialized, too */
- }
if (repl_ex_nst > 0 && MASTER(cr))
{
repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
&& (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
}
+ bDoReplEx = ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step, repl_ex_nst));
+
if (bSimAnn)
{
update_annealing_target_temp(&(ir->opts), t);
do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
- if (do_ene || do_log)
+ if (do_ene || do_log || bDoReplEx)
{
bCalcVir = TRUE;
bCalcEner = TRUE;
/* Replica exchange */
bExchanged = FALSE;
- if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step, repl_ex_nst))
+ if (bDoReplEx)
{
bExchanged = replica_exchange(fplog, cr, repl_ex,
state_global, enerd,
logo->bQuitOnClick = bQuitOnClick;
InitWin(&logo->wd, 0, 0, 360, 270, 1, "GROMACS");
bg = LIGHTGREY;
- if ((newcol = getenv("LOGO")) != NULL)
+ if ((newcol = getenv("GMX_LOGO_COLOR")) != NULL)
{
GetNamedColor(x11, newcol, &bg);
}
title = strdup(argv[0]);
/* First check environment */
- fontname = getenv("GMXFONT");
+ fontname = getenv("GMX_FONT");
display = getenv("DISPLAY");
snew(ARGV, *argc);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff