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}
% 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
#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
"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);
/* 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)
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 (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);
}
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);
/* 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);
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