#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, 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.
add_subdirectory(analysisdata)
add_subdirectory(selection)
add_subdirectory(trajectoryanalysis)
+ add_subdirectory(energyanalysis)
add_subdirectory(tools)
endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015,2016,2017, 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
+# 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.
+#
+# 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.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# 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.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015,2016,2017, 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
+# 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.
+#
+# 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.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# 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.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(EnergyAnalysisUnitTests energyanalysis-test
+ legacyenergy.cpp
+)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, 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
+ * 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.
+ *
+ * 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.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * 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.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx energy
+ *
+ * \todo These will be superseded by tests of the energyanalysis
+ * modules.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+
+#include "gmxpre.h"
+
+#include <cstring>
+
+#include <string>
+
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/path.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/xvgtest.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+class DhdlTest : public IntegrationTestFixture
+{
+ public:
+ DhdlTest() : data_(), checker_(data_.rootChecker()) {}
+
+ void runTest()
+ {
+ CommandLine caller;
+ caller.append("energy");
+
+ caller.addOption("-s", fileManager_.getInputFilePath("dhdl.tpr"));
+ caller.addOption("-f", fileManager_.getInputFilePath("dhdl.edr"));
+
+ std::string xvgFileName = fileManager_.getTemporaryFilePath("dhdl.xvg");
+ caller.addOption("-odh", xvgFileName);
+
+ EXPECT_EQ(0, gmx_energy(caller.argc(), caller.argv()));
+
+ EXPECT_TRUE(Path::exists(xvgFileName));
+ TextInputFile xvgFile(xvgFileName);
+ XvgMatchSettings settings;
+ auto outputFilesChecker = checker_.checkCompound("OutputFiles", "Files");
+ auto fileChecker = outputFilesChecker.checkCompound("File", "-o");
+ checkXvgFile(&xvgFile, &fileChecker, settings);
+ }
+
+ TestReferenceData data_;
+ TestReferenceChecker checker_;
+};
+
+TEST_F(DhdlTest, ExtractDhdl)
+{
+ runTest();
+}
+
+class EnergyTest : public IntegrationTestFixture
+{
+ public:
+ EnergyTest() : data_(), checker_(data_.rootChecker()) {}
+
+ void runTest(const char *stringForStdin)
+ {
+ CommandLine caller;
+ caller.append("energy");
+
+ caller.addOption("-f", fileManager_.getInputFilePath("ener.edr"));
+
+ std::string xvgFileName = fileManager_.getTemporaryFilePath("energy.xvg");
+ caller.addOption("-o", xvgFileName);
+
+ redirectStringToStdin(stringForStdin);
+ EXPECT_EQ(0, gmx_energy(caller.argc(), caller.argv()));
+
+ EXPECT_TRUE(Path::exists(xvgFileName));
+ TextInputFile xvgFile(xvgFileName);
+ XvgMatchSettings settings;
+ auto outputFilesChecker = checker_.checkCompound("OutputFiles", "Files");
+ auto fileChecker = outputFilesChecker.checkCompound("File", "-o");
+ checkXvgFile(&xvgFile, &fileChecker, settings);
+ }
+
+ TestReferenceData data_;
+ TestReferenceChecker checker_;
+};
+
+TEST_F(EnergyTest, ExtractEnergy)
+{
+ runTest("Potential\nKinetic-En.\nTotal-Energy\n");
+}
+
+TEST_F(EnergyTest, ExtractEnergyByNumber)
+{
+ runTest("4 6 9");
+}
+
+TEST_F(EnergyTest, ExtractEnergyMixed)
+{
+ runTest("Pressu\n7\nbox-z\nvol\n");
+}
+
+class ViscosityTest : public IntegrationTestFixture
+{
+ public:
+ ViscosityTest() : data_(), checker_(data_.rootChecker()) {}
+
+ std::string addFileToTest(CommandLine *caller,
+ const char *optionName,
+ const char *outputFileName)
+ {
+ std::string xvgFileName = fileManager_.getTemporaryFilePath(outputFileName);
+ caller->addOption(optionName, xvgFileName);
+ return xvgFileName;
+ }
+
+ void runTest(const char *optionName,
+ const char *outputFileName)
+ {
+ CommandLine caller;
+ caller.append("energy");
+
+ caller.addOption("-f", fileManager_.getInputFilePath("ener.edr"));
+ caller.addOption("-vis", fileManager_.getTemporaryFilePath("visco.xvg"));
+
+ std::string xvgFileNameToTest;
+
+ /* -vis can write a lot of non-conditional output files,
+ so we use temporary paths to clean up files that are
+ not the ones being tested in this test */
+ if (0 == std::strcmp(optionName, "-evisco"))
+ {
+ xvgFileNameToTest = addFileToTest(&caller, optionName, outputFileName);
+ }
+ else
+ {
+ caller.addOption("-evisco", fileManager_.getTemporaryFilePath("evisco"));
+ }
+ if (0 == std::strcmp(optionName, "-eviscoi"))
+ {
+ xvgFileNameToTest = addFileToTest(&caller, optionName, outputFileName);
+ }
+ else
+ {
+ caller.addOption("-eviscoi", fileManager_.getTemporaryFilePath("eviscoi"));
+ }
+ if (0 == std::strcmp(optionName, "-corr"))
+ {
+ xvgFileNameToTest = addFileToTest(&caller, optionName, outputFileName);
+ }
+ else
+ {
+ caller.addOption("-corr", fileManager_.getTemporaryFilePath("enecorr"));
+ }
+
+ caller.addOption("-o", fileManager_.getTemporaryFilePath("energy"));
+
+ EXPECT_EQ(0, gmx_energy(caller.argc(), caller.argv()));
+
+ EXPECT_TRUE(Path::exists(xvgFileNameToTest));
+ TextInputFile xvgFile(xvgFileNameToTest);
+ XvgMatchSettings settings;
+ settings.tolerance = relativeToleranceAsFloatingPoint(1e-4, 1e-5);
+ auto outputFilesChecker = checker_.checkCompound("OutputFiles", "Files");
+ auto fileChecker = outputFilesChecker.checkCompound("File", "-o");
+ checkXvgFile(&xvgFile, &fileChecker, settings);
+ }
+
+ TestReferenceData data_;
+ TestReferenceChecker checker_;
+};
+
+TEST_F(ViscosityTest, EinsteinViscosity)
+{
+ runTest("-evisco", "evisco.xvg");
+}
+
+TEST_F(ViscosityTest, EinsteinViscosityIntegral)
+{
+ runTest("-eviscoi", "eviscoi.xvg");
+}
+
+} // namespace
+} // namespace
+} // namespace
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "dH/d\xl\f{} and \xD\f{}H"
+xaxis label "Time (ps)"
+yaxis label "dH/d\xl\f{} and \xD\f{}H (kJ/mol [\xl\f{}]\S-1\N)"
+TYPE xy
+subtitle "T = 300 (K) \xl\f{} state 0: (mass-lambda, coul-lambda, vdw-lambda, bonded-lambda, restraint-lambda) = (0.0000, 0.0000, 0.0000, 0.0000, 0.0000)"
+s0 legend "Total Energy (kJ/mol)"
+s1 legend "dH/d\xl\f{} mass-lambda = 0.0000"
+s2 legend "dH/d\xl\f{} coul-lambda = 0.0000"
+s3 legend "dH/d\xl\f{} vdw-lambda = 0.0000"
+s4 legend "dH/d\xl\f{} bonded-lambda = 0.0000"
+s5 legend "dH/d\xl\f{} restraint-lambda = 0.0000"
+s6 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 0.0000, 0.0000, 0.0000)"
+s7 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 0.0500, 0.0000, 0.0000)"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
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#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/strconvert.h"
static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
static const int NOTSET = -23451;
gmx_bool bHaveSums;
} enerdata_t;
+static void done_enerdata_t(int nset, enerdata_t *edat)
+{
+ sfree(edat->step);
+ sfree(edat->steps);
+ sfree(edat->points);
+ for (int i = 0; i < nset; i++)
+ {
+ sfree(edat->s[i].ener);
+ sfree(edat->s[i].es);
+ }
+ sfree(edat->s);
+}
+
static double mypow(double x, double y)
{
if (x > 0)
/* all we need is the ir to be able to write the label */
read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, &mtop);
+ done_mtop(&mtop);
}
static void get_orires_parms(const char *topnm, t_inputrec *ir,
return esum;
}
-static char *ee_pr(double ee, char *buf)
+static void ee_pr(double ee, int buflen, char *buf)
{
- char tmp[100];
- double rnd;
-
- if (ee < 0)
- {
- sprintf(buf, "%s", "--");
- }
- else
+ snprintf(buf, buflen, "%s", "--");
+ if (ee >= 0)
{
/* Round to two decimals by printing. */
- sprintf(tmp, "%.1e", ee);
- sscanf(tmp, "%lf", &rnd);
- sprintf(buf, "%g", rnd);
+ char tmp[100];
+ snprintf(tmp, sizeof(tmp), "%.1e", ee);
+ double rnd = gmx::doubleFromString(tmp);
+ snprintf(buf, buflen, "%g", rnd);
}
-
- return buf;
}
static void remove_drift(int nset, int nbmin, int nbmax, real dt, enerdata_t *edat)
}
static void analyse_ener(gmx_bool bCorr, const char *corrfn,
+ const char *eviscofn, const char *eviscoifn,
gmx_bool bFee, gmx_bool bSum, gmx_bool bFluct,
gmx_bool bVisco, const char *visfn, int nmol,
gmx_int64_t start_step, double start_t,
totaldrift /= nmol;
}
+ ee_pr(pr_errest, sizeof(eebuf), eebuf);
fprintf(stdout, "%-24s %10g %10s %10g %10g",
- leg[i], pr_aver, ee_pr(pr_errest, eebuf), pr_stddev, totaldrift);
+ leg[i], pr_aver, eebuf, pr_stddev, totaldrift);
if (bFee)
{
fprintf(stdout, " %10g", fee[i]);
if (bSum)
{
totaldrift = (edat->nsteps - 1)*esum->s[0].slope;
+ ee_pr(esum->s[0].ee/nmol, sizeof(eebuf), eebuf);
fprintf(stdout, "%-24s %10g %10s %10s %10g (%s)",
- "Total", esum->s[0].av/nmol, ee_pr(esum->s[0].ee/nmol, eebuf),
+ "Total", esum->s[0].av/nmol, eebuf,
"--", totaldrift/nmol, enm[set[0]].unit);
/* pr_aver,pr_stddev,a,totaldrift */
if (bFee)
eneint[2][i+1] = eneint[2][i] + 0.5*(edat->s[5].es[i].sum + edat->s[7].es[i].sum)*Dt/edat->points[i];
}
- einstein_visco("evisco.xvg", "eviscoi.xvg",
+ einstein_visco(eviscofn, eviscoifn,
3, edat->nframes+1, eneint, Vaver, Temp, Dt, oenv);
for (i = 0; i < 3; i++)
}
}
}
-
+ // Clean up!
+ sfree(native_lambda_vec);
+ sfree(lambda_components);
if (nblock_hist == 0 && nblock_dh == 0)
{
/* don't do anything */
{ efXVG, "-oten", "oriten", ffOPTWR },
{ efXVG, "-corr", "enecorr", ffOPTWR },
{ efXVG, "-vis", "visco", ffOPTWR },
+ { efXVG, "-evisco", "evisco", ffOPTWR },
+ { efXVG, "-eviscoi", "eviscoi", ffOPTWR },
{ efXVG, "-ravg", "runavgdf", ffOPTWR },
{ efXVG, "-odh", "dhdl", ffOPTWR }
};
(gmx_strcasecmp(interaction_function[j].longname, leg[i]) == 0);
}
}
-
if (bPrAll && nset > 1)
{
gmx_fatal(FARGS, "Printing averages can only be done when a single set is selected");
}
xvgr_legend(fodt, norsel, (const char**)odtleg, oenv);
}
+ sfree(odtleg);
}
}
if (bOTEN)
while (bCont && (timecheck == 0));
fprintf(stderr, "\n");
- close_enx(fp);
+ done_ener_file(fp);
if (out)
{
xvgrclose(out);
{
double dt = (frame[cur].t-start_t)/(edat.nframes-1);
analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
+ opt2fn("-evisco", NFILE, fnm), opt2fn("-eviscoi", NFILE, fnm),
bFee, bSum, bFluct,
bVisco, opt2fn("-vis", NFILE, fnm),
nmol,
fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm),
reftemp, nset, set, leg, &edat, time, oenv);
}
-
+ // Clean up!
+ done_enerdata_t(nset, &edat);
+ sfree(time);
+ free_enxframe(&frame[0]);
+ free_enxframe(&frame[1]);
+ sfree(frame);
+ free_enxnms(nre, enm);
+ sfree(ppa);
+ sfree(set);
+ sfree(leg);
+ sfree(bIsEner);
{
const char *nxy = "-nxy";
do_view(oenv, opt2fn_null("-oten", NFILE, fnm), nxy);
do_view(oenv, opt2fn_null("-odh", NFILE, fnm), nxy);
}
+ output_env_done(oenv);
+ done_filenms(NFILE, fnm);
return 0;
}
sfree(pull->coord);
}
+static void done_lambdas(t_lambda *fep)
+{
+ if (fep->n_lambda > 0)
+ {
+ for (int i = 0; i < efptNR; i++)
+ {
+ sfree(fep->all_lambda[i]);
+ }
+ sfree(fep->all_lambda);
+ }
+}
+
void done_inputrec(t_inputrec *ir)
{
sfree(ir->opts.nrdf);
sfree(ir->opts.SAsteps);
sfree(ir->opts.bOPT);
sfree(ir->opts.bTS);
+ sfree(ir->opts.egp_flags);
+ done_lambdas(ir->fepvals);
sfree(ir->fepvals);
sfree(ir->expandedvals);
sfree(ir->simtempvals);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff