--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 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
+# 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.
+
+# Sets version information variables and provides CMake functions for
+# generating files based on them
+#
+# This script provides the following basic version variables that need to be
+# maintained manually:
+# GMX_VERSION_MAJOR Major version number.
+# GMX_VERSION_MINOR Minor version number.
+# GMX_VERSION_PATCH Patch version number.
+# Should always be defined: zero for, e.g., 5.0.
+# GMX_VERSION_SUFFIX String suffix to add to numeric version string.
+# "-dev" is automatically added when not building from a source package,
+# and does not need to be kept here.
+# LIBRARY_SOVERSION so version for the built libraries.
+# Should be increased for each binary incompatible release (in GROMACS,
+# the typical policy is to increase it for each major/minor version
+# change, but not for patch releases, even if the latter may not always
+# be fully binary compatible).
+# LIBRARY_VERSION Full library version.
+# REGRESSIONTEST_BRANCH For builds not from source packages, name of the
+# regressiontests branch at gerrit.gromacs.org whose HEAD can test this
+# code, *if* this code is recent enough (i.e., contains all changes from
+# the corresponding code branch that affects the regression test
+# results).
++# REGRESSIONTEST_MD5SUM
++# The MD5 checksum of the regressiontest tarball. Only used when building
++# from a source package.
+# They are collected into a single section below.
+# The following variables are set based on these:
+# GMX_VERSION String composed from GMX_VERSION_* numeric variables
+# above. Example: 4.6.1, 5.0
+# GMX_VERSION_STRING String with GMX_VERSION suffixed with the given
+# suffix and possibly "-dev" for builds not from a source package.
+# GMX_VERSION_NUMERIC Numeric version number (e.g., 40601 for 4.6.1).
+# GMX_API_VERSION Numeric API version.
+# This is currently set automatically to GMX_VERSION_NUMERIC, but may
+# become manually maintained in the future if there will be releases
+# where the API does not change, but programs/libraries do.
+# In such a case, this should be the first version where the current API
+# appeared.
+# REGRESSIONTEST_VERSION For source packages, version number of the
+# matching regressiontests tarball. Not used for builds not from source
+# packages.
+# The latter two are used to generate gromacs/version.h to allow software
+# written against the GROMACS API to provide some #ifdef'ed code to support
+# multiple GROMACS versions.
+#
+# The following variables are defined without manual intervention:
+# SOURCE_IS_SOURCE_DISTRIBUTION The source tree is from a source tarball.
+# SOURCE_IS_GIT_REPOSITORY The source tree is a git repository.
+# Note that both can be false if the tree has been extracted, e.g., as a
+# tarball directly from git.
+#
+# This script also declares machinery to generate and obtain version
+# information from a git repository. This is enabled by default if the source
+# tree is a git, but can be disabled with
+# GMX_GIT_VERSION_INFO Advanced CMake variable to disable git
+# version info generation.
+# The main interface to this machinery is the gmx_configure_version_file()
+# CMake function. The signature is
+# gmx_configure_version_file(<input> <output>
+# [REMOTE_HASH] [SOURCE_FILE]
+# [TARGET <target>]
+# [COMMENT <comment>])
+# <input> Specify the input and output files as for configure_file().
+# <output> The configuration is done with configure_file(... @ONLY) with
+# the following variables defined (as well as all the
+# GMX_VERSION* variables from above):
+# GMX_VERSION_STRING_FULL
+# GMX_VERSION_FULL_HASH
+# GMX_VERSION_CENTRAL_BASE_HASH
+# The output file is created during build time, so any dependent
+# targets should specify it as a dependency.
+# REMOTE_HASH Currently, this has no effect, but it signifies that the
+# <input> file is using the CENTRAL_BASE_HASH variable.
+# This variable is much more expensive to initialize than the
+# others, so this allows local changes in this file to only
+# compute that value when required if that becomes necessary.
+# SOURCE_FILE Signals that <output> will be used as a source file.
+# The function will set properties for the source file
+# appropriately to signify that it is generated.
+# TARGET By default, this function uses add_custom_command() to
+# generate the output file. If TARGET is specified, then
+# add_custom_target() is used to create a target with the given
+# name <target> that runs this custom command. Use this if
+# the same file will be used for multiple downstream targets,
+# or if the explicit target for the file is otherwise
+# necessary.
+# COMMENT Set a custom comment to be shown when building the rule
+# (see add_custom_command(... COMMENT <comment>)).
+# As an alternative to using this script, also the following variables are
+# provided (can be useful when generating more complex CMake scripts that do
+# build-time tasks):
+# VERSION_INFO_CMAKE_SCRIPT
+# Absolute path to a CMake script that can be included using include()
+# to declare the GMX_VERSION_* variables documented for
+# gmx_configure_version_file().
+# VERSION_INFO_DEPS
+# If a custom command depends on VERSION_INFO_CMAKE_SCRIPT, then it
+# should add ${VERSION_INFO_DEPS} to its DEPENDS list to get the
+# appropriate dependencies.
+# TODO: If someone wants to add a custom target that depends on
+# VERSION_INFO_CMAKE_SCRIPT, a separate variable may be needed for those
+# dependencies.
+#
+# The version string printed by 'gmx -version' (and also printed in the startup
+# header) can provide useful information for, e.g., diagnosing bug reports and
+# identifying what exact version the user was using. The following formats are
+# possible (with examples given for a particular version):
+# 4.6.1 Plain version number without any suffix signifies a build from
+# a released source tarball.
+# 4.6.1-dev '-dev' suffix signifies all other builds. If there is no other
+# information, either the user built the code outside any git
+# repository, or disabled the version info generation.
+# 4.6.1-dev-YYYYMMDD-1234abc
+# The YYYYMMDD part shows the commit date (not author date) of
+# the HEAD commit from which the code was built. The abbreviated
+# hash is the hash of that commit (the full hash is available in
+# 'gmx -version' output).
+# If the HEAD hash is not identified as coming from branches in
+# "authoritative" GROMACS repositories, 'gmx -version' will show
+# the nearest ancestor commit that is identified as such (but see
+# the '-local' and '-unknown' suffixes below).
+# 4.6.1-dev-YYYYMMDD-1234abc-dirty
+# As above, but there were local modifications in the source tree
+# when the code was built.
+# 4.6.1-dev-YYYYMMDD-1234abc-unknown
+# As above, but there were no remotes in the repository that
+# could be identified as "authoritative" GROMACS repositories.
+# This happens if the code is not cloned from git.gromacs.org
+# or gerrit.gromacs.org.
+# 4.6.1-dev-YYYYMMDD-1234abc-local
+# As above, but there were no commits in the recent history of
+# the branch that could be identified as coming from
+# "authoritative" GROMACS repositories. This should be
+# relatively rare.
+#
+# Other variables set here are not intended for use outside this file.
+# The scripts gmxGenerateVersionInfo.cmake and gmxConfigureVersionInfo.cmake
+# are used internally by this machinery, as well as VersionInfo.cmake.cmakein.
+
+#####################################################################
+# Basic nature of the source tree
+
+set(SOURCE_IS_GIT_REPOSITORY OFF)
+set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
+if (EXISTS "${PROJECT_SOURCE_DIR}/.git")
+ set(SOURCE_IS_GIT_REPOSITORY ON)
+endif()
+# This file is excluded from CPack source packages, but part of the repository,
+# so it should get included everywhere else.
+if (NOT EXISTS "${PROJECT_SOURCE_DIR}/admin/.isreposource")
+ set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
+endif()
+
+#####################################################################
+# Manually maintained version info
+
+# The GROMACS convention is that these are the version number of the next
+# release that is going to be made from this branch.
+set(GMX_VERSION_MAJOR 5)
+set(GMX_VERSION_MINOR 1)
+set(GMX_VERSION_PATCH 0)
+# The suffix, on the other hand, is used mainly for betas and release
+# candidates, where it signifies the last such release from this branch;
+# it will be empty before the first such release, as well as after the
+# final release is out.
+set(GMX_VERSION_SUFFIX "")
+
+set(LIBRARY_SOVERSION 1)
+set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
+
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
++set(REGRESSIONTEST_MD5SUM "a07524afebca5013540d4f2f72df2dce")
+
+#####################################################################
+# General version management based on manually set numbers
+
+if (GMX_VERSION_PATCH)
+ set(GMX_VERSION "${GMX_VERSION_MAJOR}.${GMX_VERSION_MINOR}.${GMX_VERSION_PATCH}")
+else()
+ set(GMX_VERSION "${GMX_VERSION_MAJOR}.${GMX_VERSION_MINOR}")
+endif()
+set(GMX_VERSION_STRING "${GMX_VERSION}${GMX_VERSION_SUFFIX}")
+if (NOT SOURCE_IS_SOURCE_DISTRIBUTION)
+ set(GMX_VERSION_STRING "${GMX_VERSION_STRING}-dev")
+endif()
+
+set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
+
+math(EXPR GMX_VERSION_NUMERIC
+ "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_MINOR}*100 + ${GMX_VERSION_PATCH}")
+set(GMX_API_VERSION ${NUM_VERSION})
+
+#####################################################################
+# git version info management
+
+# There can be clusters where git and CMake can run on nodes where the other is
+# not available, accessing the same source tree.
+# Should be unlikely, but doesn't hurt to check.
+set(_git_info_default OFF)
+if (SOURCE_IS_GIT_REPOSITORY)
+ find_package(Git)
+ if (GIT_FOUND)
+ set(_git_info_default ON)
+ endif()
+endif()
+option(GMX_GIT_VERSION_INFO "Generate git version information" ${_git_info_default})
+mark_as_advanced(GMX_GIT_VERSION_INFO)
+# Detect preconditions for version info generation if it is requested.
+if (GMX_GIT_VERSION_INFO)
+ if (NOT SOURCE_IS_GIT_REPOSITORY)
+ message(FATAL_ERROR
+ "Cannot generate git version information from source tree not under git. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif()
+ # We need at least git v1.5.3 be able to parse git's date output.
+ if (NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
+ message(FATAL_ERROR
+ "No compatible git version found (>= 1.5.3 required). "
+ "Won't be able to generate development version information. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif()
+endif()
+
+# The first two are also for use outside this file, encapsulating the details
+# of how to use the generated VersionInfo.cmake.
+set(VERSION_INFO_CMAKE_FILE ${PROJECT_BINARY_DIR}/VersionInfo.cmake)
+set(VERSION_INFO_DEPS ${VERSION_INFO_CMAKE_FILE})
+# Capture the location of the necessary files in internal variables for use in
+# the function below.
+set(VERSION_INFO_CMAKEIN_FILE ${CMAKE_CURRENT_LIST_DIR}/VersionInfo.cmake.cmakein)
+set(VERSION_INFO_CONFIGURE_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/gmxConfigureVersionInfo.cmake)
+
+# Rules to create the VersionInfo.cmake file.
+# For git info, the sequence is:
+# 1. (configure time) VersionInfo.cmake.cmakein -> VersionInfo-partial.cmake.cmakein
+# - Set all variables that are known at configure time.
+# 2. (build time) VersionInfo-partial.cmake.cmakein -> VersionInfo.cmake
+# - Set variables that may change as result of repository state changes
+# (i.e., everything that requires running git).
+# - Runs every time as a git-version-info target, but the output file
+# timestamp only changes if its contents actually change.
+# - Depending on the native build system, this may run once per build
+# or once per each time it is required for step 3.
+# 3. (build time) VersionInfo.cmake -> other files
+# - Set variables in files specified with gmx_configure_version_file()
+# using the values generated in step 2.
+# - Each file runs as a custom command that depends on the previous
+# steps, and runs only if the VersionInfo.cmake file is newer than the
+# output file.
+# Without git info, the sequence is:
+# 1. (configure time) VersionInfo.cmake.cmakein -> VersionInfo.cmake
+# - Everything is known at configure time, so the output is generated
+# immediately with all variables set (git info will be empty).
+# 2. (build time) VersionInfo.cmake -> other files
+# - As with git info, processes files from gmx_configure_version_file().
+# - These are again custom commands that depend on the output from
+# step 1, so they get regenerated only when the static version info
+# changes.
+if (GMX_GIT_VERSION_INFO)
+ # Configure information known at this time into a partially filled
+ # version info file.
+ set(VERSION_INFO_CMAKEIN_FILE_PARTIAL
+ ${PROJECT_BINARY_DIR}/VersionInfo-partial.cmake.cmakein)
+ # Leave these to be substituted by the custom target below.
+ set(GMX_VERSION_STRING_FULL "\@GMX_VERSION_STRING_FULL\@")
+ set(GMX_VERSION_FULL_HASH "\@GMX_VERSION_FULL_HASH\@")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "\@GMX_VERSION_CENTRAL_BASE_HASH\@")
+ configure_file(${VERSION_INFO_CMAKEIN_FILE}
+ ${VERSION_INFO_CMAKEIN_FILE_PARTIAL}
+ @ONLY)
+ # If generating the version info, create a target that runs on every build
+ # and does the actual git calls, storing the results into a CMake script.
+ # This needs to be run at build time to update the version information
+ # properly when the git hash changes, but the build system does not.
+ # All targets added by gmx_configure_version_file() use the information
+ # from this script to get their variables from, removing the need to run
+ # git multiple times and simplifying reuse for other purposes.
+ #
+ # Ninja requires all generated files mentioned in dependencies of custom
+ # commands (in gmx_configure_version_info()) to be actually mentioned in
+ # the build system, and luckily add_custom_command() makes that possible.
+ # But it seems impossible to create a robust custom command that would be
+ # always run, so other generators that do not have this constraint simply
+ # use an add_custom_target().
+ if (CMAKE_GENERATOR STREQUAL "Ninja")
+ # The second, phony file is never created, so the rule is always
+ # triggered again. TODO: Figure out why this works, even though ninja
+ # very eagerly complains about missing files.
+ # This unfortunately does not work with the make generator, as
+ # the non-existent second file causes some part of the generated system
+ # erase the first file at the beginning of every build, causing a full
+ # rebuild of the dependencies.
+ add_custom_command(OUTPUT ${VERSION_INFO_CMAKE_FILE} git-version-phony
+ COMMAND ${CMAKE_COMMAND}
+ -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+ -D PROJECT_VERSION=${GMX_VERSION_STRING}
+ -D PROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR}
+ -D VERSION_CMAKEIN=${VERSION_INFO_CMAKEIN_FILE_PARTIAL}
+ -D VERSION_OUT=${VERSION_INFO_CMAKE_FILE}
+ -P ${CMAKE_CURRENT_LIST_DIR}/gmxGenerateVersionInfo.cmake
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ COMMENT "Generating git version information"
+ VERBATIM)
+ # The generated Ninja build system would probably work fine even
+ # without this target, but CMake requires all custom commands to belong
+ # to a target in the same CMakeLists.txt to generate anything for them.
+ add_custom_target(git-version-info DEPENDS ${VERSION_INFO_CMAKE_FILE})
+ else()
+ # For other generators, a target-level dependency on git-version-info
+ # ensures that VERSION_INFO_CMAKE_FILE is created before the dependent
+ # target's dependencies are even evaluated.
+ add_custom_target(git-version-info
+ COMMAND ${CMAKE_COMMAND}
+ -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+ -D PROJECT_VERSION=${GMX_VERSION_STRING}
+ -D PROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR}
+ -D VERSION_CMAKEIN=${VERSION_INFO_CMAKEIN_FILE_PARTIAL}
+ -D VERSION_OUT=${VERSION_INFO_CMAKE_FILE}
+ -P ${CMAKE_CURRENT_LIST_DIR}/gmxGenerateVersionInfo.cmake
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ COMMENT "Generating git version information"
+ VERBATIM)
+ endif()
+ list(APPEND VERSION_INFO_DEPS git-version-info)
+else()
+ # If the version info is static, just generate the CMake script with the
+ # version variables during the CMake run.
+ set(GMX_VERSION_STRING_FULL ${GMX_VERSION_STRING})
+ set(GMX_VERSION_FULL_HASH "")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "")
+ configure_file(${VERSION_INFO_CMAKEIN_FILE} ${VERSION_INFO_CMAKE_FILE})
+endif()
+unset(GMX_VERSION_STRING_FULL)
+unset(GMX_VERSION_FULL_HASH)
+unset(GMX_VERSION_CENTRAL_BASE_HASH)
+
+# The main user-visible interface to the machinery.
+# See documentation at the top of the script.
+function (gmx_configure_version_file INFILE OUTFILE)
+ include(CMakeParseArguments)
+ set(_options REMOTE_HASH SOURCE_FILE)
+ set(_one_value_args COMMENT TARGET)
+ cmake_parse_arguments(ARG "${_options}" "${_one_value_args}" "" ${ARGN})
+ if (ARG_UNPARSED_ARGUMENTS)
+ message(FATAL_ERROR "Unknown arguments: ${ARG_UNPARSED_ARGUMENTS}")
+ endif()
+ # Some callers may pass partial paths that do not really make sense,
+ # so create a default comment that only contains the actual file name.
+ get_filename_component(_basename ${OUTFILE} NAME)
+ set(_comment "Generating ${_basename}")
+ if (ARG_COMMENT)
+ set(_comment ${ARG_COMMENT})
+ endif()
+ # Mimic configure_file()
+ if (NOT IS_ABSOLUTE ${INFILE})
+ set(INFILE ${CMAKE_CURRENT_SOURCE_DIR}/${INFILE})
+ endif()
+ # The touch command is necessary to ensure that after the target is run,
+ # the timestamp is newer than in the input files.
+ add_custom_command(OUTPUT ${OUTFILE}
+ COMMAND ${CMAKE_COMMAND}
+ -D VERSION_VARIABLES=${VERSION_INFO_CMAKE_FILE}
+ -D VERSION_CMAKEIN=${INFILE}
+ -D VERSION_OUT=${OUTFILE}
+ -P ${VERSION_INFO_CONFIGURE_SCRIPT}
+ COMMAND ${CMAKE_COMMAND} -E touch ${OUTFILE}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS ${INFILE} ${VERSION_INFO_DEPS} ${VERSION_INFO_CONFIGURE_SCRIPT}
+ COMMENT "${_comment}"
+ VERBATIM)
+ if (ARG_TARGET)
+ add_custom_target(${ARG_TARGET} DEPENDS ${OUTFILE} VERBATIM)
+ endif()
+ if (ARG_SOURCE_FILE)
+ set_source_files_properties(${OUTFILE} PROPERTIES GENERATED true)
+ endif()
+endfunction()
// The FF macro returns whether or not the bit is set
#define FF(arg) ((Flags & arg) == arg)
- /* Check for double arguments */
- for (i = 1; (i < *argc); i++)
+ try
{
- if (argv[i] && (strlen(argv[i]) > 1) && (!std::isdigit(argv[i][1])))
+ int nicelevel = 0;
+ double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
+ bool bView = false;
+ int xvgFormat = 0;
+ gmx::TimeUnitManager timeUnitManager;
+ gmx::OptionsAdapter adapter(*argc, argv);
+ gmx::Options options(NULL, NULL);
+ gmx::FileNameOptionManager fileOptManager;
+
+ fileOptManager.disableInputOptionChecking(
+ FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
+ options.addManager(&fileOptManager);
- options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
++ options.setDescription(gmx::constArrayRefFromArray<const char *>(desc, ndesc));
+
+ options.addOption(
+ gmx::IntegerOption("nice").store(&nicelevel)
+ .defaultValue(FF(PCA_BE_NICE) ? 19 : 0)
+ .description("Set the nicelevel"));
+
+ if (FF(PCA_CAN_SET_DEFFNM))
{
- for (j = i+1; (j < *argc); j++)
- {
- if ( (argv[i][0] == '-') && (argv[j][0] == '-') &&
- (strcmp(argv[i], argv[j]) == 0) )
- {
- if (FF(PCA_NOEXIT_ON_ARGS))
- {
- fprintf(stderr, "Double command line argument %s\n",
- argv[i]);
- }
- else
- {
- gmx_fatal(FARGS, "Double command line argument %s\n",
- argv[i]);
- }
- }
- }
+ fileOptManager.addDefaultFileNameOption(&options, "deffnm");
}
- }
- debug_gmx();
-
- /* Check ALL the flags ... */
- max_pa = NPCA_PA + EXTRA_PA + npargs+1;
- snew(all_pa, max_pa);
-
- for (i = npall = 0; (i < static_cast<int>(NPCA_PA)); i++)
- {
- npall = add_parg(npall, all_pa, &(pca_pa[i]));
- }
-
- if (FF(PCA_BE_NICE))
- {
- nicelevel = 19;
- }
- npall = add_parg(npall, all_pa, &nice_pa);
-
- if (FF(PCA_CAN_SET_DEFFNM))
- {
- npall = add_parg(npall, all_pa, &deffnm_pa);
- }
- if (FF(PCA_CAN_BEGIN))
- {
- npall = add_parg(npall, all_pa, &begin_pa);
- }
- if (FF(PCA_CAN_END))
- {
- npall = add_parg(npall, all_pa, &end_pa);
- }
- if (FF(PCA_CAN_DT))
- {
- npall = add_parg(npall, all_pa, &dt_pa);
- }
- if (FF(PCA_TIME_UNIT))
- {
- npall = add_parg(npall, all_pa, &time_pa);
- }
- if (FF(PCA_CAN_VIEW))
- {
- npall = add_parg(npall, all_pa, &view_pa);
- }
-
- bXvgr = FALSE;
- for (i = 0; (i < nfile); i++)
- {
- bXvgr = bXvgr || (fnm[i].ftp == efXVG);
- }
- if (bXvgr)
- {
- npall = add_parg(npall, all_pa, &xvg_pa);
- }
-
- /* Now append the program specific arguments */
- for (i = 0; (i < npargs); i++)
- {
- npall = add_parg(npall, all_pa, &(pa[i]));
- }
-
- /* set etENUM options to default */
- for (i = 0; (i < npall); i++)
- {
- if (all_pa[i].type == etENUM)
+ if (FF(PCA_CAN_BEGIN))
{
- all_pa[i].u.c[0] = all_pa[i].u.c[1];
+ options.addOption(
+ gmx::DoubleOption("b").store(&tbegin).timeValue()
+ .description("First frame (%t) to read from trajectory"));
}
- }
- set_default_time_unit(time_units, FF(PCA_TIME_UNIT));
- set_default_xvg_format(xvg_format);
-
- /* Now parse all the command-line options */
- get_pargs(argc, argv, npall, all_pa);
-
- /* set program name, command line, and default values for output options */
- output_env_init(oenv, gmx::getProgramContext(), (time_unit_t)nenum(time_units), bView,
- (xvg_format_t)nenum(xvg_format), 0, debug_level);
-
- /* Parse the file args */
- parse_file_args(argc, argv, nfile, fnm, deffnm, !FF(PCA_NOT_READ_NODE));
-
- /* Open the debug file */
- if (debug_level > 0)
- {
- char buf[256];
-
- if (gmx_mpi_initialized())
+ if (FF(PCA_CAN_END))
{
- sprintf(buf, "%s%d.debug", output_env_get_short_program_name(*oenv),
- gmx_node_rank());
+ options.addOption(
+ gmx::DoubleOption("e").store(&tend).timeValue()
+ .description("Last frame (%t) to read from trajectory"));
}
- else
+ if (FF(PCA_CAN_DT))
+ {
+ options.addOption(
+ gmx::DoubleOption("dt").store(&tdelta).timeValue()
+ .description("Only use frame when t MOD dt = first time (%t)"));
+ }
+ if (FF(PCA_TIME_UNIT))
+ {
+ timeUnitManager.setTimeUnitFromEnvironment();
+ timeUnitManager.addTimeUnitOption(&options, "tu");
+ }
+ if (FF(PCA_CAN_VIEW))
{
- sprintf(buf, "%s.debug", output_env_get_short_program_name(*oenv));
+ options.addOption(
+ gmx::BooleanOption("w").store(&bView)
+ .description("View output [TT].xvg[tt], [TT].xpm[tt], "
+ "[TT].eps[tt] and [TT].pdb[tt] files"));
}
- init_debug(debug_level, buf);
- fprintf(stderr, "Opening debug file %s (src code file %s, line %d)\n",
- buf, __FILE__, __LINE__);
- }
+ bool bXvgr = false;
+ for (int i = 0; i < nfile; i++)
+ {
+ bXvgr = bXvgr || (fnm[i].ftp == efXVG);
+ }
+ xvgFormat = gmx::getDefaultXvgFormat(xvg_formats);
+ if (bXvgr)
+ {
+ options.addOption(
+ gmx::StringOption("xvg").enumValue(xvg_formats)
+ .storeEnumIndex(&xvgFormat)
+ .description("xvg plot formatting"));
+ }
- /* Now copy the results back... */
- for (i = 0, k = npall-npargs; (i < npargs); i++, k++)
- {
- memcpy(&(pa[i]), &(all_pa[k]), (size_t)sizeof(pa[i]));
- }
+ /* Now append the program specific arguments */
+ for (int i = 0; i < nfile; i++)
+ {
+ adapter.filenmToOptions(&options, &fnm[i]);
+ }
+ for (int i = 0; i < npargs; i++)
+ {
+ adapter.pargsToOptions(&options, &pa[i]);
+ }
- bool bExit = false;
- try
- {
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
- bExit = (context != NULL);
- if (context != NULL && !(FF(PCA_QUIET)))
+ if (context != NULL)
{
- gmx::Options options(NULL, NULL);
- options.setDescription(gmx::constArrayRefFromArray(desc, ndesc));
- for (i = 0; i < nfile; i++)
- {
- gmx::filenmToOptions(&options, &fnm[i]);
- }
- for (i = 0; i < npall; i++)
- {
- gmx::pargsToOptions(&options, &all_pa[i]);
- }
+ GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
+ "Help output should be handled higher up and "
+ "only get called only on the master rank");
gmx::CommandLineHelpWriter(options)
.setShowDescriptions(true)
- .setTimeUnitString(output_env_get_time_unit(*oenv))
+ .setTimeUnitString(timeUnitManager.timeUnitAsString())
- .setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
+ .setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
.writeHelp(*context);
+ return FALSE;
}
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- /* Set the nice level */
+ /* Now parse all the command-line options */
+ gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
+ .parse(argc, argv);
+ options.finish();
+
+ /* set program name, command line, and default values for output options */
+ output_env_init(oenv, gmx::getProgramContext(),
+ (time_unit_t)(timeUnitManager.timeUnit() + 1), bView,
+ (xvg_format_t)(xvgFormat + 1), 0);
+
+ /* Set the nice level */
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
- /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
- if (nicelevel != 0 && !bExit)
- {
- static gmx_bool nice_set = FALSE; /* only set it once */
- static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
- tMPI_Thread_mutex_lock(&init_mutex);
- if (!nice_set)
+ /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
+ if (nicelevel != 0)
{
- if (nice(nicelevel) == -1)
+ static gmx_bool nice_set = FALSE; /* only set it once */
+ static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+ tMPI_Thread_mutex_lock(&init_mutex);
+ if (!nice_set)
{
- /* Do nothing, but use the return value to avoid warnings. */
+ if (nice(nicelevel) == -1)
+ {
+ /* Do nothing, but use the return value to avoid warnings. */
+ }
+ nice_set = TRUE;
}
- nice_set = TRUE;
+ tMPI_Thread_mutex_unlock(&init_mutex);
}
- tMPI_Thread_mutex_unlock(&init_mutex);
- }
#endif
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff