# NOTE: when releasing the "-dev" suffix needs to be stripped off!
# REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
# defined.
-set(PROJECT_VERSION "5.0-rc1-dev")
+set(PROJECT_VERSION "5.1-dev")
# If this is a released tarball, "-dev" will not be present in
# PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
# number of the regressiontest tarball against which the code tarball
# PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
# gerrit.gromacs.org branch whose HEAD can test this code, *if* this
# code contains all recent fixes from the corresponding code branch.
-set(REGRESSIONTEST_BRANCH "refs/heads/release-5-0")
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "5")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
#SET(CPACK_PACKAGE_VERSION_PATCH "0")
# The numerical gromacs version. It is 40600 for 4.6.0.
@CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.h \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/scanner.cpp @NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN@
EXCLUDE_SYMBOLS = YY* yy* _gmx_sel_yy*
+EXCLUDE_SYMBOLS += __STDC*
EXCLUDE_SYMBOLS += TEST TEST_F TEST_P TYPED_TEST_CASE TYPED_TEST INSTANTIATE_TEST_CASE_P
EXCLUDE_SYMBOLS += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES = YES
# TODO: Add rule to exclude examples from this check
if fileobj.is_installed():
reporter.file_error(fileobj, "source file is installed")
- if fileobj.get_documentation_type() != DocType.internal:
+ if fileobj.get_doc_type() != DocType.internal:
reporter.file_error(fileobj,
"source file documentation appears outside full documentation")
elif fileobj.get_api_type() != DocType.internal:
elif fileobj.is_test_file() and fileobj.is_installed():
reporter.file_error(fileobj, "test file is installed")
elif fileobj.is_installed():
- if fileobj.get_documentation_type() != DocType.public:
+ if fileobj.get_doc_type() != DocType.public:
reporter.file_error(fileobj,
"public header has non-public documentation")
- elif fileobj.get_documentation_type() == DocType.public:
+ elif fileobj.get_doc_type() == DocType.public:
reporter.file_error(fileobj,
"non-installed header has public documentation")
elif fileobj.get_api_type() == DocType.public:
reporter.file_error(fileobj,
"non-installed header specified as part of public API")
- elif fileobj.get_documentation_type() < fileobj.get_api_type():
+ elif fileobj.get_doc_type() < fileobj.get_api_type():
reporter.file_error(fileobj,
"API type ({0}) conflicts with documentation visibility ({1})"
- .format(fileobj.get_api_type(), fileobj.get_documentation_type()))
+ .format(fileobj.get_api_type(), fileobj.get_doc_type()))
if not fileobj.has_brief_description():
reporter.file_error(fileobj,
filemodule = fileobj.get_module()
othermodule = otherfile.get_module()
if fileobj.is_documented() and otherfile.is_documented():
- filetype = fileobj.get_documentation_type()
- othertype = otherfile.get_documentation_type()
+ filetype = fileobj.get_doc_type()
+ othertype = otherfile.get_doc_type()
if filetype > othertype:
reporter.code_issue(includedfile,
"{0} file includes {1} file {2}"
.format(filetype, othertype, includedfile))
- check_api = (othermodule and othermodule.is_documented() and
- filemodule != othermodule)
+ check_api = (otherfile.api_type_is_reliable() and filemodule != othermodule)
if check_api and otherfile.get_api_type() < DocType.library:
reporter.code_issue(includedfile,
"included file {0} is not documented as exposed outside its module"
"""Check documentation for a class/struct/union."""
check_entity(classobj, reporter)
if classobj.is_documented():
- classtype = classobj.get_documentation_type()
- filetype = classobj.get_file_documentation_type()
+ classtype = classobj.get_doc_type()
+ filetype = classobj.get_file_doc_type()
if classtype == DocType.public and not classobj.is_in_installed_file():
reporter.doc_error(classobj,
"has public documentation, but is not in installed header")
"is in {0} file(s), but appears in {1} documentation"
.format(filetype, classtype))
-def check_member(member, reporter):
+def check_member(member, reporter, check_ignored):
"""Check documentation for a generic member."""
check_entity(member, reporter)
if member.is_documented():
- if not member.is_visible():
- # TODO: This is triggered by members in anonymous namespaces.
+ if check_ignored and not member.is_visible():
reporter.doc_note(member,
"is documented, but is ignored by Doxygen, because its scope is not documented")
if member.has_inbody_description():
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
parser.add_option('--check-ignored', action='store_true',
- help='Check documentation ignored by Doxygen')
+ help='Issue notes for comments ignored by Doxygen')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
check_class(classobj, reporter)
for memberobj in tree.get_members():
- if memberobj.is_visible() or options.check_ignored:
- check_member(memberobj, reporter)
+ check_member(memberobj, reporter, options.check_ignored)
reporter.write_pending()
reporter.report_unused_filters()
def __init__(self, name, refid):
Entity.__init__(self, name, refid)
self._parents = set()
+ self._class = None
+ self._namespace = None
+ self._files = set()
+ self._group = None
self._location = None
self._alternates = set()
self._loaded = False
def add_parent_compound(self, compound):
"""Add a compound that contains this member."""
self._parents.add(compound)
+ if isinstance(compound, Class):
+ assert self._class is None
+ self._class = compound
+ elif isinstance(compound, Namespace):
+ assert self._namespace is None
+ self._namespace = compound
+ elif isinstance(compound, File):
+ self._files.add(compound)
+ elif isinstance(compound, Group):
+ assert self._group is None
+ self._group = compound
+ else:
+ assert False
- def _get_raw_location(self):
- """Returns the BodyLocation object associated with this member.
+ def merge_definition(self, definition):
+ """Merge another member into this.
- This is necessary so that EnumValue can override it report a non-empty
- location: Doxygen doesn't provide any location for <enumvalue>.
+ See DocumentationSet.merge_duplicates().
"""
- return self._location
-
- def get_parent_compounds(self):
- return self._parents
-
- def get_inherited_visibility(self):
- return max([parent.get_visibility() for parent in self._parents])
-
- def is_visible(self):
- return self.get_inherited_visibility() != DocType.none
-
- def has_same_body_location(self):
- return self._get_raw_location().has_same_body_location()
-
- def get_reporter_location(self):
- return self._get_raw_location().get_reporter_location()
-
- def get_location(self):
- return self._get_raw_location().get_location()
-
- def get_body_location(self):
- return self._get_raw_location().get_body_location()
-
- def merge_definition(self, definition):
+ assert self._class is None
+ assert definition._class is None
+ assert self._group == definition._group
+ assert self._namespace == definition._namespace
self._parents.update(definition._parents)
+ self._files.update(definition._files)
self._alternates.add(definition)
def load_details_from_element(self, rootelem, xmlpath):
"""
return False
+ def _get_raw_location(self):
+ """Returns the BodyLocation object associated with this member.
+
+ This is necessary so that EnumValue can override it report a non-empty
+ location: Doxygen doesn't provide any location for <enumvalue>.
+ """
+ return self._location
+
+ def get_reporter_location(self):
+ return self._get_raw_location().get_reporter_location()
+
+ def get_location(self):
+ """Return main location for the member.
+
+ This typically corresponds to the declaration.
+ """
+ return self._get_raw_location().get_location()
+
+ def get_body_location(self):
+ """Return location of the body for the member.
+
+ Some types of members do not have a body location, in which case this
+ returns None.
+ """
+ return self._get_raw_location().get_body_location()
+
+ def has_same_body_location(self):
+ """Check whether the main location is the same as body location."""
+ return self._get_raw_location().has_same_body_location()
+
+ def get_namespace(self):
+ return self._namespace
+
+ def get_parent_compounds(self):
+ return self._parents
+
+ def get_inherited_visibility(self):
+ return max([parent.get_visibility() for parent in self._parents])
+
def show(self):
self.show_base()
+ if self._alternates:
+ idlist = [x.get_id() for x in self._alternates]
+ print 'Alt. IDs: {0}'.format(', '.join(idlist))
print 'Parent vis: {0}'.format(self.get_inherited_visibility())
print 'Location: {0}'.format(self.get_location().get_full_string())
print 'Body loc: {0}'.format(self.get_body_location().get_full_string())
contains references to contained compounds, and details of all members
within the compound.
"""
+
def __init__(self, name, refid):
Entity.__init__(self, name, refid)
self._members = dict()
def get_reporter_location(self):
return self._doclocation.get_reporter_location()
+ def is_anonymous(self):
+ return 'anonymous_namespace{' in self.get_name()
+
def show(self):
self.show_base()
print 'Doc. loc.: {0}'.format(self._doclocation.get_full_string())
def merge_duplicates(self):
"""Merge duplicate member definitions based on body location.
- At least for functions that are declared in a header, but have their
- body in a source file, Doxygen seems to create two different IDs, but
- the contents of the members are the same, except for the location
+ At least for some functions that are declared in a header, but have
+ their body in a source file, Doxygen seems to create two different IDs,
+ but the contents of the members are the same, except for the location
attribute. This method merges members that have identical name and
body location into a single member that keeps the information from both
instances (they should only differ in the location attribute and in
def get_groups(self, name):
return self.get_compounds(Group, lambda x: x.get_name() in name)
- def get_namespaces(self, name):
- return self.get_compounds(Namespace, lambda x: x.get_name() in name)
+ def get_namespaces(self, name=None):
+ if name:
+ return self.get_compounds(Namespace, lambda x: x.get_name() in name)
+ else:
+ return self.get_compounds(Namespace)
def get_classes(self, name=None):
if name:
def get_name(self):
return os.path.basename(self._abspath)
- def get_documentation_type(self):
+ def get_doc_type(self):
if not self._rawdoc:
return DocType.none
return self._rawdoc.get_visibility()
def get_api_type(self):
return self._apitype
+ def api_type_is_reliable(self):
+ if self._apitype > DocType.internal:
+ return True
+ module = self.get_module()
+ return module and module.is_documented()
+
+ def is_public(self):
+ if self.api_type_is_reliable():
+ return self.get_api_type() == DocType.public
+ return self.get_api_type() == DocType.public or self.is_installed()
+
+ def is_module_internal(self):
+ if self.is_source_file():
+ return True
+ return not self.is_installed() and self.get_api_type() <= DocType.internal
+
def get_expected_module(self):
return self._dir.get_module()
def get_group(self):
return self._group
+class Namespace(object):
+
+ """Namespace in the GROMACS source code."""
+
+ def __init__(self, rawdoc):
+ self._rawdoc = rawdoc
+
+ def is_anonymous(self):
+ return self._rawdoc.is_anonymous()
class Class(object):
def has_brief_description(self):
return self._rawdoc.has_brief_description()
- def get_documentation_type(self):
+ def get_doc_type(self):
+ """Return documentation type (visibility) for the class.
+
+ In addition to the actual code, this encodes GROMACS-specific logic
+ of setting EXTRACT_LOCAL_CLASSES=YES only for the full documentation.
+ Local classes never appear outside the full documentation, no matter
+ what is their visibility.
+ """
if not self.is_documented():
return DocType.none
if self._rawdoc.is_local():
return DocType.internal
return self._rawdoc.get_visibility()
- def get_file_documentation_type(self):
- return max([fileobj.get_documentation_type() for fileobj in self._files])
+ def get_file_doc_type(self):
+ return max([fileobj.get_doc_type() for fileobj in self._files])
def is_in_installed_file(self):
return any([fileobj.is_installed() for fileobj in self._files])
+class Member(object):
+
+ """Member (in Doxygen terminology) in the GROMACS source tree.
+
+ Currently, modeling is limited to the minimal set of properties that the
+ checker uses.
+ """
+
+ def __init__(self, rawdoc, namespace):
+ self._rawdoc = rawdoc
+ self._namespace = namespace
+
+ def get_name(self):
+ return self._rawdoc.get_name()
+
+ def get_reporter_location(self):
+ return self._rawdoc.get_reporter_location()
+
+ def is_documented(self):
+ return self._rawdoc.is_documented()
+
+ def has_brief_description(self):
+ return self._rawdoc.has_brief_description()
+
+ def has_inbody_description(self):
+ return self._rawdoc.has_inbody_description()
+
+ def is_visible(self):
+ """Return whether the member is visible in Doxygen documentation.
+
+ Doxygen ignores members whose parent compounds are not documented.
+ However, when EXTRACT_ANON_NPACES=ON (which is set for our full
+ documentation), members of anonymous namespaces are extracted even if
+ the namespace is the only parent and is not documented.
+ """
+ if self._namespace and self._namespace.is_anonymous():
+ return True
+ return self._rawdoc.get_inherited_visibility() != DocType.none
+
+
class GromacsTree(object):
"""Root object for navigating the GROMACS source tree.
self._files = dict()
self._modules = dict()
self._classes = set()
+ self._namespaces = set()
+ self._members = set()
self._walk_dir(os.path.join(self._source_root, 'src'))
rootdir = self._get_dir(os.path.join('src', 'gromacs'))
for subdir in rootdir.get_subdirectories():
self._load_modules()
self._load_files()
if not only_files:
+ self._load_namespaces()
self._load_classes()
+ self._load_members()
def _load_dirs(self):
"""Load Doxygen XML directory information."""
fileobj.set_doc_xml(filedoc, self)
self._docmap[filedoc] = fileobj
+ def _load_namespaces(self):
+ """Load Doxygen XML namespace information."""
+ nsdocs = self._docset.get_namespaces()
+ for nsdoc in nsdocs:
+ nsobj = Namespace(nsdoc)
+ self._docmap[nsdoc] = nsobj
+ self._namespaces.add(nsobj)
+
def _load_classes(self):
"""Load Doxygen XML class information."""
classdocs = self._docset.get_classes()
self._docmap[classdoc] = classobj
self._classes.add(classobj)
+ def _load_members(self):
+ """Load Doxygen XML member information."""
+ memberdocs = self._docset.get_members()
+ for memberdoc in memberdocs:
+ nsdoc = memberdoc.get_namespace()
+ nsobj = self.get_object(nsdoc)
+ memberobj = Member(memberdoc, nsobj)
+ self._docmap[memberdoc] = memberobj
+ self._members.add(memberobj)
+
def _get_dir(self, relpath):
"""Get directory object for a path relative to source tree root."""
return self._dirs.get(relpath)
def get_object(self, docobj):
"""Get tree object for a Doxygen XML object."""
+ if docobj is None:
+ return None
return self._docmap.get(docobj)
def get_files(self):
def get_members(self):
"""Get iterable for all members (in Doxygen terms) in the source tree."""
- # TODO: Add wrappers to solve some issues.
- return self._docset.get_members()
+ return self._members
gmxtree.
"""
intramodule = (fromfile.get_module() == tofile.get_module())
- is_legacy = not tofile.get_module().is_documented()
+ is_legacy = not tofile.api_type_is_reliable()
if fromfile.get_module() == tofile.get_module():
edgetype = EdgeType.intramodule
- elif tofile.get_api_type() == DocType.internal:
+ elif tofile.get_api_type() == DocType.internal and not tofile.is_public():
if is_legacy:
edgetype = EdgeType.legacy
else:
edgetype = EdgeType.test
elif tofile.is_test_file():
edgetype = EdgeType.undocumented
- elif fromfile.is_source_file() or \
- (fromfile.get_api_type() <= DocType.internal and \
- not fromfile.is_installed()):
- if tofile.get_api_type() == DocType.public:
+ elif fromfile.is_module_internal():
+ if tofile.is_public():
edgetype = EdgeType.pubimpl
elif tofile.get_api_type() == DocType.library:
edgetype = EdgeType.libimpl
- elif is_legacy or not tofile.is_documented():
+ elif is_legacy:
edgetype = EdgeType.legacy
+ elif not tofile.is_documented():
+ edgetype = EdgeType.undocumented
else:
raise ValueError('Unknown edge type between {0} and {1}'
- .format(fromfile.path, tofile.path))
+ .format(fromfile.get_relpath(), tofile.get_relpath()))
elif fromfile.get_api_type() == DocType.library:
edgetype = EdgeType.library
- elif fromfile.get_api_type() == DocType.public or fromfile.is_installed():
- if tofile.get_api_type() == DocType.public or \
- tofile.get_documentation_type() == DocType.public or \
- (tofile.is_installed() and not tofile.is_documented()):
+ elif fromfile.is_public() or fromfile.is_installed():
+ if tofile.is_public() or tofile.is_installed():
edgetype = EdgeType.public
else:
edgetype = EdgeType.undocumented
+ elif is_legacy:
+ edgetype = EdgeType.legacy
else:
raise ValueError('Unknown edge type between {0} and {1}'
- .format(fromfile.path, tofile.path))
+ .format(fromfile.get_relpath(), tofile.get_relpath()))
return Edge(filenodes[fromfile], filenodes[tofile], edgetype)
def _create_file_edges(self, filenodes):
edges.append(edge)
return edges
+ def _get_module_color(self, modulegroup):
+ if modulegroup == 'legacy':
+ return 'fillcolor=grey75'
+ elif modulegroup == 'analysismodules':
+ return 'fillcolor="0 .2 1"'
+ elif modulegroup == 'utilitymodules':
+ return 'fillcolor=".08 .2 1"'
+ elif modulegroup == 'mdrun':
+ return 'fillcolor=".75 .2 1"'
+ return None
+
def _create_module_node(self, module, filenodes):
"""Create node for a module.
properties.append('shape=ellipse')
properties.append('URL="\\ref module_{0}"'.format(module.get_name()))
if not module.is_documented():
+ fillcolor = self._get_module_color('legacy')
+ else:
+ fillcolor = self._get_module_color(module.get_group())
+ if fillcolor:
style.append('filled')
- properties.append('fillcolor=grey75')
- elif module.get_group() == 'analysismodules':
- style.append('filled')
- properties.append('fillcolor="0 .2 1"')
- elif module.get_group() == 'utilitymodules':
- style.append('filled')
- properties.append('fillcolor=".08 .2 1"')
- elif module.get_group() == 'mdrun':
- style.append('filled')
- properties.append('fillcolor=".75 .2 1"')
+ properties.append(fillcolor)
rootdir = module.get_root_dir()
if rootdir.has_installed_files():
properties.append('color=".66 .5 1"')
node.add_child(self._create_file_node(childfile, filenodes))
return node
+ def _create_legend_node(self, label, modulegroup):
+ if modulegroup:
+ nodename = 'legend_' + modulegroup
+ fillcolor = self._get_module_color(modulegroup)
+ else:
+ nodename = 'legend_' + label
+ fillcolor = None
+ style = []
+ properties = []
+ if fillcolor:
+ style.append('filled')
+ properties.append(fillcolor)
+ return Node(nodename, label, style, properties)
+
def create_modules_graph(self):
"""Create module dependency graph."""
filenodes = dict()
nodes.append(node)
modulenodes.append(node)
edges = self._create_file_edges(filenodes)
+ # TODO: Consider adding invisible edges to order the nodes better.
+ # TODO: Consider adding legend for the edge types as well.
+ legendnode = Node('legend', 'legend')
+ legendnode.add_child(self._create_legend_node('legacy', 'legacy'))
+ legendnode.add_child(self._create_legend_node('analysis', 'analysismodules'))
+ legendnode.add_child(self._create_legend_node('utility', 'utilitymodules'))
+ legendnode.add_child(self._create_legend_node('mdrun', 'mdrun'))
+ legendnode.add_child(Node('legend_installed', 'installed', properties=['color=".66 .5 1"', 'penwidth=3']))
+ nodes.append(legendnode)
graph = Graph(nodes, edges)
for node in modulenodes:
graph.collapse_node(node)
So, you want to build the manual? This is now easy.
1. Configure the main GROMACS repo with GMX_BUILD_MANUAL=on
-2. cmake will run some detection about whetehr this is possible
+2. cmake will run some detection about whether this is possible
3. Later, use "make manual," which will build GROMACS in the
usual way, and use the generated binaries to build the manual.
-398
+399
If You Want Something Done You Have to Do It Yourself_(Highlander II)
I Live the Life They Wish They Did_(Tricky)
Jesus Built My Hotrod_(Ministry)
It was something to at least have a choice of nightmares_(Joseph Conrad)
You fight, work, sweat, nearly kill yourself, sometimes you do kill yourself, trying to accomplish something - and you can't._(Joseph Conrad)
And after some more talk we agreed that the wisdom of rats had been grossly overrated, being in fact no greater than that of men_(Joseph Conrad)
+It's an easy game, just don't let the ball past!_(Szilard Pall)
K Ion
NA Ion
CA Ion
-MK Ion
+MG Ion
CL Ion
ZN Ion
CU1 Ion
#include <stdio.h>
#include <string.h>
#include <math.h>
-#include "main.h"
+
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "sysstuff.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/utility/smalloc.h"
#endif
#include "typedefs.h"
-#include "main.h"
#include "vec.h"
#include "txtdump.h"
#include "ns.h"
#include "gromacs/utility/smalloc.h"
#include "wnblist.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include <config.h>
#endif
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/matio.h"
#include "index.h"
#include "gstat.h"
#include <stdlib.h>
#include "errno.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "physics.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "vec.h"
#include "names.h"
#include "ehdata.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "physics.h"
#include "ehdata.h"
#include "macros.h"
#include "copyrite.h"
#include "gromacs/commandline/pargs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "physics.h"
-#include "xvgr.h"
#include "vec.h"
#include "names.h"
#include "ehdata.h"
#include <config.h>
#endif
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
#include "physics.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "copyrite.h"
-#include "xvgr.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
#include "rmpbc.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "index.h"
#include "nrnb.h"
#include "gstat.h"
#include "gromacs/fileio/matio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define G_REF1 0
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/pdbio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "copyrite.h"
-#include "main.h"
#include "nrnb.h"
#include "txtdump.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "mdatoms.h"
#include "coulomb.h"
#include "rmpbc.h"
#include "pme.h"
#include "force.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "pbc.h"
#include "gromacs/utility/gmxmpi.h"
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/fileio/pdbio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void my_func(char *msg)
{
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "complex.h"
#include "fftgrid.h"
#include "mdrun.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/writeps.h"
#include "copyrite.h"
-#include "xvgr.h"
#include "minvert.h"
#include "pppm.h"
#include "readinp.h"
-#include "main.h"
#include "force.h"
#include "nrnb.h"
#include "coulomb.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "mdrun.h"
#include "main.h"
#include "gromacs/legacyheaders/oenv.h"
#include "gromacs/legacyheaders/vec.h"
-#include "gromacs/legacyheaders/xvgr.h"
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/options/timeunitmanager.h"
#include <utility>
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/network.h"
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinehelpmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
#include "thread_mpi/mutex.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
namespace gmx
#include "thread_mpi/threads.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/network.h"
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinehelpwriter.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
}
}
}
- debug_gmx();
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs+1;
#include <gtest/gtest.h>
#include "gromacs/commandline/cmdlineprogramcontext.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/utility/common.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/uniqueptr.h"
#include "testutils/cmdlinetest.h"
#include "mtop_util.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/gmxfio.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/linearalgebra/nrjac.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* We use the same defines as in mvdata.c here */
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#define GMX_ESSENTIALDYNAMICS_EDSAM_H
#include "typedefs.h"
+#include "gromacs/fileio/filenm.h"
#ifdef __cplusplus
extern "C" {
#include <errno.h>
#include "types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fft/fft.h"
#include "gromacs/math/gmxcomplex.h"
FILE* debug = 0;
#endif
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef GMX_FFT_FFTW3
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 "gromacs/fft/fft.h"
#include "gromacs/legacyheaders/types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "external/fftpack/fftpack.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 <fftw3.h>
#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef GMX_DOUBLE
#define FFTWPREFIX(name) fftw_ ## name
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 <mkl_service.h>
#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* For MKL version (<10.0), we should define MKL_LONG. */
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "fft5d.h"
confio.h
enxio.h
filenm.h
- futil.h
gmxfio.h
matio.h
mdoutf.h
trxio.h
xdr_datatype.h
xtcio.h
+ xvgr.h
)
gmx_install_headers(fileio ${FILEIO_PUBLIC_HEADERS})
#endif
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include <errno.h>
#include "macros.h"
#include "gromacs/utility/cstringutil.h"
#include "confio.h"
#include "vec.h"
#include "symtab.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "xdrf.h"
#include "filenm.h"
#include "pdbio.h"
#include "tpxio.h"
#include "trxio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "copyrite.h"
#include "pbc.h"
#include "mtop_util.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
-#include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gmxfio.h"
#include "enxio.h"
{
if (sb->fval_alloc)
{
- free(sb->fval);
+ sfree(sb->fval);
sb->fval_alloc = 0;
sb->fval = NULL;
}
if (sb->dval_alloc)
{
- free(sb->dval);
+ sfree(sb->dval);
sb->dval_alloc = 0;
sb->dval = NULL;
}
if (sb->ival_alloc)
{
- free(sb->ival);
+ sfree(sb->ival);
sb->ival_alloc = 0;
sb->ival = NULL;
}
if (sb->lval_alloc)
{
- free(sb->lval);
+ sfree(sb->lval);
sb->lval_alloc = 0;
sb->lval = NULL;
}
if (sb->cval_alloc)
{
- free(sb->cval);
+ sfree(sb->cval);
sb->cval_alloc = 0;
sb->cval = NULL;
}
{
if (sb->sval[i])
{
- free(sb->sval[i]);
+ sfree(sb->sval[i]);
}
}
- free(sb->sval);
+ sfree(sb->sval);
sb->sval_alloc = 0;
sb->sval = NULL;
}
{
enxsubblock_free(&(eb->sub[i]));
}
- free(eb->sub);
+ sfree(eb->sub);
eb->nsub_alloc = 0;
eb->sub = NULL;
}
{
enxblock_free(&(fr->block[b]));
}
- free(fr->block);
+ sfree(fr->block);
}
void add_blocks_enxframe(t_enxframe *fr, int n)
#include <stdlib.h>
#include <string.h>
-#include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 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.
- *
- * 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.
- */
-
-#ifndef GMX_FILEIO_FUTIL_H
-#define GMX_FILEIO_FUTIL_H
-
-#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-/* Native windows uses backslash path separators.
- * Cygwin and everybody else in the world use slash.
- */
-#include "../utility/gmx_header_config.h"
-#ifdef GMX_NATIVE_WINDOWS
-#define DIR_SEPARATOR '\\'
-#else
-#define DIR_SEPARATOR '/'
-#endif
-
-/* Now get the maximum path size. */
-#ifdef PATH_MAX
-# define GMX_PATH_MAX PATH_MAX
-#elif defined MAX_PATH
-# define GMX_PATH_MAX MAX_PATH
-#else
-# define GMX_PATH_MAX 4096
-#endif
-
-typedef gmx_int64_t gmx_off_t;
-
-void no_buffers(void);
-/* Turn off buffering of files (which is default) for debugging purposes */
-
-gmx_bool gmx_fexist(const char *fname);
-/* Return TRUE when fname exists, FALSE otherwise */
-
-gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr);
-/* Return TRUE when fname exists, FALSE otherwise, bcast from master to others */
-
-gmx_bool gmx_eof(FILE *fp);
-/* Return TRUE on end-of-file, FALSE otherwise */
-
-gmx_bool is_pipe(FILE *fp);
-/* Check whether the file (opened by gmx_ffopen) is a pipe */
-
-/* Make a backup of file if necessary.
- Return false if there was a problem.
- */
-gmx_bool make_backup(const char * file);
-
-FILE *gmx_ffopen(const char *file, const char *mode);
-/* Return a valid file pointer when successful, exits otherwise
- * If the file is in compressed format, open a pipe which uncompresses
- * the file! Therefore, files must be closed with gmx_ffclose (see below)
- */
-
-int gmx_ffclose(FILE *fp);
-/* Close files or pipes */
-
-
-void frewind(FILE *fp);
-/* Does not rewind pipes, but does so for normal files */
-
-#define rewind frewind
-
-
-int gmx_fseek(FILE *stream, gmx_off_t offset, int whence);
-/* OS-independent fseek. 64-bit when available */
-
-gmx_off_t gmx_ftell(FILE *stream);
-/* OS-independent fseek. 64-bit when available. */
-
-
-gmx_bool is_pipe(FILE *fp);
-
-char *gmxlibfn(const char *file);
-/* allocates and returns a string with the full file name for a library file */
-
-FILE *libopen(const char *file);
-/* Open a library file for reading. This looks in the current directory
- * first, and then in the library directory. If the file is not found,
- * it terminates with a fatal_error
- */
-
-/* Opaque data type to list directories */
-typedef struct gmx_directory *
- gmx_directory_t;
-
-/* Open a directory for reading. The first argument should be a pointer
- * to a declared gmx_directory_t variable. Returns 0 on success.
- */
-int
-gmx_directory_open(gmx_directory_t *p_gmxdir, const char *dirname);
-
-
-/* Given an initialized gmx_directory_t, if there are more files in
- * the directory this routine returns 0 and write the next name
- * into the USER-PROVIDED buffer name. The last argument is the max
- * number of characters that will be written. Just as strncpy, the
- * string will NOT be terminated it it is longer than maxlength_name.
- */
-int
-gmx_directory_nextfile(gmx_directory_t gmxdir, char *name, int maxlength_name);
-
-/* Release all data for a directory structure */
-int
-gmx_directory_close(gmx_directory_t gmxdir);
-
-
-char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal);
-
-FILE *low_libopen(const char *file, gmx_bool bFatal);
-/* The same as the above, but does not terminate if (!bFatal) */
-
-/* Create unique name for temp file (wrapper around mkstemp).
- * Buf should be at least 7 bytes long
- */
-void gmx_tmpnam(char *buf);
-
-/* truncte the file to the specified length */
-int gmx_truncatefile(char *path, gmx_off_t length);
-
-/* rename/move the file (atomically, if the OS makes that available) oldname
- to newname */
-int gmx_file_rename(const char *oldname, const char *newname);
-
-/* copy the file (data only) oldname to newname. if copy_if_empty==FALSE,
- the file won't be copied if it's empty.*/
-int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty);
-
-/* do an fsync() on an open file pointer.
- Only use this during checkpointing! */
-int gmx_fsync(FILE *fp);
-
-void gmx_chdir(const char *directory);
-void gmx_getcwd(char *buffer, size_t size);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* GMX_FILEIO_FUTIL_H */
#include "thread_mpi/threads.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gromacs/utility/cstringutil.h"
#include "gmxfio.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
#define GMX_FILEIO_GMXFIO_H
#include <stdio.h>
+
#include "../legacyheaders/typedefs.h"
-#include "futil.h"
+#include "../utility/cstringutil.h"
+#include "../utility/futil.h"
#ifdef __cplusplus
extern "C" {
#include <io.h>
#endif
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gromacs/utility/cstringutil.h"
#include "gmxfio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gmxfio.h"
#include "md5.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gmxfio.h"
#include "md5.h"
#include <io.h>
#endif
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gmxfio.h"
#include "md5.h"
#include "xdrf.h"
#include "xdr_datatype.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
/* This is just for clarity - it can never be anything but 4! */
#define XDR_INT_SIZE 4
#include <algorithm>
-#include "sysstuff.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/cstringutil.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "matio.h"
#include "gmxfio.h"
#include "gromacs/math/utilities.h"
*/
#include "mdoutf.h"
-#include "gromacs/legacyheaders/xvgr.h"
#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/legacyheaders/mvdata.h"
#include "checkpoint.h"
#include "copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
struct gmx_mdoutf {
#endif
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/cstringutil.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "pdbio.h"
#include "vec.h"
#include "copyrite.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "atomprop.h"
#include "physics.h"
#include "pbc.h"
#include "gmxfio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
int ai, aj;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
#ifndef GMX_FILEIO_PDBIO_H
#define GMX_FILEIO_PDBIO_H
-#include "../legacyheaders/sysstuff.h"
+#include <stdio.h>
+
#include "../legacyheaders/typedefs.h"
#include "../legacyheaders/symtab.h"
#include "../legacyheaders/atomprop.h"
#include <stdlib.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
gmx_bool get_a_line(FILE *fp, char line[], int n)
{
#include <gtest/gtest.h>
#include <string>
-#include "gromacs/fileio/path.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/utility/path.h"
#include "testutils/testfilemanager.h"
#include "thread_mpi/threads.h"
#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
#endif
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/physics.h"
+
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/common.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
-#include "gmxfio.h"
static const char *modeToVerb(char mode)
{
#include "gromacs/legacyheaders/types/atoms.h"
#include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/utility/common.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
void gmx_prepare_tng_writing(const char *filename,
/* This file is completely threadsafe - keep it that way! */
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "names.h"
#include "symtab.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gmxfio.h"
#include "tpxio.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "vec.h"
#include "sim_util.h"
#include "mdrun.h"
#endif
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "names.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "trnio.h"
#include "gmxfio.h"
#include <assert.h>
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#ifdef GMX_USE_PLUGINS
#include "vmdio.h"
#include "tngio_for_tools.h"
#include "names.h"
#include "vec.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "xtcio.h"
#include "pdbio.h"
#include "confio.h"
#include "xdrf.h"
#include "gromacs/fileio/timecontrol.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* defines for frame counter output */
#define SKIP1 10
#include <shlobj.h>
#endif
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
+#include "gromacs/utility/futil.h"
#include "vmdio.h"
#include <stdio.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
const char *fontnm[efontNR] = {
#include "typedefs.h"
#include "xdrf.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
int xdr_real(XDR *xdrs, real *r)
#include "xtcio.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
-#include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#define XTC_MAGIC 1995
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gromacs/fileio/xvgr.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <sys/time.h>
#endif
-#include "sysstuff.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
-#include "copyrite.h"
-#include "oenv.h"
-#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "viewit.h"
-#include "vec.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/vec.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
gmx_bool output_env_get_print_xvgr_codes(const output_env_t oenv)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_FILEIO_XVGR_H
+#define GMX_FILEIO_XVGR_H
-#ifndef _xvgr_h
-#define _xvgr_h
+#include <stdio.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "viewit.h"
+#include "../legacyheaders/types/oenv.h"
+#include "../legacyheaders/types/simple.h"
+#include "../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _xvgr_h */
+#endif
#include "macros.h"
#include "txtdump.h"
#include "bondf.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "typedefs.h"
#include "vec.h"
#include "gstat.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void print_one(const output_env_t oenv, const char *base, const char *name,
const char *title, const char *ylabel, int nf, real time[],
#include "typedefs.h"
#include "physics.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "correl.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, 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.
#endif
#include <stdio.h>
#include "types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*Make range-array (Permutation identity) for sorting */
void rangeArray(int *ar, int size)
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
t_mat *init_mat(int n1, gmx_bool b1D)
{
#include "gromacs/utility/smalloc.h"
#include "gstat.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "index.h"
t_dlist *mk_dlist(FILE *log,
#endif
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "symtab.h"
void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
#include "eigio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
rvec **xref, gmx_bool *bDMR,
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "vec.h"
#include "index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
const int nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3};
#include "vec.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
static void my_calc_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
#endif
#include <math.h>
+#include <stdlib.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
#include "geminate.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
static void missing_code_message()
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
#include "gromacs/fileio/confio.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "vec.h"
#include "gromacs/statistics/statistics.h"
#include "gromacs/commandline/pargs.h"
#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "macros.h"
static const char *etitles[] = { "E-docked", "Free Energy" };
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/matio.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "eigio.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "readinp.h"
#include "txtdump.h"
#include "gstat.h"
#include "gromacs/statistics/statistics.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gmx_ana.h"
#include "geminate.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "physics.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "vec.h"
#include "index.h"
#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gstat.h"
#include "gromacs/fileio/trnio.h"
#include "gmx_ana.h"
#include <config.h>
#endif
-#include <math.h>
-#include <string.h>
#include <ctype.h>
-#include <math.h>
#include <float.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "macros.h"
#include "gromacs/fileio/enxio.h"
#include "physics.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gmx_ana.h"
#include "gromacs/math/utilities.h"
#include "gromacs/utility/cstringutil.h"
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "physics.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define MAX_ENDS 3
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <stdio.h>
+
#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
-#include <string.h>
-#include "sysstuff.h"
#include "txtdump.h"
#include "typedefs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/fileio/matio.h"
#include "gmx_ana.h"
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include "macros.h"
#include "gromacs/random/random.h"
#include "pbc.h"
#include "rmpbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/matio.h"
#include "cmat.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* print to two file pointers at once (i.e. stderr and log) */
static gmx_inline
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
#include "rmpbc.h"
#include "gromacs/commandline/pargs.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "index.h"
#include "mtop_util.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void clust_size(const char *ndx, const char *trx, const char *xpm,
const char *xpmw, const char *ncl, const char *acl,
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "typedefs.h"
-#include "xvgr.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "vec.h"
#include "index.h"
#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
#include "txtdump.h"
#endif
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trnio.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
int gmx_covar(int argc, char *argv[])
{
#include <config.h>
#endif
+#include <stdlib.h>
+
#include "gromacs/commandline/pargs.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "rmpbc.h"
#include "pbc.h"
#include "physics.h"
#include "gmx_ana.h"
#include "macros.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define SQR(x) (pow(x, 2.0))
#define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <math.h>
-#include <ctype.h>
-#include "sysstuff.h"
+#include <ctype.h>
+#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/utility/cstringutil.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gmx_ana.h"
#include "macros.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
char *atomname;
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
#include "princ.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "gstat.h"
#include "gromacs/fileio/matio.h"
#include "pbc.h"
+#include "viewit.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
int gmx_densmap(int argc, char *argv[])
{
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/cstringutil.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "copyrite.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/programcontext.h"
#ifdef GMX_DOUBLE
#include "gstat.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "correl.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/utilities.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
#include "pbc.h"
#include "bondf.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "txtdump.h"
#include "gromacs/statistics/statistics.h"
#include "gstat.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/programcontext.h"
#define e2d(x) ENM2DEBYE*(x)
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include "typedefs.h"
#include "macros.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "vec.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/utility/smalloc.h"
#include "gmx_ana.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
int n;
#include <config.h>
#endif
-#include "sysstuff.h"
+#include <stdlib.h>
+
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/strdb.h"
#include "mshift.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/matio.h"
#include "index.h"
#include "gstat.h"
#include "gromacs/fileio/trxio.h"
#include "viewit.h"
-
static int strip_dssp(char *dsspfile, int nres,
gmx_bool bPhobres[], real t,
real *acc, FILE *fTArea,
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <stdio.h>
+
#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "gromacs/fileio/confio.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
#include "txtdump.h"
#include "typedefs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "correl.h"
#include "gmx_ana.h"
#include "gromacs/fft/fft.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
int gmx_dyecoupl(int argc, char *argv[])
{
#include "gromacs/utility/smalloc.h"
#include "index.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "physics.h"
#include "gmx_ana.h"
#include "rmpbc.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct
{
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <string.h>
+
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "disre.h"
#include "names.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/enxio.h"
#include "vec.h"
#include "gmx_ana.h"
#include "gromacs/utility/cstringutil.h"
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/commandline/pargs.h"
#include "names.h"
#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
#include "physics.h"
#include "gromacs/fileio/matio.h"
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "names.h"
#include "copyrite.h"
#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
#include "physics.h"
#include "gromacs/fileio/tpxio.h"
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#endif
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "pbc.h"
#include "force.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/math/utilities.h"
#include "macros.h"
#include "vec.h"
#include "gromacs/fileio/tpxio.h"
#include "mdrun.h"
-#include "main.h"
#include "gromacs/random/random.h"
#include "index.h"
#include "mtop_util.h"
#endif
#include <math.h>
-#include "sysstuff.h"
-#include "gromacs/commandline/pargs.h"
#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
#include "vec.h"
#include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gmx_ana.h"
int gmx_genpr(int argc, char *argv[])
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "princ.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "gstat.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
#endif
#include <math.h>
-
-#include "sysstuff.h"
#include <string.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "princ.h"
#include "rmpbc.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/****************************************************************************/
/* This program calculates the ordering of water molecules across a box, as */
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "sysstuff.h"
#include "txtdump.h"
#include "physics.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gstat.h"
#include "gromacs/utility/cstringutil.h"
#include "pbc.h"
#include "gmx_ana.h"
#include "geminate.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#endif
#include <math.h>
+#include <string.h>
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "fitahx.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "hxprops.h"
#include "macros.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
#include "txtdump.h"
#include "typedefs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gmx_ana.h"
int gmx_helix(int argc, char *argv[])
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "index.h"
#include "pbc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gstat.h"
#include "pbc.h"
#include "gmx_ana.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/do_fit.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "binsearch.h"
#include "powerspect.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* Print name of first atom in all groups in index file */
static void print_types(atom_id index[], atom_id a[], int ngrps,
#include <config.h>
#endif
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "txtdump.h"
#include "gromacs/fileio/enxio.h"
#include "gstat.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
#include <string.h>
#include "readinp.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/matio.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "eigio.h"
#include <ctype.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define MAXNAMES 30
#define NAME_LEN 30
#include "macros.h"
#include "vec.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/matio.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include <math.h>
#include <stdlib.h>
-
-#include "sysstuff.h"
#include <string.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/trxio.h"
static int calc_ntype(int nft, int *ft, t_idef *idef)
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/fileio/confio.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "index.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/do_fit.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gstat.h"
#include "gromacs/statistics/statistics.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/confio.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define FACTOR 1000.0 /* Convert nm^2/ps to 10e-5 cm^2/s */
/* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
#include "txtdump.h"
#include "eigio.h"
#include "mtop_util.h"
#include "physics.h"
-#include "main.h"
#include "gmx_ana.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "cmat.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/****************************************************************************/
/* This program calculates the order parameter per atom for an interface or */
#include "main.h"
#include "macros.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* We use the same defines as in mvdata.c here */
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "physics.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "index.h"
#include "macros.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include <config.h>
#endif
-#include <math.h>
#include <ctype.h>
-
-#include "sysstuff.h"
+#include <math.h>
#include <string.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "princ.h"
#include "rmpbc.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gmx_ana.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define EPS0 8.85419E-12
#define ELC 1.60219E-19
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
#include "princ.h"
#include "rmpbc.h"
#include "txtdump.h"
#endif
#include <math.h>
-#include "sysstuff.h"
#include <string.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "physics.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "nrama.h"
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
#include "names.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void check_box_c(matrix box)
{
#include <config.h>
#endif
-#include "gromacs/utility/smalloc.h"
#include <math.h>
+#include <stdlib.h>
+
+#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "index.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "princ.h"
#include "rmpbc.h"
#include "gromacs/fileio/matio.h"
#include "macros.h"
#include "index.h"
#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/matio.h"
#include "gmx_ana.h"
#include <config.h>
#endif
-#include "gromacs/utility/smalloc.h"
#include <math.h>
+
+#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "princ.h"
#include "rmpbc.h"
#include "gromacs/fileio/confio.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
+
#include "physics.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
#include "gstat.h"
#include "vec.h"
+#include "viewit.h"
#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "macros.h"
#include "vec.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "pbc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
char *label;
#endif
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "gromacs/commandline/pargs.h"
#include "index.h"
#include "gmx_ana.h"
#include "nsfactor.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
int gmx_sans(int argc, char *argv[])
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "xvgr.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "physics.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "readinp.h"
#include "txtdump.h"
#include "gstat.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "physics.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/matio.h"
#include <config.h>
#endif
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/fileio/pdbio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/smalloc.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, gmx_bool bPBC)
#include <config.h>
#endif
-
+#include <math.h>
+#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
#include "typedefs.h"
#include "vec.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include <math.h>
#include "index.h"
#include "pbc.h"
#include "rmpbc.h"
#include "gmx_ana.h"
#include "macros.h"
-
static const double bohr = 0.529177249; /* conversion factor to compensate for VMD plugin conversion... */
-static void mequit(void)
-{
- printf("Memory allocation error\n");
- exit(1);
-}
-
int gmx_spatial(int argc, char *argv[])
{
const char *desc[] = {
MINBIN[i] -= (double)iNAB*rBINWIDTH;
nbin[i] = (long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
}
- bin = (long ***)malloc(nbin[XX]*sizeof(long **));
- if (!bin)
- {
- mequit();
- }
+ snew(bin, nbin[XX]);
for (i = 0; i < nbin[XX]; ++i)
{
- bin[i] = (long **)malloc(nbin[YY]*sizeof(long *));
- if (!bin[i])
- {
- mequit();
- }
+ snew(bin[i], nbin[YY]);
for (j = 0; j < nbin[YY]; ++j)
{
- bin[i][j] = (long *)calloc(nbin[ZZ], sizeof(long));
- if (!bin[i][j])
- {
- mequit();
- }
+ snew(bin[i][j], nbin[ZZ]);
}
}
copy_mat(box, box_pbc);
#include "gromacs/utility/smalloc.h"
#include "gstat.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "physics.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, int ePBC)
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
+#include <string.h>
+
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
#include "txtdump.h"
#include "typedefs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "pbc.h"
#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "rmpbc.h"
#include "gmx_ana.h"
#include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
gmx_bool bDim[], const char *sffmt)
#include <config.h>
#endif
-#include <string.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+
#include "macros.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
#include "names.h"
#include "gromacs/fileio/xtcio.h"
#include "rmpbc.h"
#include "pbc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
#include <config.h>
#endif
-#include <string.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "copyrite.h"
#include "macros.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
#include "names.h"
#include "rmpbc.h"
#include "pbc.h"
#include "viewit.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gmx_ana.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "princ.h"
#include "rmpbc.h"
#include "txtdump.h"
#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
atom_id i;
#include <config.h>
#endif
+#include <stdlib.h>
#include <time.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/math/utilities.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* Enum for situations that can occur during log file parsing, the
* corresponding string entries can be found in do_the_tests() in
}
-static gmx_bool is_equal(real a, real b)
-{
- real diff, eps = 1.0e-7;
-
-
- diff = a - b;
-
- if (diff < 0.0)
- {
- diff = -diff;
- }
-
- if (diff < eps)
- {
- return TRUE;
- }
- else
- {
- return FALSE;
- }
-}
-
-
static void remove_if_exists(const char *fn)
{
if (gmx_fexist(fn))
fprintf(fp, "\n");
/* Only mention settings if they were modified: */
- bRefinedCoul = !is_equal(info->rcoulomb[k_win], info->rcoulomb[0]);
- bRefinedVdW = !is_equal(info->rvdw[k_win], info->rvdw[0] );
+ bRefinedCoul = !gmx_within_tol(info->rcoulomb[k_win], info->rcoulomb[0], GMX_REAL_EPS);
+ bRefinedCoul = !gmx_within_tol(info->rcoulomb[k_win], info->rcoulomb[0], GMX_REAL_EPS);
+ bRefinedVdW = !gmx_within_tol(info->rvdw[k_win], info->rvdw[0], GMX_REAL_EPS);
bRefinedGrid = !(info->nkx[k_win] == info->nkx[0] &&
info->nky[k_win] == info->nky[0] &&
info->nkz[k_win] == info->nkz[0]);
{
/* Determine which Coulomb radii rc to use in the benchmarks */
add = (rmax-rmin)/(*ntprs-1);
- if (is_equal(rmin, info->rcoulomb[0]))
+ if (gmx_within_tol(rmin, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + j*add;
}
- else if (is_equal(rmax, info->rcoulomb[0]))
+ else if (gmx_within_tol(rmax, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + (j-1)*add;
}
fprintf(fp, " %-14s\n", fn_bench_tprs[j]);
/* Make it clear to the user that some additional settings were modified */
- if (!is_equal(ir->rvdw, info->rvdw[0])
- || !is_equal(ir->rlistlong, info->rlistlong[0]) )
+ if (!gmx_within_tol(ir->rvdw, info->rvdw[0], GMX_REAL_EPS)
+ || !gmx_within_tol(ir->rlistlong, info->rlistlong[0], GMX_REAL_EPS) )
{
bNote = TRUE;
}
/* Add test scenarios if rmin or rmax were set */
if (*ntprs <= 2)
{
- if (!is_equal(*rmin, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmin to %g changed -ntpr to %d\n",
*rmin, *ntprs);
}
- if (!is_equal(*rmax, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmax to %g changed -ntpr to %d\n",
}
old = *ntprs;
/* If one of rmin, rmax is set, we need 2 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) || !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) || !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 2);
}
/* If both rmin, rmax are set, we need 3 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) && !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 3);
}
if (*ntprs > 1)
{
- if (is_equal(*rmin, rcoulomb) && is_equal(rcoulomb, *rmax)) /* We have just a single rc */
+ if (gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && gmx_within_tol(rcoulomb, *rmax, GMX_REAL_EPS)) /* We have just a single rc */
{
fprintf(stderr, "WARNING: Resetting -ntpr to 1 since no Coulomb radius scaling is requested.\n"
"Please set rmin < rmax to test Coulomb radii in the [rmin, rmax] interval\n"
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gstat.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <stdio.h>
+
#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
#include "txtdump.h"
#include "typedefs.h"
#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gmx_ana.h"
#include "gromacs/fft/fft.h"
#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
#include "macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
//! longest file names allowed in input files
#define WHAM_MAXFILELEN 2048
#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "physics.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "xvgr.h"
#include "pbc.h"
#include "pbc.h"
#include "index.h"
#include "gstat.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gmx_ana.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/writeps.h"
#include <math.h>
#include "typedefs.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "viewit.h"
#include "gmx_ana.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/writeps.h"
#include "gromacs/utility/smalloc.h"
#include "bondf.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
real ellipticity(int nres, t_bb bb[])
{
#include <config.h>
#endif
-#include "nrama.h"
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
+
+#include "nrama.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "bondf.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "rmpbc.h"
static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
#include <string.h>
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "vec.h"
#include "nsfactor.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
void check_binwidth(real binwidth)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 <stdio.h>
#include <math.h>
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gstat.h"
real LegendreP(real x, unsigned long m)
#include "gromacs/utility/smalloc.h"
#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "interf.h"
#include "powerspect.h"
/*Prepare data structures for FFT, with time averaging of power spectrum*/
if ( (status = gmx_fft_init_2d_real(&fftp, xbins, ybins, GMX_FFT_FLAG_NONE) ) != 0)
{
- free(fftp);
gmx_fatal(status, __FILE__, __LINE__, "Error allocating FFT");
}
gmx_ffclose(datfile1);
gmx_ffclose(datfile2);
- free(ftspect1);
- free(ftspect2);
+ sfree(ftspect1);
+ sfree(ftspect2);
}
#include <stdlib.h>
#include <math.h>
#include "typedefs.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
#include "physics.h"
#include "gromacs/utility/smalloc.h"
#include "gstat.h"
#include "gromacs/fileio/matio.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
int nx, ny;
#include <ctype.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "atomprop.h"
#include "macros.h"
#include "index.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/math/utilities.h"
#include "ns.h"
#include "macros.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mshift.h"
-#include "main.h"
#include "disre.h"
#include "orires.h"
#include "force.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "calcgrid.h"
/* The grid sizes below are based on timing of a 3D cubic grid in fftw
#include "vec.h"
#include "physics.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define xAI xa[0]
#define xAJ xa[1]
#endif
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "vec.h"
#include "pbc.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "chargegroup.h"
#include <config.h>
#endif
+#include <errno.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
+#include <fcntl.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#include "vec.h"
#include "network.h"
#include "checkpoint.h"
-#include "main.h"
#include "gromacs/utility/cstringutil.h"
-#include <fcntl.h>
#include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xdrf.h"
#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/baseversion.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "buildinfo.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
struct gmx_invsqrtdata
{
- unsigned int exptab[256]; /*!< Exponential lookup table */
- unsigned int fracttab[4096]; /*!< Mantissa lookup table */
+ unsigned int exptab[256]; /**< Exponential lookup table */
+ unsigned int fracttab[4096]; /**< Mantissa lookup table */
};
#include "gromacs/legacyheaders/vec.h"
#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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 <stdio.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* CUDA library and hardware related defines */
/* TODO list some constants instead that can be used for consistency checks to
#include "cudautils.cuh"
#include "pmalloc_cuda.h"
+#include "gromacs/utility/cstringutil.h"
+
/*! Allocates nbytes of page-locked memory.
* This memory should always be freed using pfree (or with the page-locked
* free functions provied by the CUDA library).
#endif
#include <math.h>
+#include <stdlib.h>
+
#include "typedefs.h"
#include "types/commrec.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "bondf.h"
#include "copyrite.h"
#include "disre.h"
#include "gromacs/utility/smalloc.h"
#include "physics.h"
#include "txtdump.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "names.h"
#include "macros.h"
#include <config.h>
#endif
-#include <stdlib.h>
#include <assert.h>
+#include <errno.h>
+#include <stdlib.h>
#include <string.h>
#ifdef HAVE_UNISTD_H
#include "types/enums.h"
#include "types/hw_info.h"
#include "types/commrec.h"
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
+#include "network.h"
#include "md_logging.h"
#include "gmx_cpuid.h"
-#include "gromacs/utility/smalloc.h"
#include "gpu_utils.h"
#include "copyrite.h"
#include "gmx_detect_hardware.h"
-#include "main.h"
#include "md_logging.h"
-#include "gromacs/utility/gmxomp.h"
+
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
#include "thread_mpi/threads.h"
#include <config.h>
#endif
-#include "gmx_fatal.h"
#include "typedefs.h"
+#include "types/commrec.h"
#include "macros.h"
#include "network.h"
#include "copyrite.h"
#include "gmx_omp_nthreads.h"
#include "md_logging.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
/** Structure with the number of threads for each OpenMP multi-threaded
#include "md_logging.h"
#include "gmx_thread_affinity.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
static int
get_thread_affinity_layout(FILE *fplog,
* Note that this will only work on Linux as we use a GNU feature.
*/
void
-gmx_check_thread_affinity_set(FILE gmx_unused *fplog,
- const t_commrec gmx_unused *cr,
- gmx_hw_opt_t gmx_unused *hw_opt,
- int gmx_unused ncpus,
- gmx_bool gmx_unused bAfterOpenmpInit)
+gmx_check_thread_affinity_set(FILE *fplog,
+ const t_commrec *cr,
+ gmx_hw_opt_t *hw_opt,
+ int gmx_unused ncpus,
+ gmx_bool bAfterOpenmpInit)
{
#ifdef HAVE_SCHED_GETAFFINITY
cpu_set_t mask_current;
int i, ret, cpu_count, cpu_set;
gmx_bool bAllSet;
+#endif
assert(hw_opt);
+ if (!bAfterOpenmpInit)
+ {
+ /* Check for externally set OpenMP affinity and turn off internal
+ * pinning if any is found. We need to do this check early to tell
+ * thread-MPI whether it should do pinning when spawning threads.
+ * TODO: the above no longer holds, we should move these checks later
+ */
+ if (hw_opt->thread_affinity != threadaffOFF)
+ {
+ char *message;
+ if (!gmx_omp_check_thread_affinity(&message))
+ {
+ /* TODO: with -pin auto we should only warn when using all cores */
+ md_print_warn(cr, fplog, "%s", message);
+ sfree(message);
+ hw_opt->thread_affinity = threadaffOFF;
+ }
+ }
+
+ /* With thread-MPI this is needed as pinning might get turned off,
+ * which needs to be known before starting thread-MPI.
+ * With thread-MPI hw_opt is processed here on the master rank
+ * and passed to the other ranks later, so we only do this on master.
+ */
+ if (!SIMMASTER(cr))
+ {
+ return;
+ }
+#ifndef GMX_THREAD_MPI
+ return;
+#endif
+ }
+
+#ifdef HAVE_SCHED_GETAFFINITY
if (hw_opt->thread_affinity == threadaffOFF)
{
/* internal affinity setting is off, don't bother checking process affinity */
#include <stdlib.h>
#include <assert.h>
-#include "gromacs/utility/smalloc.h"
#include "types/hw_info.h"
#include "gpu_utils.h"
#include "../cuda_tools/cudautils.cuh"
#include "memtestG80_core.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
/** Amount of memory to be used in quick memtest. */
#define QUICK_MEM 250
/** Bit flag with type of tests to run in quick memtest. */
#include <config.h>
#endif
+#include <assert.h>
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include "sysstuff.h"
+
#include "macros.h"
#include "names.h"
-#include "gromacs/utility/cstringutil.h"
-#include "main.h"
#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "invblock.h"
#include "macros.h"
#include "index.h"
#include "txtdump.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
const char gmx_residuetype_undefined[] = "Other";
#include "typedefs.h"
#include "macros.h"
#include "inputrec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* The minimum number of integration steps required for reasonably accurate
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "invblock.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
atom_id *make_invblock(const t_block *block, int nr)
{
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+#ifdef GMX_NATIVE_WINDOWS
+#include <process.h>
+#endif
-#include "gromacs/utility/smalloc.h"
#include "types/commrec.h"
-#include "gmx_fatal.h"
#include "network.h"
#include "main.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/utility/cstringutil.h"
#include "copyrite.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
-
#define BUFSIZE 1024
-
static void par_fn(char *base, int ftp, const t_commrec *cr,
gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
char buf[], int bufsize)
}
-int gmx_gethostname(char *name, size_t len)
-{
- if (len < 8)
- {
- gmx_incons("gmx_gethostname called with len<8");
- }
-#if defined(HAVE_UNISTD_H) && !defined(__native_client__)
- if (gethostname(name, len-1) != 0)
- {
- strncpy(name, "unknown", 8);
- return -1;
- }
- return 0;
-#else
- strncpy(name, "unknown", 8);
- return -1;
-#endif
-}
-
-
void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
gmx_bool bAppendFiles, FILE** fplog)
{
#include <string.h>
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "mshift.h"
-#include "main.h"
#include "pbc.h"
/************************************************************
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "mtop_util.h"
#include "topsort.h"
#include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static int gmx_mtop_maxresnr(const gmx_mtop_t *mtop, int maxres_renum)
{
#include "types/commrec.h"
#include "network.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "symtab.h"
#include "vec.h"
#include "tgroup.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "network.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+#include <ctype.h>
+#include <stdarg.h>
+#include <stdlib.h>
#include <string.h>
-#include "gmx_fatal.h"
-#include "main.h"
-#include "gromacs/utility/smalloc.h"
+
#include "types/commrec.h"
-#include "network.h"
#include "copyrite.h"
-#include <ctype.h>
#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
-
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-gmx_bool gmx_mpi_initialized(void)
-{
- int n;
-#ifndef GMX_MPI
- return 0;
-#else
- MPI_Initialized(&n);
-
- return n;
-#endif
-}
-
void gmx_fill_commrec_from_mpi(t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
#endif
}
-int gmx_node_num(void)
-{
-#ifndef GMX_MPI
- return 1;
-#else
- int i;
- (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
-
-int gmx_node_rank(void)
-{
-#ifndef GMX_MPI
- return 0;
-#else
- int i;
- (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
-
-#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
-#include <spi/include/kernel/location.h>
-#endif
-
-int gmx_physicalnode_id_hash(void)
-{
- int hash_int;
-
-#ifndef GMX_LIB_MPI
- /* We have a single physical node */
- hash_int = 0;
-#else
- int resultlen;
- char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
-
- /* This procedure can only differentiate nodes with different names.
- * Architectures where different physical nodes have identical names,
- * such as IBM Blue Gene, should use an architecture specific solution.
- */
- MPI_Get_processor_name(mpi_hostname, &resultlen);
-
- /* The string hash function returns an unsigned int. We cast to an int.
- * Negative numbers are converted to positive by setting the sign bit to 0.
- * This makes the hash one bit smaller.
- * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
- * even on a million node machine. 31 bits might not be enough though!
- */
- hash_int =
- (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
- if (hash_int < 0)
- {
- hash_int -= INT_MIN;
- }
-#endif
-
- return hash_int;
-}
-
-/* TODO: this function should be fully replaced by gmx_physicalnode_id_hash */
-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];
-
- MPI_Get_processor_name(mpi_hostname, &resultlen);
-#ifdef GMX_TARGET_BGQ
- Personality_t personality;
- Kernel_GetPersonality(&personality, sizeof(personality));
- /* Each MPI rank has a unique coordinate in a 6-dimensional space
- (A,B,C,D,E,T), with dimensions A-E corresponding to different
- physical nodes, and T within each node. Each node has sixteen
- physical cores, each of which can have up to four hardware
- threads, so 0 <= T <= 63 (but the maximum value of T depends on
- the confituration of ranks and OpenMP threads per
- node). However, T is irrelevant for computing a suitable return
- value for gmx_hostname_num().
- */
- hostnum = personality.Network_Config.Acoord;
- hostnum *= personality.Network_Config.Bnodes;
- hostnum += personality.Network_Config.Bcoord;
- hostnum *= personality.Network_Config.Cnodes;
- hostnum += personality.Network_Config.Ccoord;
- hostnum *= personality.Network_Config.Dnodes;
- 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 (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 = strtol(hostnum_str + max(0, j-9), NULL, 10);
- }
-#endif
-
- if (debug)
- {
- fprintf(debug, "In gmx_hostname_num: hostname '%s', hostnum %d\n",
- mpi_hostname, hostnum);
-#ifdef GMX_TARGET_BGQ
- fprintf(debug,
- "Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\nNode ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
- personality.Network_Config.Acoord,
- personality.Network_Config.Anodes,
- personality.Network_Config.Bcoord,
- personality.Network_Config.Bnodes,
- personality.Network_Config.Ccoord,
- personality.Network_Config.Cnodes,
- personality.Network_Config.Dcoord,
- personality.Network_Config.Dnodes,
- personality.Network_Config.Ecoord,
- personality.Network_Config.Enodes,
- Kernel_ProcessorCoreID(),
- 16,
- Kernel_ProcessorID(),
- 64,
- Kernel_ProcessorThreadID(),
- 4);
-#endif
- }
- return hostnum;
-#endif
-#endif
-}
-
void gmx_setup_nodecomm(FILE gmx_unused *fplog, t_commrec *cr)
{
gmx_nodecomm_t *nc;
#endif
}
-void gmx_abort(int gmx_unused noderank, int gmx_unused nnodes, int gmx_unused errorno)
-{
-#ifndef GMX_MPI
- gmx_call("gmx_abort");
-#else
-#ifdef GMX_THREAD_MPI
- fprintf(stderr, "Halting program %s\n", ShortProgram());
- gmx_thanx(stderr);
- exit(1);
-#else
- if (nnodes > 1)
- {
- fprintf(stderr, "Halting parallel program %s on CPU %d out of %d\n",
- ShortProgram(), noderank, nnodes);
- }
- else
- {
- fprintf(stderr, "Halting program %s\n", ShortProgram());
- }
-
- gmx_thanx(stderr);
- MPI_Abort(MPI_COMM_WORLD, errorno);
- exit(1);
-#endif
-#endif
-}
-
void gmx_bcast(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
#endif
#endif
}
+
+gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
+{
+ gmx_bool bExist;
+
+ if (SIMMASTER(cr))
+ {
+ bExist = gmx_fexist(fname);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(bExist), &bExist, cr);
+ }
+ return bExist;
+}
+
+void gmx_fatal_collective(int f_errno, const char *file, int line,
+ const t_commrec *cr, gmx_domdec_t *dd,
+ const char *fmt, ...)
+{
+ va_list ap;
+ gmx_bool bMaster, bFinalize;
+#ifdef GMX_MPI
+ int result;
+ /* Check if we are calling on all processes in MPI_COMM_WORLD */
+ if (cr != NULL)
+ {
+ MPI_Comm_compare(cr->mpi_comm_mysim, MPI_COMM_WORLD, &result);
+ }
+ else
+ {
+ MPI_Comm_compare(dd->mpi_comm_all, MPI_COMM_WORLD, &result);
+ }
+ /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
+ bFinalize = (result != MPI_UNEQUAL);
+#else
+ bFinalize = TRUE;
+#endif
+ bMaster = (cr != NULL && MASTER(cr)) || (dd != NULL && DDMASTER(dd));
+
+ va_start(ap, fmt);
+ gmx_fatal_mpi_va(f_errno, file, line, bMaster, bFinalize, fmt, ap);
+ va_end(ap);
+}
#include "macros.h"
#include "nb_free_energy.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void
gmx_nb_free_energy_kernel(const t_nblist * gmx_restrict nlist,
#include "nb_generic.h"
#include "nrnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "nonbonded.h"
#include "nb_kernel.h"
#include "nb_generic_adress.h"
#include "nrnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "nonbonded.h"
#include "nb_kernel.h"
#include "nb_kernel.h"
#include "nrnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void
gmx_nb_generic_cg_kernel(t_nblist * nlist,
#include "nb_kernel.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* Static data structures to find kernels */
#include "gromacs/utility/cstringutil.h"
#include "force.h"
#include "names.h"
-#include "main.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "physics.h"
#include "force.h"
#include "bondf.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
+
#include "types/commrec.h"
-#include "sysstuff.h"
#include "names.h"
#include "macros.h"
#include "nrnb.h"
-#include "main.h"
#include "gromacs/utility/smalloc.h"
typedef struct {
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
rvec xref[],
#include <math.h>
#include <assert.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "vec.h"
#include "gromacs/math/utilities.h"
-#include "main.h"
#include "pbc.h"
#include "gromacs/utility/smalloc.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "names.h"
#include "macros.h"
#include "gmx_omp_nthreads.h"
#endif
#include "typedefs.h"
-#include "main.h"
#include "network.h"
#include "rbin.h"
#include "gromacs/utility/smalloc.h"
#include <stdlib.h>
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "readinp.h"
#include "macros.h"
#include "gromacs/fileio/gmxfio.h"
#include "names.h"
#include "warninp.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
t_inpfile *read_inpfile(const char *fn, int *ninp,
warninp_t wi)
#include "macros.h"
#include "names.h"
#include "mshift.h"
-#include "main.h"
#include "disre.h"
#include "orires.h"
#include "force.h"
#include <config.h>
#endif
-#include "sysstuff.h"
#include "typedefs.h"
#include "mshift.h"
#include "pbc.h"
#include "rmpbc.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
typedef struct {
#include <config.h>
#endif
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/math/utilities.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "macros.h"
#include "index.h"
#include "typedefs.h"
#include "oenv.h"
#include "gromacs/fileio/gmxfio.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/matio.h"
#include "names.h"
#include "sfactor.h"
t_complex ***t;
int i, j;
- t = (t_complex ***)calloc(x, sizeof(t_complex**));
- if (!t)
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
- t[0] = (t_complex **)calloc(x*y, sizeof(t_complex*));
- if (!t[0])
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
- t[0][0] = (t_complex *)calloc(x*y*z, sizeof(t_complex));
- if (!t[0][0])
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
+ snew(t, x);
+ snew(t[0], x*y);
+ snew(t[0][0], x*y*z);
for (j = 1; j < y; j++)
{
}
}
}
- sfree (counter); free(tmpSF[0][0]); free(tmpSF[0]); free(tmpSF);
+ sfree(counter);
+ sfree(tmpSF[0][0]);
+ sfree(tmpSF[0]);
+ sfree(tmpSF);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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 <config.h>
#endif
+#include <stdlib.h>
+
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "sighandler.h"
-
const char *gmx_stop_cond_name[] =
{
"None",
#endif
#include <assert.h>
+#include <stdlib.h>
#include <string.h>
+
#include "macros.h"
-#include "gromacs/utility/smalloc.h"
#include "mshift.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int atom, sid;
#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "txtdump.h"
#include "symtab.h"
#include "typedefs.h"
#include "topsort.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static gmx_bool ip_pert(int ftype, const t_iparams *ip)
{
/* This file is completely threadsafe - please keep it that way! */
#include <stdio.h>
+#include <stdlib.h>
+
#include "typedefs.h"
#include "types/commrec.h"
#include "names.h"
#include "vec.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
int pr_indent(FILE *fp, int n)
if (molb->nposres_xA > 0)
{
molb->nposres_xA = 0;
- free(molb->posres_xA);
+ sfree(molb->posres_xA);
}
if (molb->nposres_xB > 0)
{
molb->nposres_xB = 0;
- free(molb->posres_xB);
+ sfree(molb->posres_xB);
}
}
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
+#include "viewit.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
#include "oenv.h"
-#include "viewit.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/filenm.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
static const int can_view_ftp[] = {
0,
"ghostview", "display", NULL, "xterm -e rasmol"
};
-int can_view(int ftp)
+static int can_view(int ftp)
{
int i;
#include "gromacs/utility/smalloc.h"
#include "copyrite.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "warninp.h"
typedef struct warninp {
#include "toputil.h"
#include "hackblock.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void clear_atom_list(int i0, atom_id a[])
{
#endif
#include <assert.h>
+#include <math.h>
+#include <stdlib.h>
#include <sys/types.h>
-#include <math.h>
+
#include "typedefs.h"
#include "physics.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
#include "macros.h"
#include "vec.h"
#include "coulomb.h"
#include "calc_verletbuf.h"
#include "../mdlib/nbnxn_consts.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
#ifdef GMX_NBNXN_SIMD
/* The include below sets the SIMD instruction type (precision+width)
* for all nbnxn SIMD search and non-bonded kernel code.
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "physics.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "topio.h"
#include "toputil.h"
#include "convparm.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+
+#include <fcntl.h>
#include <sys/types.h>
#include <sys/stat.h>
-#include <fcntl.h>
-#include "sysstuff.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
+#include "network.h"
#include "fflibutil.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/path.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
const char *fflib_forcefield_dir_ext()
{
#include <ctype.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gpp_nextnb.h"
#include "symtab.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "pgutil.h"
#include "resall.h"
#include "gen_ad.h"
#include <math.h>
#include "gromacs/random/random.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "physics.h"
#include "typedefs.h"
#include <math.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
#include "gen_vsite.h"
-#include "gromacs/utility/smalloc.h"
#include "resall.h"
#include "add_par.h"
#include "vec.h"
#include "physics.h"
#include "index.h"
#include "names.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gpp_atomtype.h"
#include "fflibutil.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define MAXNAME 32
#define OPENDIR '[' /* starting sign for directive */
#include "gromacs/math/utilities.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "vec.h"
#include "sortwater.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
gmx_rng_t rng, rvec max_rot)
#include <string.h>
#include <time.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/confio.h"
#include "symtab.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "physics.h"
#include "calch.h"
#include "genhydro.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gmxcpp.h"
typedef struct {
#include <string.h>
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "macros.h"
#include "topdirs.h"
#include "toputil.h"
#include "topdirs.h"
#include "toputil.h"
#include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "gpp_atomtype.h"
#endif
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "macros.h"
#include "symtab.h"
#include "gromacs/utility/cstringutil.h"
#include <config.h>
#endif
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
+#include <stdlib.h>
+
#include "macros.h"
/* #define DEBUG_NNB */
#include "gpp_nextnb.h"
-#include "gmx_fatal.h"
#include "toputil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
typedef struct {
int ai, aj;
} sortable;
#include <limits.h>
#include <assert.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "readir.h"
#include "gromacs/random/random.h"
#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "splitter.h"
#include "gromacs/gmxpreprocess/sortwater.h"
#include "convparm.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "warninp.h"
#include "index.h"
#include "gromacs/fileio/gmxfio.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "symtab.h"
#include "h_db.h"
#include "gromacs/fileio/gmxfio.h"
#include "fflibutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
/* Number of control atoms for each 'add' type.
#ifndef GMX_GMXPREPROCESS_H_DB_H
#define GMX_GMXPREPROCESS_H_DB_H
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "hackblock.h"
#ifdef __cplusplus
free_t_bondeds(&(*rtp)[i].rb[j]);
}
}
- free(*rtp);
+ sfree(*rtp);
}
void free_t_hack(int nh, t_hack **h)
#include "gromacs/utility/cstringutil.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static int in_strings(char *key, int nstr, const char **str)
{
#endif
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/math/utilities.h"
#include "gromacs/fileio/confio.h"
#include "macros.h"
#include "gromacs/random/random.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "atomprop.h"
#include "names.h"
#include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/gmxlib/conformation-utilities.h"
#include "addconf.h"
#include "read-conformation.h"
#include "pbc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+
+#include "gromacs/utility/cstringutil.h"
static gmx_bool in_box(t_pbc *pbc, rvec x)
{
#include "bondf.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "gromacs/fileio/confio.h"
#include "physics.h"
#include "vec.h"
#include "nm2type.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
{
#endif
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/utility/smalloc.h"
#include "symtab.h"
#include "vec.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/pdbio.h"
#include "toputil.h"
#include "h_db.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "symtab.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "pdb2top.h"
#include "gpp_nextnb.h"
#include "topdirs.h"
#include "gromacs/utility/cstringutil.h"
#include "pgutil.h"
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define BUFSIZE 1024
static void atom_not_found(int fatal_errno, const char *file, int line,
#include "vec.h"
#include "hackblock.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
int gmx_protonate(int argc, char *argv[])
{
*/
#include "read-conformation.h"
-#include "gromacs/fileio/confio.h"
#include "atomprop.h"
#include "types/simple.h"
#include "types/atoms.h"
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
#include "readir.h"
#include "names.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
#define MAXPTR 254
#include <ctype.h>
#include <stdlib.h>
#include <limits.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "physics.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "index.h"
#include "symtab.h"
#include <stdlib.h>
#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
#include "princ.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "index.h"
#include "symtab.h"
#include "gromacs/utility/smalloc.h"
#include "readir.h"
#include "names.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/trnio.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static char *RotStr = {"Enforced rotation:"};
#endif
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "symtab.h"
#include "macros.h"
#include "resall.h"
#include <string.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "atomprop.h"
#include "names.h"
#include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/gmxlib/conformation-utilities.h"
#include "addconf.h"
#include <config.h>
#endif
+#include <stdlib.h>
+
#include "typedefs.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
#include "vec.h"
#include "sortwater.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
+
static rvec *xptr, box_1;
static int nwat;
static matrix BOX;
#include <ctype.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "symtab.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "resall.h"
#include "h_db.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "ter_db.h"
#include "toputil.h"
#include "gromacs/fileio/gmxfio.h"
#ifndef GMX_GMXPREPROCESS_TER_DB_H
#define GMX_GMXPREPROCESS_TER_DB_H
-#include "sysstuff.h"
#include "hackblock.h"
#include "grompp-impl.h"
#include "../insert-molecules.h"
#include "testutils/integrationtests.h"
#include "testutils/cmdlinetest.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
namespace
{
#include "../solvate.h"
#include "testutils/integrationtests.h"
#include "testutils/cmdlinetest.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
namespace
{
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "grompp-impl.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "toputil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gpp_atomtype.h"
#include "macros.h"
#include <stdio.h>
#include <stdarg.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "topdirs.h"
/* Must correspond to the directive enum in grompp-impl.h */
#include <config.h>
#endif
+#include <assert.h>
+#include <ctype.h>
+#include <errno.h>
#include <math.h>
-#include <sys/types.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-#include <ctype.h>
-#include <assert.h>
-#include "gromacs/fileio/futil.h"
-#include "sysstuff.h"
+#include <sys/types.h>
+
+#include "gromacs/utility/futil.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "names.h"
#include "gromacs/utility/cstringutil.h"
#include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "warninp.h"
#include "vsite_parm.h"
#include <config.h>
#endif
+#include <assert.h>
#include <ctype.h>
#include <math.h>
-#include <assert.h>
+#include <stdlib.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
#include "names.h"
#include "toputil.h"
#include "toppush.h"
#include "topdirs.h"
#include "readir.h"
#include "symtab.h"
-#include "gmx_fatal.h"
#include "warninp.h"
#include "gpp_atomtype.h"
#include "gpp_bond_atomtype.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atype,
warninp_t wi)
{
#include <ctype.h>
#include <math.h>
-#include "sysstuff.h"
#include "physics.h"
#include "macros.h"
#include "readir.h"
#include "toputil.h"
#include "topdirs.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void copy_bond (t_params *pr, int to, int from)
/* copies an entry in a bond list to another position.
#include <string.h>
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "macros.h"
#include "topdirs.h"
#include "toputil.h"
#include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gpp_atomtype.h"
/* UTILITIES */
#include "physics.h"
#include "index.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/cstringutil.h"
#include "physics.h"
#include "macros.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "gromacs/fileio/confio.h"
#include "physics.h"
#include "gromacs/commandline/pargs.h"
#include "hackblock.h"
#include "nm2type.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
char atp[7] = "HCNOSX";
#define NATP (asize(atp)-1)
dump_hybridization(debug, atoms, nbonds);
}
close_symtab(&symtab);
- free(mymol.name);
+ sfree(mymol.name);
printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
ShortProgram());
#include "gromacs/utility/smalloc.h"
#include "symtab.h"
#include "index.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "fflibutil.h"
#include "hackblock.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "xlate.h"
#include "gromacs/fileio/strdb.h"
#include <config.h>
#endif
-
+#include <errno.h>
#include <string.h>
#ifdef GMX_NATIVE_WINDOWS
#include "mdrun.h"
#include "sighandler.h"
#include "gmx_ga2la.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/fileio/confio.h"
#include "mtop_util.h"
#include "names.h"
#include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief How long shall we wait in seconds until we check for a connection again? */
#define IMDLOOPWAIT 1
#include <config.h>
#endif
-
+#include <errno.h>
#include <string.h>
+
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "imdsocket.h"
#include "imd.h"
-
#ifdef GMX_NATIVE_WINDOWS
#ifdef GMX_HAVE_WINSOCK
/*! \brief Define socklen type on Windows. */
#endif
#else
/* On UNIX, we can use nice errors from errno.h */
-#include <errno.h>
#include <unistd.h>
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
#ifndef _chargegroup_h
#define _chargegroup_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#ifdef __cplusplus
#ifndef _disre_h
#define _disre_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#ifdef __cplusplus
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#ifndef _ebin_h
#define _ebin_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#include "../fileio/enxio.h"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2012,2014, 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.
- */
-
-#ifndef _fatal_collective_h
-#define _fatal_collective_h
-
-#include "typedefs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-void
-gmx_fatal_collective(int f_errno, const char *file, int line,
- const t_commrec *cr, gmx_domdec_t *dd,
- const char *fmt, ...);
-/* As gmx_fatal declared in gmx_fatal.h,
- * but only the master process prints the error message.
- * This should only be called one of the following two situations:
- * 1) On all nodes in cr->mpi_comm_mysim, with cr!=NULL,dd==NULL.
- * 2) On all nodes in dd->mpi_comm_all, with cr==NULL,dd!=NULL.
- * This will call MPI_Finalize instead of MPI_Abort when possible,
- * This is useful for handling errors in code that is executed identically
- * for all processes.
- */
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _fatal_collective_h */
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_OMP_NTHREADS
-#define GMX_OMP_NTHREADS
+#ifndef GMX_OMP_NTHREADS_H
+#define GMX_OMP_NTHREADS_H
#include <stdio.h>
#include "typedefs.h"
}
#endif
-/*! Enum values corresponding to multithreaded algorithmic modules. */
+/** Enum values corresponding to multithreaded algorithmic modules. */
typedef enum module_nth
{
/* Default is meant to be used in OMP regions outside the named
emntNR
} module_nth_t;
-/*! Initializes the per-module thread count. It is compatible with tMPI,
- * thread-safety is ensured (for the features available with tMPI).
- * This function should caled only once during the initialization of mdrun. */
+/*! \brief
+ * Initializes the per-module thread count.
+ *
+ * It is compatible with tMPI, thread-safety is ensured (for the features
+ * available with tMPI).
+ * This function should caled only once during the initialization of mdrun. */
void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
int nthreads_hw_avail,
int omp_nthreads_req,
gmx_bool bCurrNodePMEOnly,
gmx_bool bFullOmpSupport);
-/*! Returns the number of threads to be used in the given module m. */
+/*! \brief
+ * Returns the number of threads to be used in the given module \p mod. */
int gmx_omp_nthreads_get(int mod);
-/*! \brief Sets the number of threads to be used in module. Intended
- * for use in testing. */
+/*! \brief Sets the number of threads to be used in module.
+ *
+ * Intended for use in testing. */
void gmx_omp_nthreads_set(int mod, int nthreads);
-/*! Read the OMP_NUM_THREADS env. var. and check against the value set on the command line. */
+/*! \brief
+ * Read the OMP_NUM_THREADS env. var. and check against the value set on the
+ * command line. */
void gmx_omp_nthreads_read_env(int *nthreads_omp,
gmx_bool bIsSimMaster);
}
#endif
-#endif /* GMX_OMP_NTHREADS */
+#endif
*/
#ifndef GMX_THREAD_AFFINITY_H_
#define GMX_THREAD_AFFINITY_H_
+
#include "typedefs.h"
#ifdef __cplusplus
* made by the OpenMP library.
*
* Note that this will only work on Linux as we use a GNU feature.
+ * With bAfterOpenmpInit false, it will also detect whether OpenMP environment
+ * variables for setting the affinity are set.
*/
void
gmx_check_thread_affinity_set(FILE *fplog, const t_commrec *cr,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#ifndef _macros_h
#define _macros_h
-#include "typedefs.h" /* for real definition only */
-
/* no extern "C" for this header because it only defines Macros */
/*
* angle.a[0][3]
*/
#ifndef __cplusplus
+#include <stdlib.h>
+
#define AI a[0]
#define AJ a[1]
#define AK a[2]
extern "C" {
#endif
-int gmx_gethostname(char *name, size_t len);
-/* Sets the hostname to the value given by gethostname, if available,
- * and to "unknown" otherwise. name should have at least size len.
- * Returns 0 on success, -1 on error.
- */
-
void gmx_log_open(const char *fn, const t_commrec *cr,
gmx_bool bMasterOnly, gmx_bool bAppendFiles, FILE**);
/* Open the log file, if necessary (nprocs > 1) the logfile name is
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#ifndef _mdebin_h
#define _mdebin_h
+#include <stdio.h>
+
#include "typedefs.h"
-#include "sysstuff.h"
#include "ebin.h"
#include "../fileio/enxio.h"
#include "types/state.h"
extern "C" {
#endif
-/*! Initializes the data structures related to CUDA nonbonded calculations. */
+/** Initializes the data structures related to CUDA nonbonded calculations. */
FUNC_QUALIFIER
void nbnxn_cuda_init(FILE gmx_unused *fplog,
nbnxn_cuda_ptr_t gmx_unused *p_cu_nb,
/* true of both local and non-local are don on GPU */
gmx_bool gmx_unused bLocalAndNonlocal) FUNC_TERM
-/*! Initializes simulation constant data. */
+/** Initializes simulation constant data. */
FUNC_QUALIFIER
void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const interaction_const_t gmx_unused *ic,
const nonbonded_verlet_group_t gmx_unused *nbv_group) FUNC_TERM
-/*! Initializes pair-list data for GPU, called at every pair search step. */
+/** Initializes pair-list data for GPU, called at every pair search step. */
FUNC_QUALIFIER
void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const nbnxn_pairlist_t gmx_unused *h_nblist,
int gmx_unused iloc) FUNC_TERM
-/*! Initializes atom-data on the GPU, called at every pair search step. */
+/** Initializes atom-data on the GPU, called at every pair search step. */
FUNC_QUALIFIER
void nbnxn_cuda_init_atomdata(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const nbnxn_atomdata_t gmx_unused *atomdata) FUNC_TERM
void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const interaction_const_t gmx_unused *ic) FUNC_TERM
-/*! Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
+/** Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
FUNC_QUALIFIER
void nbnxn_cuda_upload_shiftvec(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const nbnxn_atomdata_t gmx_unused *nbatom) FUNC_TERM
-/*! Clears GPU outputs: nonbonded force, shift force and energy. */
+/** Clears GPU outputs: nonbonded force, shift force and energy. */
FUNC_QUALIFIER
void nbnxn_cuda_clear_outputs(nbnxn_cuda_ptr_t gmx_unused cu_nb,
int gmx_unused flags) FUNC_TERM
-/*! Frees all GPU resources used for the nonbonded calculations. */
+/** Frees all GPU resources used for the nonbonded calculations. */
FUNC_QUALIFIER
void nbnxn_cuda_free(nbnxn_cuda_ptr_t gmx_unused cu_nb) FUNC_TERM
-/*! Returns the GPU timings structure or NULL if GPU is not used or timing is off. */
+/** Returns the GPU timings structure or NULL if GPU is not used or timing is off. */
FUNC_QUALIFIER
wallclock_gpu_t * nbnxn_cuda_get_timings(nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
}
#endif
-/*! Resets nonbonded GPU timings. */
+/** Resets nonbonded GPU timings. */
FUNC_QUALIFIER
void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t gmx_unused cu_nb) FUNC_TERM
-/*! Calculates the minimum size of proximity lists to improve SM load balance
- with CUDA non-bonded kernels. */
+/** Calculates the minimum size of proximity lists to improve SM load balance
+ * with CUDA non-bonded kernels. */
FUNC_QUALIFIER
int nbnxn_cuda_min_ci_balanced(nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
}
#endif
-/*! Returns if analytical Ewald CUDA kernels are used. */
+/** Returns if analytical Ewald CUDA kernels are used. */
FUNC_QUALIFIER
gmx_bool nbnxn_cuda_is_kernel_ewald_analytical(const nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
#include "types/simple.h"
#include "typedefs.h"
-#include "main.h"
-#include "gmx_fatal.h"
+#include "../utility/fatalerror.h"
#ifdef __cplusplus
extern "C" {
void gmx_fill_commrec_from_mpi(t_commrec *cr);
/* Continues t_commrec construction */
-int gmx_node_num(void);
-/* return the number of nodes in the ring */
-
-int gmx_node_rank(void);
-/* return the rank of the node */
-
-int gmx_physicalnode_id_hash(void);
-/* Return a non-negative hash that is, hopefully, unique for each physical node.
- * This hash is useful for determining hardware locality.
- */
-
-int gmx_hostname_num(void);
-/* Ostensibly, returns a integer characteristic of and unique to each
- physical node in the MPI system. If the first part of the MPI
- hostname (up to the first dot) ends with a number, returns this
- number. If the first part of the MPI hostname does not ends in a
- number (0-9 characters), returns 0.
- */
-
void gmx_setup_nodecomm(FILE *fplog, t_commrec *cr);
/* Sets up fast global communication for clusters with multi-core nodes */
void gmx_init_intranode_counters(t_commrec *cr);
/* Initializes intra-physical-node MPI process/thread counts and ID. */
-gmx_bool gmx_mpi_initialized(void);
-/* return TRUE when MPI_Init has been called.
- * return FALSE when MPI_Init has not been called OR
- * when GROMACS was compiled without MPI support.
- */
-
void gmx_barrier(const t_commrec *cr);
/* Wait till all processes in cr->mpi_comm_mygroup have reached the barrier */
void gmx_sumd_sim(int nr, double r[], const gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of doubles */
-void gmx_abort(int nodeid, int nnodes, int errorno);
-/* Abort the parallel run */
-
#ifdef GMX_DOUBLE
#define gmx_sum gmx_sumd
#define gmx_sum_sim gmx_sumd_sim
#define gmx_sum_sim gmx_sumf_sim
#endif
+gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr);
+/* Return TRUE when fname exists, FALSE otherwise, bcast from master to others */
+
+void
+gmx_fatal_collective(int f_errno, const char *file, int line,
+ const t_commrec *cr, gmx_domdec_t *dd,
+ const char *fmt, ...);
+/* As gmx_fatal declared in utility/fatalerror.h,
+ * but only the master process prints the error message.
+ * This should only be called one of the following two situations:
+ * 1) On all nodes in cr->mpi_comm_mysim, with cr!=NULL,dd==NULL.
+ * 2) On all nodes in dd->mpi_comm_all, with cr==NULL,dd!=NULL.
+ * This will call MPI_Finalize instead of MPI_Abort when possible,
+ * This is useful for handling errors in code that is executed identically
+ * for all processes.
+ */
+
+/* This doesn't currently work if enabled (needs some header cleanup). */
#ifdef DEBUG_GMX
#define debug_gmx() do { FILE *fp = debug ? debug : stderr; \
if (bDebugMode()) { fprintf(fp, "NODEID=%d, %s %d\n", gmx_mpi_initialized() ? gmx_node_rank() : -1, __FILE__, __LINE__); } fflush(fp); } while (0)
#define _ns_h
#include <stdio.h>
-#include "sysstuff.h"
+
#include "typedefs.h"
#include "pbc.h"
#include "tgroup.h"
#ifndef _orires_h
#define _orires_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#ifdef __cplusplus
#ifndef _types_pbc_h
#define _types_pbc_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
-/*! Allocates nbytes of page-locked memory. */
+/** Allocates nbytes of page-locked memory. */
void pmalloc(void gmx_unused **h_ptr, size_t gmx_unused nbytes) FUNC_TERM
-/*! Allocates nbytes of page-locked memory with write-combining. */
+/** Allocates nbytes of page-locked memory with write-combining. */
void pmalloc_wc(void gmx_unused **h_ptr, size_t gmx_unused nbytes) FUNC_TERM
-/*! Frees page locked memory allocated with pmalloc. */
+/** Frees page locked memory allocated with pmalloc. */
void pfree(void gmx_unused *h_ptr) FUNC_TERM
#ifdef __cplusplus
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
#ifndef _rbin_h
#define _rbin_h
-#include "sysstuff.h"
#include "typedefs.h"
-#include "network.h"
#ifdef __cplusplus
extern "C" {
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, 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.
- */
-
-#ifndef _sysstuff_h
-#define _sysstuff_h
-
-#ifndef _386_
-#include <stdlib.h>
-#endif
-#include <stdio.h>
-#include <errno.h>
-#include <signal.h>
-#include <limits.h>
-#include <time.h>
-
-#endif /* _sysstuff_h */
#define NOTSET -12345
#include <sys/types.h>
-#include "sysstuff.h"
+
#include "types/simple.h"
#include "types/enums.h"
#include "types/block.h"
#ifndef _inputrec_h_
#define _inputrec_h_
+#include <stdio.h>
#include "simple.h"
#include "enums.h"
-#include "../sysstuff.h"
#include "../../swap/enums.h"
#ifdef __cplusplus
#endif
-/*! Nonbonded NxN kernel types: plain C, CPU SIMD, GPU CUDA, GPU emulation */
+/** Nonbonded NxN kernel types: plain C, CPU SIMD, GPU CUDA, GPU emulation */
typedef enum
{
nbnxnkNotSet = 0,
nbnxnkNR
} nbnxn_kernel_type;
-/*! Return a string indentifying the kernel type */
+/** Return a string indentifying the kernel type */
const char *lookup_nbnxn_kernel_name(int kernel_type);
enum {
#ifndef _simple_h
#define _simple_h
-/* Information about integer data type sizes */
-#include <limits.h>
-#define __STDC_LIMIT_MACROS
-#include <stdint.h>
-#ifndef _MSC_VER
-#define __STDC_FORMAT_MACROS
-#include <inttypes.h>
-#endif
+#include "../../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-
-#define XX 0 /* Defines for indexing in */
-#define YY 1 /* vectors */
+#define XX 0 /* Defines for indexing in */
+#define YY 1 /* vectors */
#define ZZ 2
-#define DIM 3 /* Dimension of vectors */
-#define XXXX 0 /* defines to index matrices */
-#define XXYY 1
-#define XXZZ 2
-#define YYXX 3
-#define YYYY 4
-#define YYZZ 5
-#define ZZXX 6
-#define ZZYY 7
-#define ZZZZ 8
-
-/* There is no standard size for 'bool' in C++, so when
- * we previously defined it to int for C code the data types
- * (and structs) would have different size depending on your compiler,
- * both at gromacs build time and when you use the library.
- * The only way around this is to NOT assume anything about the C++ type,
- * so we cannot use the name 'bool' in our C code anymore.
- */
-
-typedef int gmx_bool;
-
-#ifndef FALSE
-# define FALSE 0
-#endif
-#ifndef TRUE
-# define TRUE 1
-#endif
-#define BOOL_NR 2
-
+#define DIM 3 /* Dimension of vectors */
typedef int atom_id; /* To indicate an atoms id */
#define NO_ATID (atom_id)(~0) /* Use this to indicate invalid atid */
typedef int imatrix[DIM][DIM];
-#ifdef _MSC_VER
-typedef __int32 gmx_int32_t;
-#define GMX_PRId32 "I32d"
-#define GMX_SCNd32 "I32d"
-
-typedef __int64 gmx_int64_t;
-#define GMX_PRId64 "I64d"
-#define GMX_SCNd64 "I64d"
-
-typedef unsigned __int32 gmx_uint32_t;
-#define GMX_PRIu32 "I32u"
-#define GMX_SCNu32 "I32u"
-
-typedef unsigned __int64 gmx_uint64_t;
-#define GMX_PRIu64 "I64u"
-#define GMX_SCNu64 "I64u"
-#else
-typedef int32_t gmx_int32_t;
-#define GMX_PRId32 PRId32
-#define GMX_SCNd32 SCNd32
-
-typedef int64_t gmx_int64_t;
-#define GMX_PRId64 PRId64
-#define GMX_SCNd64 SCNd64
-
-typedef uint32_t gmx_uint32_t;
-#define GMX_PRIu32 PRIu32
-#define GMX_SCNu32 SCNu32
-
-typedef uint64_t gmx_uint64_t;
-#define GMX_PRIu64 PRIu64
-#define GMX_SCNu64 SCNu64
-#endif
-
-#define GMX_INT32_MAX INT32_MAX
-#define GMX_INT32_MIN INT32_MIN
-
-#define GMX_INT64_MAX INT64_MAX
-#define GMX_INT64_MIN INT64_MIN
-
-#define GMX_UINT32_MAX UINT32_MAX
-#define GMX_UINT32_MIN UINT32_MIN
-
-#define GMX_UINT64_MAX UINT64_MAX
-#define GMX_UINT64_MIN UINT64_MIN
-
-#if !defined __cplusplus && _MSC_VER
-#define gmx_inline __inline
-#else
-/* C++ or C99 */
-#define gmx_inline inline
-#endif
-
-/* ICC, GCC, MSVC, Pathscale, PGI, XLC support __restrict.
- * Any other compiler can be added here. We cannot
- * use restrict because it is in C99 but not in C++ */
-#define gmx_restrict __restrict
-
-/*
- * These attributes suppress compiler warnings about unused function arguments
- * by marking them as possibly unused. Some arguments are unused but
- * have to be retained to preserve a function signature
- * that must match that of another function.
- * Some arguments are only used in *some* code paths (e.g. MPI)
- */
-
-#ifndef gmx_unused
-#ifdef __GNUC__
-/* GCC, clang, and some ICC pretending to be GCC */
-# define gmx_unused __attribute__ ((unused))
-#elif (defined(__INTEL_COMPILER) || defined(__ECC)) && !defined(_MSC_VER)
-/* ICC on *nix */
-# define gmx_unused __attribute__ ((unused))
-#elif defined _MSC_VER
-/* MSVC */
-# define gmx_unused /*@unused@*/
-#elif defined(__xlC__)
-/* IBM */
-# define gmx_unused __attribute__ ((unused))
-#else
-# define gmx_unused
-#endif
-#endif
-
-/* Standard sizes for char* string buffers */
-#define STRLEN 4096
-#define BIG_STRLEN 1048576
-
-
#ifdef __cplusplus
}
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#ifndef _vcm_h
#define _vcm_h
-#include "sysstuff.h"
+#include <stdio.h>
+
#include "typedefs.h"
#ifdef __cplusplus
#include <config.h>
#endif
+#include <math.h>
+
#include "types/simple.h"
-#include "../math/utilities.h"
#include "typedefs.h"
-#include "sysstuff.h"
-#include "gmx_fatal.h"
-#include <math.h>
#include "physics.h"
+#include "../math/utilities.h"
+#include "../utility/fatalerror.h"
+
#ifdef __cplusplus
extern "C" {
#elif 0
#ifndef _viewit_h
#define _viewit_h
-#include "typedefs.h"
+#include "types/oenv.h"
#include "../fileio/filenm.h"
#ifdef __cplusplus
extern "C" {
#endif
-
void do_view(const output_env_t oenv, const char *fn, const char *opts);
/* forks off appropriate command to view file.
* currently eps, xpm, xvg and pdb are supported
#include "eigensolver.h"
#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gmx_lapack.h"
#include <stdio.h>
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gmx_lapack.h"
*/
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xdrf.h"
#include "gromacs/linearalgebra/sparsematrix.h"
-
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
/* Just a number to identify our file type */
#include <math.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
static gmx_inline
#endif
#include <math.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "physics.h"
#include "pbc.h"
#include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define N 4
#include "do_fit.h"
#include "gromacs/math/utilities.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "vec.h"
#include "txtdump.h"
#include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
real calc_similar_ind(gmx_bool bRho, int nind, atom_id *index, real mass[],
unsigned int
gmx_log2i(unsigned int x);
-/*! /brief Multiply two large ints
+/*! \brief Multiply two large ints
*
- * \return False iff overflow occured
+ * \return False iff overflow occured
*/
gmx_bool
check_int_multiply_for_overflow(gmx_int64_t a,
#include "typedefs.h"
#include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
real
adress_weight(rvec x,
#include "network.h"
#include "vec.h"
#include "physics.h"
-#include "main.h"
#include "calcmu.h"
#include "gmx_omp_nthreads.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 <config.h>
#endif
-#include "sysstuff.h"
#include "force.h"
#include "vec.h"
#include "mshift.h"
#include "macros.h"
+#define XXXX 0
+#define XXYY 1
+#define XXZZ 2
+#define YYXX 3
+#define YYYY 4
+#define YYZZ 5
+#define ZZXX 6
+#define ZZYY 7
+#define ZZZZ 8
+
static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
{
vir[XX] -= 0.5*dvx;
#endif
#include <math.h>
-#include "main.h"
+#include <stdlib.h>
+
+#include "types/commrec.h"
#include "constr.h"
#include "copyrite.h"
#include "physics.h"
#include "vec.h"
#include "pbc.h"
-#include "gromacs/utility/smalloc.h"
#include "mdrun.h"
#include "nrnb.h"
#include "domdec.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int b0; /* first constraint for this thread */
#include <config.h>
#endif
+#include <stdlib.h>
+
#include "gromacs/fileio/confio.h"
#include "types/commrec.h"
#include "constr.h"
#include "copyrite.h"
#include "invblock.h"
-#include "main.h"
#include "mdrun.h"
#include "nrnb.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/pulling/pull.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct gmx_constr {
int ncon_tot; /* The total number of constraints */
#include "macros.h"
#include "physics.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "nrnb.h"
#include "gromacs/random/random.h"
#include <stdio.h>
#include "vec.h"
#include "constr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "pbc.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
+#include "gromacs/utility/fatalerror.h"
+#include "network.h"
#include "vec.h"
#include "domdec.h"
#include "domdec_network.h"
#include "gmx_omp_nthreads.h"
#include "gpu_utils.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/swap/swapcoords.h"
#include "gromacs/utility/qsort_threadsafe.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
#define DDRANK(dd, rank) (rank)
#define DDMASTERRANK(dd) (dd->masterrank)
#include "nsgrid.h"
#include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,
t_commrec *cr_sum)
#include "gmx_omp_nthreads.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
int nsend;
#endif
#include <string.h>
+
#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "types/commrec.h"
#include "domdec.h"
#include "domdec_network.h"
#include "force.h"
#include "gmx_omp_nthreads.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* for dd_init_local_state */
#define NITEM_DD_INIT_LOCAL_STATE 5
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "ebin.h"
-#include "main.h"
#include "gromacs/math/utilities.h"
#include "vec.h"
#include "physics.h"
#include <config.h>
#endif
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
#include "typedefs.h"
#include "types/commrec.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "physics.h"
#include "coulomb.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/math/gmxcomplex.h"
#define TOL 2e-5
#include "mdrun.h"
#include "update.h"
#include "physics.h"
-#include "main.h"
#include "mdatoms.h"
#include "force.h"
#include "bondf.h"
#include "network.h"
#include "calcmu.h"
#include "constr.h"
-#include "xvgr.h"
#include "gromacs/random/random.h"
#include "domdec.h"
#include "macros.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
static void init_df_history_weights(df_history_t *dfhist, t_expanded *expand, int nlim)
#include <math.h>
#include <string.h>
#include <assert.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void ns(FILE *fp,
t_forcerec *fr,
#include <math.h>
#include <string.h>
#include <assert.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "vec.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "physics.h"
#include "force.h"
#include "tables.h"
#include "physics.h"
#include "domdec.h"
#include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mtop_util.h"
#include "pbc.h"
#include "nrnb.h"
#include "physics.h"
#include "domdec.h"
#include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mtop_util.h"
#include "genborn.h"
#include "physics.h"
#include "domdec.h"
#include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mtop_util.h"
#include "genborn.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/utility/smalloc.h"
#include "vec.h"
-#include "main.h"
#include "mvdata.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "symtab.h"
#include "txtdump.h"
#include "mdatoms.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 <math.h>
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mdrun.h"
#include "md_support.h"
#include "md_logging.h"
#include "typedefs.h"
#include "mdatoms.h"
#include "gromacs/utility/smalloc.h"
-#include "main.h"
#include "qmmm.h"
#include "mtop_util.h"
#include "gmx_omp_nthreads.h"
#include <config.h>
#endif
-#include <string.h>
#include <float.h>
+#include <stdlib.h>
+#include <string.h>
+
#include "typedefs.h"
#include "mdebin.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/enxio.h"
#include "vec.h"
#include "disre.h"
-#include "main.h"
#include "network.h"
#include "names.h"
#include "orires.h"
#include "constr.h"
#include "mtop_util.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/gmxfio.h"
#include "macros.h"
#include "mdrun.h"
#include <float.h>
#include <math.h>
#include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "mdebin.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/enxio.h"
#include <string.h>
#include <time.h>
#include <math.h>
-#include "sysstuff.h"
#include "gromacs/utility/cstringutil.h"
#include "network.h"
#include "gromacs/utility/smalloc.h"
#include "nrnb.h"
-#include "main.h"
#include "force.h"
#include "macros.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "typedefs.h"
#include "update.h"
#include <config.h>
#endif
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
+
#include "macros.h"
#include "vec.h"
#include "nbnxn_consts.h"
#include "nbnxn_internal.h"
#include "nbnxn_atomdata.h"
#include "nbnxn_search.h"
-#include "gromacs/utility/gmxomp.h"
#include "gmx_omp_nthreads.h"
#include "thread_mpi/atomic.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
/* Default nbnxn allocation routine, allocates NBNXN_MEM_ALIGN byte aligned */
void nbnxn_alloc_aligned(void **ptr, size_t nbytes)
{
#include "nbnxn_cuda.h"
#include "nbnxn_cuda_data_mgmt.h"
+#include "gromacs/utility/cstringutil.h"
+
#if defined TEXOBJ_SUPPORTED && __CUDA_ARCH__ >= 300
#define USE_TEXOBJ
#endif
extern "C" {
#endif
-/*! Launch asynchronously the nonbonded force calculations.
+/*! \brief
+ * Launch asynchronously the nonbonded force calculations.
+ *
* This consists of the following (async) steps launched:
* - upload x and q;
* - upload shift vector;
int gmx_unused flags,
int gmx_unused iloc) FUNC_TERM
-/*! Launch asynchronously the download of nonbonded forces from the GPU
- * (and energies/shift forces if required).
+/*! \brief
+ * Launch asynchronously the download of nonbonded forces from the GPU
+ * (and energies/shift forces if required).
*/
void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const nbnxn_atomdata_t gmx_unused *nbatom,
int gmx_unused flags,
int gmx_unused aloc) FUNC_TERM
-/*! Wait for the asynchronously launched nonbonded calculations and data
- * transfers to finish.
+/*! \brief
+ * Wait for the asynchronously launched nonbonded calculations and data
+ * transfers to finish.
*/
void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t gmx_unused cu_nb,
const nbnxn_atomdata_t gmx_unused *nbatom,
#include <cuda.h>
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
#include "tables.h"
#include "typedefs.h"
#include "types/enums.h"
#include "gpu_utils.h"
#include "gromacs/utility/common.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
#include "../nbnxn_kernel_common.h"
#include "gmx_omp_nthreads.h"
#include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* {0} */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* {0} */
#include "../nbnxn_kernel_common.h"
#include "gmx_omp_nthreads.h"
#include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* GMX_NBNXN_SIMD_2XNN */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#include "../nbnxn_kernel_common.h"
#include "gmx_omp_nthreads.h"
#include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* GMX_NBNXN_SIMD_4XN */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#include <string.h>
#include <assert.h>
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "types/commrec.h"
#include "macros.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * 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 "types/nlistheuristics.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
void reset_nlistheuristics(gmx_nlheur_t *nlh, gmx_int64_t step)
#endif
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
+
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "ns.h"
#include "pbc.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "nrnb.h"
#include "txtdump.h"
#include "mtop_util.h"
#include <stdlib.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "nsgrid.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "network.h"
#include "domdec.h"
#include "pbc.h"
#include <stdio.h>
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
/***********************************
#include <config.h>
#endif
+#include <assert.h>
+#include <math.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <math.h>
-#include <assert.h>
+
#include "typedefs.h"
#include "txtdump.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "coulomb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "pme.h"
#include "network.h"
#include "physics.h"
#include "macros.h"
#include "gromacs/fft/parallel_3dfft.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/timing/cyclecounter.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "pme.h"
#include "network.h"
#ifdef GMX_QMMM_GAMESS
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "qmmm.h"
#include <stdio.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include <stdlib.h>
#ifdef GMX_QMMM_GAUSSIAN
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "qmmm.h"
#include <stdio.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include <stdlib.h>
#ifdef GMX_QMMM_MOPAC
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "qmmm.h"
#include <stdio.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include <stdlib.h>
#endif
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "qmmm.h"
#include <stdio.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include <stdlib.h>
#endif
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "macros.h"
#include "qmmm.h"
#include <stdio.h>
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include <stdlib.h>
#include "mtop_util.h"
#include <config.h>
#endif
-#include "sysstuff.h"
#include "typedefs.h"
#include "force.h"
#include "names.h"
#endif
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "pbc.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
+
#include "typedefs.h"
#include "types/commrec.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "vec.h"
#include "txtdump.h"
#include "force.h"
#include "sim_util.h"
#include "update.h"
#include "physics.h"
-#include "main.h"
#include "mdatoms.h"
#include "force.h"
#include "bondf.h"
#include "network.h"
#include "calcmu.h"
#include "constr.h"
-#include "xvgr.h"
#include "copyrite.h"
#include "domdec.h"
#include "genborn.h"
#include <stdio.h>
#include "typedefs.h"
#include "types/commrec.h"
-#include "sysstuff.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "network.h"
#include "txtdump.h"
#include "names.h"
#include "physics.h"
#include "vec.h"
#include "gromacs/math/utilities.h"
-#include "main.h"
#include "force.h"
#include "vcm.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "network.h"
#include "rbin.h"
#include "tgroup.h"
#include "domdec.h"
#include "constr.h"
#include "checkpoint.h"
-#include "xvgr.h"
#include "md_support.h"
#include "mdrun.h"
#include "sim_util.h"
#include "typedefs.h"
#include "names.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/xvgr.h"
#include "vec.h"
-#include "main.h"
#include "network.h"
#include "physics.h"
#include "force.h"
#include <math.h>
#include "macros.h"
-#include "main.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "tgroup.h"
#include "vec.h"
#include "network.h"
#include <config.h>
#endif
+#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include <math.h>
-#include "sysstuff.h"
+
#include "network.h"
#include "gromacs/utility/smalloc.h"
#include "nrnb.h"
-#include "main.h"
#include "chargegroup.h"
#include "force.h"
#include "macros.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "txtdump.h"
#include "typedefs.h"
#include "update.h"
#include "domdec.h"
#include "gromacs/random/random.h"
#include "physics.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "mdatoms.h"
#include "ns.h"
#include "mtop_util.h"
#include <math.h>
#include "types/commrec.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "nrnb.h"
#include "physics.h"
#include "macros.h"
#include "vec.h"
-#include "main.h"
#include "update.h"
#include "gromacs/random/random.h"
#include "mshift.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/pulling/pull.h"
#endif
#include <stdio.h>
+
#include "typedefs.h"
+#include "types/commrec.h"
#include "vsite.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include <math.h>
#include <string.h>
-#include "gromacs/math/utilities.h"
-#include "sysstuff.h"
+
#include "typedefs.h"
#include "macros.h"
-#include "gromacs/utility/smalloc.h"
#include "force.h"
-#include "gromacs/fileio/filenm.h"
#include "nrnb.h"
#include "vec.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
void make_wall_tables(FILE *fplog, const output_env_t oenv,
const t_inputrec *ir, const char *tabfn,
const gmx_groups_t *groups,
#include "types/commrec.h"
#include "ns.h"
#include "nrnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "names.h"
#include "domdec.h"
#include "gromacs/fileio/gmxfio.h"
#include <string>
-#include "../legacyheaders/types/simple.h"
+#include "../utility/basedefinitions.h"
#include "../utility/gmxassert.h"
#include "abstractoption.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "index.h"
#include "gromacs/fileio/gmxfio.h"
#include "vec.h"
#include <string.h>
#include "gromacs/utility/smalloc.h"
#include "pull.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "names.h"
#include "pbc.h"
#include "mtop_util.h"
#include "names.h"
#include "vec.h"
#include "gmx_ga2la.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/linearalgebra/nrjac.h"
#include <stdlib.h>
-#include "sysstuff.h"
#include "princ.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "vec.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "types/commrec.h"
#include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "macros.h"
#include "symtab.h"
#include "index.h"
#endif
/*! Fixed random number seeds for different types of RNG */
-#define RND_SEED_UPDATE 1 /*!< For coordinate update (sd, bd, ..) */
-#define RND_SEED_REPLEX 2 /*!< For replica exchange */
-#define RND_SEED_VRESCALE 3 /*!< For V-rescale thermostat */
-#define RND_SEED_ANDERSEN 4 /*!< For Andersen thermostat */
-#define RND_SEED_TPI 5 /*!< For test particle insertion */
-#define RND_SEED_EXPANDED 6 /*!< For expanded emseble methods */
+#define RND_SEED_UPDATE 1 /**< For coordinate update (sd, bd, ..) */
+#define RND_SEED_REPLEX 2 /**< For replica exchange */
+#define RND_SEED_VRESCALE 3 /**< For V-rescale thermostat */
+#define RND_SEED_ANDERSEN 4 /**< For Andersen thermostat */
+#define RND_SEED_TPI 5 /**< For test particle insertion */
+#define RND_SEED_EXPANDED 6 /**< For expanded emseble methods */
/*! \brief Abstract datatype for a random number generator
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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 "gromacs/selection/centerofmass.h"
+#include <errno.h>
+
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/pbc.h"
#include "gromacs/legacyheaders/vec.h"
*/
#include "gromacs/selection/indexutil.h"
+#include <cstdlib>
#include <cstring>
#include <string>
#include <vector>
#include "gromacs/legacyheaders/index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
/********************************************************************
void
gmx_ana_index_sort(gmx_ana_index_t *g)
{
- qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
+ std::qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
}
/*!
break;
default: /* Should not be reached */
- gmx_bug("internal error");
+ GMX_RELEASE_ASSERT(false, "Unreachable code was reached");
break;
}
}
#include <boost/exception_ptr.hpp>
#include <boost/shared_ptr.hpp>
-#include "gromacs/fileio/futil.h"
#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selmethod.h"
#include <boost/shared_ptr.hpp>
#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/xvgr.h"
#include "gromacs/onlinehelp/helpmanager.h"
#include "gromacs/onlinehelp/helpwritercontext.h"
#include <math.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \cond libapi */
/*! \addtogroup module_simd */
#endif
#include <stddef.h>
-#include "gromacs/legacyheaders/types/simple.h"
+
+#include "gromacs/utility/basedefinitions.h"
/* Forward declarations so memory allocation can be used in implementations */
static gmx_inline float * gmx_simd_align_f(float *p);
* \ingroup module_simd
*/
#include <vector>
+
#include <gtest/gtest.h>
-#include "gromacs/simd/simd.h"
+#include "gromacs/legacyheaders/types/simple.h"
+
+#include "gromacs/simd/simd.h"
namespace gmx
{
*/
#include <gtest/gtest.h>
+
+#include "gromacs/legacyheaders/types/simple.h"
+
#include "gromacs/simd/simd.h"
namespace
#include "names.h"
#include "network.h"
#include "mdrun.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/timing/wallcycle.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
#include "md_logging.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
/* DEBUG_WCYCLE adds consistency checking for the counters.
* It checks if you stop a counter different from the last
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/types/simple.h"
-
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/smalloc.h"
/* TODO in future: convert gmx_walltime_accounting to a class,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
#ifndef GMX_TIMING_WALLTIME_ACCOUNTING_H
#define GMX_TIMING_WALLTIME_ACCOUNTING_H
-#include "../legacyheaders/types/simple.h"
+#include "../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-/*! Contains per-process and per-thread data about elapsed wall-clock
- * times and integration steps performed. */
+/*! \brief
+ * Contains per-process and per-thread data about elapsed wall-clock
+ * times and integration steps performed. */
typedef struct gmx_walltime_accounting *gmx_walltime_accounting_t;
//! Constructor
void
walltime_accounting_destroy(gmx_walltime_accounting_t walltime_accounting);
-/*! Record initial time stamps, e.g. at run end or counter
- * re-initalization time */
+/*! \brief
+ * Record initial time stamps, e.g. at run end or counter re-initalization time
+ */
void
walltime_accounting_start(gmx_walltime_accounting_t walltime_accounting);
-/*! Measure and cache the elapsed wall-clock time since
- * walltime_accounting_start */
+/*! \brief
+ * Measure and cache the elapsed wall-clock time since
+ * walltime_accounting_start() */
void
walltime_accounting_end(gmx_walltime_accounting_t walltime_accounting);
-/*! Measure and return the elapsed wall-clock time since
- * walltime_accounting_start */
+/*! \brief
+ * Measure and return the elapsed wall-clock time since
+ * walltime_accounting_start() */
double
walltime_accounting_get_current_elapsed_time(gmx_walltime_accounting_t walltime_accounting);
double
walltime_accounting_get_nsteps_done(gmx_walltime_accounting_t walltime_accounting);
-/*! Set the number of integration steps done
+/*! \brief Set the number of integration steps done
*
* TODO consider whether this should get done in walltime_accounting_end */
void
walltime_accounting_set_nsteps_done(gmx_walltime_accounting_t walltime_accounting,
gmx_int64_t nsteps_done);
-/*! \brief Calls system timing routines (e.g. clock_gettime) to get the
- * (fractional) number of seconds elapsed since the epoch.
+/*! \brief
+ * Calls system timing routines (e.g. clock_gettime) to get the (fractional)
+ * number of seconds elapsed since the epoch.
*
* Resolution is implementation-dependent, but typically nanoseconds
* or microseconds. */
#include <stdio.h>
#include <string.h>
-#include "main.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "atomprop.h"
#include "vec.h"
#include "pbc.h"
#include "gromacs/utility/smalloc.h"
#include "names.h"
#include "mtop_util.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/xtcio.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "main.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "sysstuff.h"
+#include "gromacs/utility/futil.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "names.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include <math.h>
#include "index.h"
-#include "gmx_fatal.h"
-#include "sysstuff.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "names.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/random/random.h"
#define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))
#include <string.h>
#include <math.h>
#include <assert.h>
-#include "main.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "names.h"
#include "txtdump.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/scoped_ptr_sfree.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
* The header file.h declares a gmx::File class for basic I/O support.
*
* The header path.h declares helpers for manipulating paths and for managing
- * directories (this has been moved to src/gromacs/fileio/ to wait for
- * resolution of #950).
+ * directories.
*
* The fate of these headers depends on what is decided in Redmine issue #950.
*
set(UTILITY_PUBLIC_HEADERS
arrayref.h
+ basedefinitions.h
cstringutil.h
common.h
errorcodes.h
exceptions.h
+ fatalerror.h
file.h
flags.h
+ futil.h
gmx_header_config.h
gmxassert.h
init.h
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * 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.
+ */
+/*! \file
+ * \brief
+ * Basic types and macros used throughout \Gromacs.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_BASEDEFINITIONS_H
+#define GMX_UTILITY_BASEDEFINITIONS_H
+
+/* Information about integer data type sizes */
+#include <limits.h>
+#define __STDC_LIMIT_MACROS
+#include <stdint.h>
+#ifndef _MSC_VER
+#define __STDC_FORMAT_MACROS
+#include <inttypes.h>
+#endif
+
+/*! \brief
+ * Boolean type for use in \Gromacs C code.
+ *
+ * There is no standard size for 'bool' in C++, so when
+ * we previously defined it to int for C code the data types
+ * (and structs) would have different size depending on your compiler,
+ * both at \Gromacs build time and when you use the library.
+ * The only way around this is to NOT assume anything about the C++ type,
+ * so we cannot use the name 'bool' in our C code anymore.
+ */
+typedef int gmx_bool;
+
+#ifndef FALSE
+/** False value for ::gmx_bool. */
+# define FALSE 0
+#endif
+#ifndef TRUE
+/** True value for ::gmx_bool. */
+# define TRUE 1
+#endif
+/** Number of gmx_bool values. */
+#define BOOL_NR 2
+
+/*! \name Fixed-width integer types
+ *
+ * These types and macros provide the equivalent of 32- and 64-bit integer
+ * types from C99 headers `stdint.h` and `inttypes.h`. These headers are also
+ * there in C++11. The types and macros from here should be used instead of
+ * `int32_t` etc.
+ * MSVC doesn't support these before Visual Studio 2013.
+ */
+/*! \{ */
+#ifdef _MSC_VER
+typedef __int32 gmx_int32_t;
+#define GMX_PRId32 "I32d"
+#define GMX_SCNd32 "I32d"
+
+typedef __int64 gmx_int64_t;
+#define GMX_PRId64 "I64d"
+#define GMX_SCNd64 "I64d"
+
+typedef unsigned __int32 gmx_uint32_t;
+#define GMX_PRIu32 "I32u"
+#define GMX_SCNu32 "I32u"
+
+typedef unsigned __int64 gmx_uint64_t;
+#define GMX_PRIu64 "I64u"
+#define GMX_SCNu64 "I64u"
+#else
+typedef int32_t gmx_int32_t;
+#define GMX_PRId32 PRId32
+#define GMX_SCNd32 SCNd32
+
+typedef int64_t gmx_int64_t;
+#define GMX_PRId64 PRId64
+#define GMX_SCNd64 SCNd64
+
+typedef uint32_t gmx_uint32_t;
+#define GMX_PRIu32 PRIu32
+#define GMX_SCNu32 SCNu32
+
+typedef uint64_t gmx_uint64_t;
+#define GMX_PRIu64 PRIu64
+#define GMX_SCNu64 SCNu64
+#endif
+
+#define GMX_INT32_MAX INT32_MAX
+#define GMX_INT32_MIN INT32_MIN
+
+#define GMX_INT64_MAX INT64_MAX
+#define GMX_INT64_MIN INT64_MIN
+
+#define GMX_UINT32_MAX UINT32_MAX
+#define GMX_UINT32_MIN UINT32_MIN
+
+#define GMX_UINT64_MAX UINT64_MAX
+#define GMX_UINT64_MIN UINT64_MIN
+/*! \} */
+
+/*! \def gmx_inline
+ * \brief
+ * Keyword to use in C code instead of C99 `inline`.
+ *
+ * Some of the C compilers we support do not recognize the C99 keyword
+ * `inline`. This macro should be used in C code and in shared C/C++ headers
+ * to indicate a function is inlined.
+ * C++ code should use plain `inline`, as that is already in C++98.
+ */
+#if !defined __cplusplus && _MSC_VER
+#define gmx_inline __inline
+#else
+/* C++ or C99 */
+#define gmx_inline inline
+#endif
+
+/* ICC, GCC, MSVC, Pathscale, PGI, XLC support __restrict.
+ * Any other compiler can be added here. */
+/*! \brief
+ * Keyword to use in instead of C99 `restrict`.
+ *
+ * We cannot use `restrict` because it is only in C99, but not in C++.
+ * This macro should instead be used to allow easily supporting different
+ * compilers.
+ */
+#define gmx_restrict __restrict
+
+/*! \def gmx_unused
+ * \brief
+ * Attribute to suppres compiler warnings about unused function parameters.
+ *
+ * This attribute suppresses compiler warnings about unused function arguments
+ * by marking them as possibly unused. Some arguments are unused but
+ * have to be retained to preserve a function signature
+ * that must match that of another function.
+ * Some arguments are only used in *some* conditional compilation code paths
+ * (e.g. MPI).
+ */
+#ifndef gmx_unused
+#ifdef __GNUC__
+/* GCC, clang, and some ICC pretending to be GCC */
+# define gmx_unused __attribute__ ((unused))
+#elif (defined(__INTEL_COMPILER) || defined(__ECC)) && !defined(_MSC_VER)
+/* ICC on *nix */
+# define gmx_unused __attribute__ ((unused))
+#elif defined _MSC_VER
+/* MSVC */
+# define gmx_unused /*@unused@*/
+#elif defined(__xlC__)
+/* IBM */
+# define gmx_unused __attribute__ ((unused))
+#else
+# define gmx_unused
+#endif
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * 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.
+ */
+#include "basenetwork.h"
+
+#include "config.h"
+
+#include <cctype>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
+#include <exception>
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/programcontext.h"
+
+int gmx_gethostname(char *name, size_t len)
+{
+ if (len < 8)
+ {
+ gmx_incons("gmx_gethostname called with len<8");
+ }
+#if defined(HAVE_UNISTD_H) && !defined(__native_client__)
+ if (gethostname(name, len-1) != 0)
+ {
+ std::strncpy(name, "unknown", 8);
+ return -1;
+ }
+ return 0;
+#else
+ std::strncpy(name, "unknown", 8);
+ return -1;
+#endif
+}
+
+gmx_bool gmx_mpi_initialized(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+ int n;
+ MPI_Initialized(&n);
+
+ return n;
+#endif
+}
+
+int gmx_node_num(void)
+{
+#ifndef GMX_MPI
+ return 1;
+#else
+ int i;
+ (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+int gmx_node_rank(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+ int i;
+ (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
+#include <spi/include/kernel/location.h>
+#endif
+
+int gmx_physicalnode_id_hash(void)
+{
+ int hash_int;
+
+#ifndef GMX_LIB_MPI
+ /* We have a single physical node */
+ hash_int = 0;
+#else
+ int resultlen;
+ char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
+
+ /* This procedure can only differentiate nodes with different names.
+ * Architectures where different physical nodes have identical names,
+ * such as IBM Blue Gene, should use an architecture specific solution.
+ */
+ MPI_Get_processor_name(mpi_hostname, &resultlen);
+
+ /* The string hash function returns an unsigned int. We cast to an int.
+ * Negative numbers are converted to positive by setting the sign bit to 0.
+ * This makes the hash one bit smaller.
+ * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
+ * even on a million node machine. 31 bits might not be enough though!
+ */
+ hash_int =
+ (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
+ if (hash_int < 0)
+ {
+ hash_int -= INT_MIN;
+ }
+#endif
+
+ 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];
+
+ MPI_Get_processor_name(mpi_hostname, &resultlen);
+#ifdef GMX_TARGET_BGQ
+ Personality_t personality;
+ Kernel_GetPersonality(&personality, sizeof(personality));
+ /* Each MPI rank has a unique coordinate in a 6-dimensional space
+ (A,B,C,D,E,T), with dimensions A-E corresponding to different
+ physical nodes, and T within each node. Each node has sixteen
+ physical cores, each of which can have up to four hardware
+ threads, so 0 <= T <= 63 (but the maximum value of T depends on
+ the confituration of ranks and OpenMP threads per
+ node). However, T is irrelevant for computing a suitable return
+ value for gmx_hostname_num().
+ */
+ hostnum = personality.Network_Config.Acoord;
+ hostnum *= personality.Network_Config.Bnodes;
+ hostnum += personality.Network_Config.Bcoord;
+ hostnum *= personality.Network_Config.Cnodes;
+ hostnum += personality.Network_Config.Ccoord;
+ hostnum *= personality.Network_Config.Dnodes;
+ 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",
+ personality.Network_Config.Acoord,
+ personality.Network_Config.Anodes,
+ personality.Network_Config.Bcoord,
+ personality.Network_Config.Bnodes,
+ personality.Network_Config.Ccoord,
+ personality.Network_Config.Cnodes,
+ personality.Network_Config.Dcoord,
+ personality.Network_Config.Dnodes,
+ personality.Network_Config.Ecoord,
+ personality.Network_Config.Enodes,
+ Kernel_ProcessorCoreID(),
+ 16,
+ Kernel_ProcessorID(),
+ 64,
+ Kernel_ProcessorThreadID(),
+ 4);
+#endif
+ }
+ return hostnum;
+#endif
+#endif
+}
+
+#ifdef GMX_LIB_MPI
+void gmx_abort(int errorno)
+{
+ const char *programName = "GROMACS";
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ catch (const std::exception &)
+ {
+ }
+ const int nnodes = gmx_node_num();
+ const int noderank = gmx_node_rank();
+ if (nnodes > 1)
+ {
+ std::fprintf(stderr, "Halting parallel program %s on node %d out of %d\n",
+ programName, noderank, nnodes);
+ }
+ else
+ {
+ std::fprintf(stderr, "Halting program %s\n", programName);
+ }
+
+ MPI_Abort(MPI_COMM_WORLD, errorno);
+ std::exit(errorno);
+}
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief
+ * Utility functions for basic MPI and network functionality.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_BASENETWORK_H
+#define GMX_UTILITY_BASENETWORK_H
-#ifndef _shift_h
-#define _shift_h
+#include <stddef.h>
-#include "typedefs.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
-real *mk_shift_tab(int n, real r1, real rc, real dr, real *sfac);
-/* Return a table of length n, containing the parabolic
- * shift function from HJC Berendsen
+/*! \brief
+ * Sets the hostname to the value given by gethostname(), if available.
+ *
+ * \param[out] name Buffer to receive the hostname.
+ * \param[in] len Length of buffer \p name (must be >= 8).
+ * \returns 0 on success, -1 on error.
+ *
+ * If the value is not available, "unknown" is returned.
+ * \p name should have at least size \p len.
+ */
+int gmx_gethostname(char *name, size_t len);
+
+/*! \brief
+ * Returns whether MPI has been initialized.
+ *
+ * The return value is `FALSE` if MPI_Init() has not been called, or if
+ * \Gromacs has been compiled without MPI support.
+ * For thread-MPI, always returns `TRUE`.
+ */
+gmx_bool gmx_mpi_initialized(void);
+
+/** Returns the number of nodes. */
+int gmx_node_num(void);
+
+/** Returns the rank of the node. */
+int gmx_node_rank(void);
+
+/*! \brief
+ * Return a non-negative hash that is, hopefully, unique for each physical
+ * node.
+ *
+ * This hash is useful for determining hardware locality.
*/
+int gmx_physicalnode_id_hash(void);
+
+/*! \brief
+ * Returns an integer characteristic of and, hopefully, unique to each
+ * physical node in the MPI system.
+ *
+ * If the first part of the MPI hostname (up to the first dot) ends with a
+ * number, returns this number. If the first part of the MPI hostname does not
+ * ends in a number (0-9 characters), returns 0.
+ *
+ * \todo
+ * This function should be fully replaced by gmx_physicalnode_id_hash().
+ */
+int gmx_hostname_num(void);
+
+/** Abort the parallel run */
+void gmx_abort(int errorno);
#ifdef __cplusplus
}
#endif
-#endif /* _shift_h */
+#endif
#include <unistd.h>
#endif
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/main.h"
-
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
int continuing(char *s)
#include <stdio.h>
#include <time.h>
-#include "../legacyheaders/types/simple.h"
+#include "basedefinitions.h"
#include "gmx_header_config.h"
#define CONTINUE '\\'
/** Comment sign to use. */
#define COMMENTSIGN ';'
+/** Standard size for char* string buffers. */
+#define STRLEN 4096
/*! \brief
* Strip trailing spaces and if s ends with a ::CONTINUE remove that too.
#include "thread_mpi/system_error.h"
-#include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/errorcodes.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
#ifdef GMX_LIB_MPI
// TODO: Consider moving the output done in gmx_abort() into the message
// printing routine above, so that this could become a simple MPI_Abort().
- gmx_abort(gmx_node_rank(), gmx_node_num(), returnCode);
+ gmx_abort(returnCode);
#endif
return returnCode;
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
+#include "fatalerror.h"
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <ctype.h>
-#include <errno.h>
-#include <stdarg.h>
-#include <string.h>
+#include <cerrno>
+#include <cstdarg>
+#include <cstdlib>
+#include <cstring>
-#include "thread_mpi/threads.h"
+#include <exception>
-#include "main.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "copyrite.h"
-#include "macros.h"
+#include "thread_mpi/threads.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/common.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
static gmx_bool bDebug = FALSE;
static FILE *log_file = NULL;
-static tMPI_Thread_mutex_t debug_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-static tMPI_Thread_mutex_t where_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static tMPI_Thread_mutex_t debug_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static tMPI_Thread_mutex_t where_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+
+static const char *const gmxuser
+ = "Please report this to the mailing list (gmx-users@gromacs.org)";
gmx_bool bDebugMode(void)
{
- gmx_bool ret;
-#if 0
- tMPI_Thread_mutex_lock(&debug_mutex);
-#endif
- ret = bDebug;
-#if 0
- tMPI_Thread_mutex_unlock(&debug_mutex);
-#endif
return bDebug;
}
static int fatal_errno = 0;
-static void quit_gmx(const char *msg)
+static void default_error_handler(const char *msg)
{
tMPI_Thread_mutex_lock(&debug_mutex);
if (fatal_errno == 0)
}
perror(msg);
}
+ tMPI_Thread_mutex_unlock(&debug_mutex);
+}
-#ifdef GMX_LIB_MPI
- if (gmx_mpi_initialized())
- {
- int nnodes;
- int noderank;
+static void (*gmx_error_handler)(const char *msg) = default_error_handler;
- nnodes = gmx_node_num();
- noderank = gmx_node_rank();
+void set_gmx_error_handler(void (*func)(const char *msg))
+{
+ // TODO: Either this is unnecessary, or also reads to the handler should be
+ // protected by a mutex.
+ tMPI_Thread_mutex_lock(&debug_mutex);
+ gmx_error_handler = func;
+ tMPI_Thread_mutex_unlock(&debug_mutex);
+}
- if (nnodes > 1)
- {
- fprintf(stderr, "Error on node %d, will try to stop all the nodes\n",
- noderank);
- }
- gmx_abort(noderank, nnodes, -1);
- }
-#endif
+static void call_error_handler(const char *key, const char *file, int line, const char *msg)
+{
+ char buf[10240], errerrbuf[1024];
+ const char *llines = "-------------------------------------------------------";
+ char *strerr;
- if (debug)
+ if (msg == NULL)
{
- fflush(debug);
+ sprintf(errerrbuf, "Empty fatal_error message. %s", gmxuser);
}
- if (bDebugMode())
+ // In case ProgramInfo is not initialized and there is an issue with the
+ // initialization, fall back to "GROMACS".
+ const char *programName = "GROMACS";
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ catch (const std::exception &)
{
- fprintf(stderr, "dump core (y/n):");
- fflush(stderr);
- if (toupper(getc(stdin)) != 'N')
- {
- (void) abort();
- }
}
- exit(fatal_errno);
- tMPI_Thread_mutex_unlock(&debug_mutex);
+ strerr = gmx_strerror(key);
+ sprintf(buf, "\n%s\nProgram %s, %s\n"
+ "Source code file: %s, line: %d\n\n"
+ "%s:\n%s\nFor more information and tips for troubleshooting, please check the GROMACS\n"
+ "website at http://www.gromacs.org/Documentation/Errors\n%s\n",
+ llines, programName, gmx_version(), file, line,
+ strerr, msg ? msg : errerrbuf, llines);
+ free(strerr);
+
+ gmx_error_handler(buf);
}
-/* The function below should be identical to quit_gmx,
- * except that is does not actually quit and call gmx_abort.
- */
-static void quit_gmx_noquit(const char *msg)
+static void do_exit(bool bMaster, bool bFinalize)
{
- tMPI_Thread_mutex_lock(&debug_mutex);
- if (!fatal_errno)
- {
- if (log_file)
- {
- fprintf(log_file, "%s\n", msg);
- }
- fprintf(stderr, "%s\n", msg);
- /* we set it to no-zero because if this function is called, something
- has gone wrong */
- fatal_errno = 255;
- }
- else
- {
- if (fatal_errno != -1)
- {
- errno = fatal_errno;
- }
- perror(msg);
- }
-
-#ifndef GMX_LIB_MPI
if (debug)
{
fflush(debug);
}
- if (bDebugMode())
+
+#ifdef GMX_MPI
+ if (gmx_mpi_initialized())
{
- fprintf(stderr, "dump core (y/n):");
- fflush(stderr);
- if (toupper(getc(stdin)) != 'N')
+ if (bFinalize)
{
- (void) abort();
+ /* Broadcast the fatal error number possibly modified
+ * on the master process, in case the user would like
+ * to use the return status on a non-master process.
+ * The master process in cr and dd always has global rank 0.
+ */
+ MPI_Bcast(&fatal_errno, sizeof(fatal_errno), MPI_BYTE,
+ 0, MPI_COMM_WORLD);
+
+ /* Finalize nicely instead of aborting */
+ MPI_Finalize();
}
- }
+ else if (bMaster)
+ {
+#ifdef GMX_LIB_MPI
+ gmx_abort(1);
#endif
-
- tMPI_Thread_mutex_unlock(&debug_mutex);
-}
-
-void gmx_fatal(int f_errno, const char *file, int line, const char *fmt, ...)
-{
- va_list ap;
- char msg[STRLEN];
-
- va_start(ap, fmt);
- vsprintf(msg, fmt, ap);
- va_end(ap);
-
- tMPI_Thread_mutex_lock(&debug_mutex);
- fatal_errno = f_errno;
- tMPI_Thread_mutex_unlock(&debug_mutex);
-
- _gmx_error("fatal", msg, file, line);
-}
-
-void gmx_fatal_collective(int f_errno, const char *file, int line,
- const t_commrec *cr, gmx_domdec_t *dd,
- const char *fmt, ...)
-{
- gmx_bool bFinalize;
- va_list ap;
- char msg[STRLEN];
-#ifdef GMX_MPI
- int result;
+ }
+ else
+ {
+ /* Let all other processes wait till the master has printed
+ * the error message and issued MPI_Abort.
+ */
+ MPI_Barrier(MPI_COMM_WORLD);
+ }
+ }
+#else
+ GMX_UNUSED_VALUE(bMaster);
+ GMX_UNUSED_VALUE(bFinalize);
#endif
- bFinalize = TRUE;
-
-#ifdef GMX_MPI
- /* Check if we are calling on all processes in MPI_COMM_WORLD */
- if (cr != NULL)
- {
- MPI_Comm_compare(cr->mpi_comm_mysim, MPI_COMM_WORLD, &result);
- }
- else
+ if (bDebugMode())
{
- MPI_Comm_compare(dd->mpi_comm_all, MPI_COMM_WORLD, &result);
+ std::abort();
}
- /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
- bFinalize = (result != MPI_UNEQUAL);
-#endif
+ std::exit(1);
+}
- if ((cr != NULL && MASTER(cr) ) ||
- (dd != NULL && DDMASTER(dd)))
+void gmx_fatal_mpi_va(int f_errno, const char *file, int line,
+ gmx_bool bMaster, gmx_bool bFinalize,
+ const char *fmt, va_list ap)
+{
+ if (bMaster)
{
- va_start(ap, fmt);
+ char msg[STRLEN];
vsprintf(msg, fmt, ap);
- va_end(ap);
tMPI_Thread_mutex_lock(&debug_mutex);
fatal_errno = f_errno;
tMPI_Thread_mutex_unlock(&debug_mutex);
- if (bFinalize)
- {
- /* Use an error handler that does not quit */
- set_gmx_error_handler(quit_gmx_noquit);
- }
-
- _gmx_error("fatal", msg, file, line);
+ call_error_handler("fatal", file, line, msg);
}
-#ifdef GMX_MPI
- if (bFinalize)
- {
- /* Broadcast the fatal error number possibly modified
- * on the master process, in case the user would like
- * to use the return status on a non-master process.
- * The master process in cr and dd always has global rank 0.
- */
- MPI_Bcast(&fatal_errno, sizeof(fatal_errno), MPI_BYTE,
- 0, MPI_COMM_WORLD);
-
- /* Finalize nicely instead of aborting */
- MPI_Finalize();
- }
- else
- {
- /* Let all other processes wait till the master has printed
- * the error message and issued MPI_Abort.
- */
- MPI_Barrier(MPI_COMM_WORLD);
- }
-#endif
+ do_exit(bMaster, bFinalize);
+}
- exit(fatal_errno);
+void gmx_fatal(int f_errno, const char *file, int line, const char *fmt, ...)
+{
+ va_list ap;
+ va_start(ap, fmt);
+ gmx_fatal_mpi_va(f_errno, file, line, TRUE, FALSE, fmt, ap);
+ va_end(ap);
}
/*
if (!bDebug) /* another thread hasn't already run this*/
{
no_buffers();
- debug = gmx_fio_fopen(dbgfile, "w+");
+ debug = gmx_ffopen(dbgfile, "w+");
bDebug = TRUE;
if (dbglevel >= 2)
{
tMPI_Thread_mutex_unlock(&debug_mutex);
}
-static const char *gmxuser = "Please report this to the mailing list (gmx-users@gromacs.org)";
-
-static void (*gmx_error_handler)(const char *msg) = quit_gmx;
-
-void set_gmx_error_handler(void (*func)(const char *msg))
-{
- tMPI_Thread_mutex_lock(&debug_mutex);
- gmx_error_handler = func;
- tMPI_Thread_mutex_unlock(&debug_mutex);
-}
-
char *gmx_strerror(const char *key)
{
typedef struct {
{ "input", "Input error or input inconsistency" },
{ "mem", "Memory allocation/freeing error" },
{ "open", "Can not open file" },
- { "range", "Range checking error" }
+ { "range", "Range checking error" },
+ { NULL, NULL}
};
-#define NMSG asize(msg)
- char buf[1024];
- size_t i;
if (key == NULL)
{
}
else
{
- for (i = 0; (i < NMSG); i++)
+ for (size_t i = 0; msg[i].key != NULL; ++i)
{
if (strcmp(key, msg[i].key) == 0)
{
- break;
+ return strdup(msg[i].msg);
}
}
- if (i == NMSG)
- {
- sprintf(buf, "No error message associated with key %s\n%s", key, gmxuser);
- return strdup(buf);
- }
- else
- {
- return strdup(msg[i].msg);
- }
+ char buf[1024];
+ sprintf(buf, "No error message associated with key %s\n%s", key, gmxuser);
+ return strdup(buf);
}
}
void _gmx_error(const char *key, const char *msg, const char *file, int line)
{
- char buf[10240], errerrbuf[1024];
- const char *llines = "-------------------------------------------------------";
- char *strerr;
-
- /* protect the audience from suggestive discussions */
-
- if (msg == NULL)
- {
- sprintf(errerrbuf, "Empty fatal_error message. %s", gmxuser);
- }
-
- strerr = gmx_strerror(key);
- sprintf(buf, "\n%s\nProgram %s, %s\n"
- "Source code file: %s, line: %d\n\n"
- "%s:\n%s\nFor more information and tips for troubleshooting, please check the GROMACS\n"
- "website at http://www.gromacs.org/Documentation/Errors\n%s\n",
- llines, ShortProgram(), GromacsVersion(), file, line,
- strerr, msg ? msg : errerrbuf, llines);
- free(strerr);
-
- gmx_error_handler(buf);
+ call_error_handler(key, file, line, msg);
+ do_exit(true, false);
}
void _range_check(int n, int n_min, int n_max, const char *warn_str,
* Declares fatal error handling and debugging routines for C code.
*
* \inpublicapi
+ * \ingroup module_utility
*/
-#ifndef _fatal_h
-#define _fatal_h
+#ifndef GMX_UTILITY_FATALERROR_H
+#define GMX_UTILITY_FATALERROR_H
+#include <stdarg.h>
#include <stdio.h>
-#include "types/simple.h"
+#include "basedefinitions.h"
#ifdef __cplusplus
extern "C" {
/** Prints filename and line to stdlog. */
#define where() _where(__FILE__, __LINE__)
+/*! \brief
+ * Low-level fatal error reporting routine for collective MPI errors.
+ *
+ * This function works as gmx_fatal(), but provides additional control for
+ * cases where it is known that the same error occurs on multiple MPI ranks.
+ * The error handler is called only if \p bMaster is `TRUE`, and MPI_Finalize()
+ * is called instead of MPI_Abort() in MPI-enabled \Gromacs if \p bFinalize is
+ * `TRUE`.
+ *
+ * This is used to implement gmx_fatal_collective() (which cannot be declared
+ * here, since it would bring with it mdrun-specific dependencies).
+ */
+void
+gmx_fatal_mpi_va(int fatal_errno, const char *file, int line, gmx_bool bMaster,
+ gmx_bool bFinalize, const char *fmt, va_list ap) GMX_ATTRIBUTE_NORETURN;
+
/*! \brief
* Fatal error reporting routine for \Gromacs.
*
* The format of \p fmt uses printf()-like formatting.
*
* In case all MPI processes want to stop with the same fatal error,
- * use gmx_fatal_collective(), declared in gmx_fatal_collective.h,
+ * use gmx_fatal_collective(), declared in network.h,
* to avoid having as many error messages as processes.
*
* The first three parameters can be provided through ::FARGS:
/*! \brief
* Sets an error handler for gmx_fatal() and other fatal error routines.
*
- * The default handler prints the message and aborts the program.
- * If you set a custom handler, it must also abort the program, otherwise
- * \Gromacs will behave unpredictably (most likely, it crashes shortly after
- * the fatal error).
+ * The default handler prints the message.
+ * \Gromacs will terminate the program after the error handler returns.
+ * To make gmx_fatal_collective() work, the error handler should not terminate
+ * the program, as it cannot know what is the desired way of termination.
* The string passed to the handler may be a multi-line string.
*
* \see gmx_fatal()
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gromacs/utility/futil.h"
+
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "thread_mpi/threads.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
}
-#ifdef rewind
-#undef rewind
-#endif
-
void frewind(FILE *fp)
{
tMPI_Thread_mutex_lock(&pstack_mutex);
}
-gmx_bool is_pipe(FILE *fp)
+//! Check whether the file (opened by gmx_ffopen()) is a pipe.
+static bool is_pipe(FILE *fp)
{
tMPI_Thread_mutex_lock(&pstack_mutex);
if (ps->fp == fp)
{
tMPI_Thread_mutex_unlock(&pstack_mutex);
- return TRUE;
+ return true;
}
ps = ps->prev;
}
tMPI_Thread_mutex_unlock(&pstack_mutex);
- return FALSE;
+ return false;
}
}
}
-
-gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
-{
- gmx_bool bExist;
-
- if (SIMMASTER(cr))
- {
- bExist = gmx_fexist(fname);
- }
- if (PAR(cr))
- {
- gmx_bcast(sizeof(bExist), &bExist, cr);
- }
- return bExist;
-}
-
gmx_bool gmx_eof(FILE *fp)
{
char data[4];
/* name in Buf should now be OK */
}
-int gmx_truncatefile(char *path, gmx_off_t length)
-{
-#ifdef _MSC_VER
- /* Microsoft visual studio does not have "truncate" */
- HANDLE fh;
- LARGE_INTEGER win_length;
-
- win_length.QuadPart = length;
-
- fh = CreateFile(path, GENERIC_READ | GENERIC_WRITE, 0, NULL,
- OPEN_EXISTING, 0, NULL);
- SetFilePointerEx(fh, win_length, NULL, FILE_BEGIN);
- SetEndOfFile(fh);
- CloseHandle(fh);
-
- return 0;
-#else
- return truncate(path, length);
-#endif
-}
-
-
int gmx_file_rename(const char *oldname, const char *newname)
{
#ifndef GMX_NATIVE_WINDOWS
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 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.
+ *
+ * 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.
+ */
+/*! \file
+ * \brief
+ * Low-level wrappers for OS-specific file handling with some \Gromacs
+ * customizations.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_FUTIL_H
+#define GMX_UTILITY_FUTIL_H
+
+#include <limits.h>
+#include <stdio.h>
+
+#include "basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+#include "gmx_header_config.h"
+/*! \def DIR_SEPARATOR
+ * \brief
+ * Directory separator on this OS.
+ *
+ * Native Windows uses backslash path separators (but accepts also slashes).
+ * Cygwin and most other systems use slash.
+ *
+ * \todo
+ * Get rid of this (Redmine #950), or at least remove this from an installed
+ * header. It is not necessary for constructing paths on the systems that it
+ * currently supports, and is not reliable in parsing input paths either, since
+ * Windows needs to accept both instead of only DIR_SEPARATOR.
+ */
+#ifdef GMX_NATIVE_WINDOWS
+#define DIR_SEPARATOR '\\'
+#else
+#define DIR_SEPARATOR '/'
+#endif
+
+/*! \def GMX_PATH_MAX
+ * \brief
+ * Maximum path length, if the OS provides one, otherwise a fixed constant.
+ */
+#ifdef PATH_MAX
+# define GMX_PATH_MAX PATH_MAX
+#elif defined MAX_PATH
+# define GMX_PATH_MAX MAX_PATH
+#else
+# define GMX_PATH_MAX 4096
+#endif
+
+/** \Gromacs definition to use instead of `off_t`. */
+typedef gmx_int64_t gmx_off_t;
+
+/*! \brief
+ * Turn off buffering of files (which is default) for debugging purposes.
+ *
+ * This only has effect on files opened with gmx_ffopen().
+ */
+void no_buffers(void);
+
+/*! \brief
+ * Check whether a path exists.
+ *
+ * \returns `TRUE` when \p fname exists.
+ *
+ * Note that this returns `TRUE` even if \p fname is a directory instead of a
+ * file.
+ */
+gmx_bool gmx_fexist(const char *fname);
+
+/*! \brief
+ * Checks for end of file.
+ *
+ * \returns `TRUE` on end-of-file
+ *
+ * \todo
+ * There are only two callers for this function, while there are ~20 direct
+ * calls to feof(). Probably this is unnecessary.
+ */
+gmx_bool gmx_eof(FILE *fp);
+
+/*! \brief
+ * Makes a backup of file if the file exists.
+ *
+ * \returns `FALSE` if there was a problem.
+ */
+gmx_bool make_backup(const char *file);
+
+/*! \brief
+ * Opens a file, with \Gromacs-specific additions.
+ *
+ * If the file is in compressed format, opens a pipe which uncompresses the
+ * file on the fly. For this to work, gmx_ffclose() and frewind() should
+ * always be used for files opened with gmx_ffopen() instead of fclose() and
+ * rewind(). For compressed files, the \p file parameter should be passed
+ * without the compressed extension; if that file is not found, then a few
+ * compression extensions are tried.
+ * Creates a backup if a file opened for writing already exists before
+ * overwriting it.
+ * A fatal error results if the file cannot be opened, for whatever reason.
+ */
+FILE *gmx_ffopen(const char *file, const char *mode);
+
+/** Closes a file opened with gmx_ffopen(). */
+int gmx_ffclose(FILE *fp);
+
+/*! \brief
+ * Wraps rewind() for files opened with gmx_ffopen().
+ *
+ * A fatal error results if this function is called for a pipe (a compressed
+ * input file).
+ */
+void frewind(FILE *fp);
+
+/** OS-independent 64-bit fseek(). */
+int gmx_fseek(FILE *stream, gmx_off_t offset, int whence);
+
+/** OS-independent 64-bit ftell(). */
+gmx_off_t gmx_ftell(FILE *stream);
+
+/*! \brief
+ * Finds full path for a library file.
+ *
+ * Searches first in the current directory, and then in the configured library
+ * directories.
+ * Fatal error results if the file is not found in any location.
+ * The caller is responsible of freeing the returned string.
+ */
+char *gmxlibfn(const char *file);
+
+/*! \brief
+ * Opens a library file for reading.
+ *
+ * Works as gmxlibfn(), except that it opens the file and returns a file
+ * handle.
+ */
+FILE *libopen(const char *file);
+
+/*! \brief
+ * More flexible gmxlibfn().
+ *
+ * Works as gmxlibfn(), but provides control whether the current working
+ * directory is searched or not, and whether a missing file is a fatal error or
+ * not.
+ */
+char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal);
+
+/*! \brief
+ * Alternative for libopen() that optionally does not exit.
+ *
+ * Works as libopen(), but provides control whether a missing file is a fatal
+ * error or not.
+ */
+FILE *low_libopen(const char *file, gmx_bool bFatal);
+
+/** Opaque data type to list directories. */
+typedef struct gmx_directory *gmx_directory_t;
+
+/*! \brief
+ * Opens a directory for reading.
+ *
+ * \param[out] p_gmxdir Handle to the opened directory.
+ * \param[in] dirname Path to directory to open.
+ * \returns 0 on success.
+ */
+int
+gmx_directory_open(gmx_directory_t *p_gmxdir, const char *dirname);
+
+/*! \brief
+ * Gets next file in a directory.
+ *
+ * Given an initialized gmx_directory_t, if there are more files in
+ * the directory this routine returns 0 and write the next name
+ * into the USER-PROVIDED buffer \p name. The last argument is the max
+ * number of characters that will be written. Just as strncpy(), the
+ * string will NOT be terminated it it is longer than \p maxlength_name.
+ */
+int
+gmx_directory_nextfile(gmx_directory_t gmxdir, char *name, int maxlength_name);
+
+/** Releases all data for a directory structure. */
+int
+gmx_directory_close(gmx_directory_t gmxdir);
+
+
+/*! \brief
+ * Creates unique name for temp file (wrapper around mkstemp).
+ *
+ * \p buf should be at least 7 bytes long
+ */
+void gmx_tmpnam(char *buf);
+
+/*! \brief
+ * OS-independent rename().
+ *
+ * Renames/moves a file atomically, if the OS makes that available.
+ */
+int gmx_file_rename(const char *oldname, const char *newname);
+
+/*! \brief
+ * Copies a file (data only) oldname to newname.
+ *
+ * If \p copy_if_empty is `FALSE`, the file won't be copied if it's empty.
+ */
+int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty);
+
+/*! \brief
+ * OS-independent fsync().
+ *
+ * Only use this during checkpointing!
+ */
+int gmx_fsync(FILE *fp);
+
+/*! \brief
+ * OS-independent chdir().
+ *
+ * Exits with a fatal error if changing the directory fails.
+ */
+void gmx_chdir(const char *directory);
+/*! \brief
+ * OS-independent getcwd().
+ *
+ * Exits with a fatal error if the call fails.
+ */
+void gmx_getcwd(char *buffer, size_t size);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
#include "config.h"
#include <stdio.h>
+#include <stdlib.h>
#ifdef GMX_OPENMP
#include <omp.h>
#endif
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/md_logging.h"
-
#include "gromacs/utility/common.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/stringutil.h"
int gmx_omp_get_max_threads(void)
{
#endif
}
-/*!
- * Thread affinity set by the OpenMP library can conflict with the GROMACS
- * internal affinity setting.
- *
- * While GNU OpenMP does not set affinity by default, the Intel OpenMP library
- * does. This conflicts with the internal affinity (especially thread-MPI)
- * setting, results in incorrectly locked threads, and causes dreadful performance.
- *
- * The KMP_AFFINITY environment variable is used by Intel, GOMP_CPU_AFFINITY
- * by the GNU compilers (Intel also honors it well). If any of the variables
- * is set, we honor it, disable the internal pinning, and warn the user.
- * When using Intel OpenMP, we will disable affinity if the user did not set it
- * anually through one of the aforementioned environment variables.
- *
- * Note that the Intel OpenMP affinity disabling iwll only take effect if this
- * function is called before the OpenMP library gets initialized which happens
- * when the first call is made into a compilation unit that contains OpenMP
- * pragmas.
- */
-void gmx_omp_check_thread_affinity(FILE *fplog,
- const t_commrec *cr,
- gmx_hw_opt_t *hw_opt)
+gmx_bool gmx_omp_check_thread_affinity(char **message)
{
- /* no need to worry if internal thread pinning is turned off */
- if (hw_opt->thread_affinity == threadaffOFF)
- {
- return;
- }
+ bool shouldSetAffinity = true;
-#ifndef GMX_OPENMP
- GMX_UNUSED_VALUE(fplog);
- GMX_UNUSED_VALUE(cr);
-#else
+ *message = NULL;
+#ifdef GMX_OPENMP
/* We assume that the affinity setting is available on all platforms
* gcc supports. Even if this is not the case (e.g. Mac OS) the user
* will only get a warning. */
#if defined(__GNUC__) || defined(__INTEL_COMPILER)
+ const char *programName;
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
const char *const gomp_env = getenv("GOMP_CPU_AFFINITY");
const bool bGompCpuAffinitySet = (gomp_env != NULL);
/* turn off internal pinning if GOMP_CPU_AFFINITY is set & non-empty */
if (bGompCpuAffinitySet && *gomp_env != '\0')
{
- /* TODO: with -pin auto we should only warn when using all cores */
- md_print_warn(cr, fplog,
- "NOTE: GOMP_CPU_AFFINITY set, will turn off %s internal affinity\n"
- " setting as the two can conflict and cause performance degradation.\n"
- " To keep using the %s internal affinity setting, unset the\n"
- " GOMP_CPU_AFFINITY environment variable.",
- ShortProgram(), ShortProgram());
-
- hw_opt->thread_affinity = threadaffOFF;
+ try
+ {
+ std::string buf = gmx::formatString(
+ "NOTE: GOMP_CPU_AFFINITY set, will turn off %s internal affinity\n"
+ " setting as the two can conflict and cause performance degradation.\n"
+ " To keep using the %s internal affinity setting, unset the\n"
+ " GOMP_CPU_AFFINITY environment variable.",
+ programName, programName);
+ *message = gmx_strdup(buf.c_str());
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ shouldSetAffinity = false;
}
#endif /* __GNUC__ || __INTEL_COMPILER */
/* turn off internal pinning KMP_AFFINITY != "disabled" */
if (bKmpAffinitySet && (gmx_strncasecmp(kmp_env, "disabled", 8) != 0))
{
- /* TODO: with -pin auto we should only warn when using all cores */
- md_print_warn(cr, fplog,
- "NOTE: KMP_AFFINITY set, will turn off %s internal affinity\n"
- " setting as the two can conflict and cause performance degradation.\n"
- " To keep using the %s internal affinity setting, set the\n"
- " KMP_AFFINITY=disabled environment variable.",
- ShortProgram(), ShortProgram());
-
- hw_opt->thread_affinity = threadaffOFF;
+ try
+ {
+ std::string buf = gmx::formatString(
+ "NOTE: KMP_AFFINITY set, will turn off %s internal affinity\n"
+ " setting as the two can conflict and cause performance degradation.\n"
+ " To keep using the %s internal affinity setting, set the\n"
+ " KMP_AFFINITY=disabled environment variable.",
+ programName, programName);
+ *message = gmx_strdup(buf.c_str());
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ shouldSetAffinity = false;
}
#endif /* __INTEL_COMPILER */
#endif /* GMX_OPENMP */
+ return shouldSetAffinity;
}
#include "config.h"
#endif
+#include <stdio.h>
+
#ifndef GMX_NATIVE_WINDOWS
/* Ugly hack because the openmp implementation below hacks into the SIMD
* settings to decide when to use _mm_pause(). This should eventually be
#include <windows.h>
#endif
-#include "types/commrec.h"
-#include "mdrun.h"
+#include "basedefinitions.h"
#ifdef __cplusplus
extern "C"
/*! \brief
* Check for externally set thread affinity to avoid conflicts with \Gromacs
* internal setting.
+ *
+ * \param[out] message Receives the message to be shown to the user.
+ * \returns `true` if we can set thread affinity ourselves.
+ *
+ * While GNU OpenMP does not set affinity by default, the Intel OpenMP library
+ * does. This conflicts with the internal affinity (especially thread-MPI)
+ * setting, results in incorrectly locked threads, and causes dreadful performance.
+ *
+ * The KMP_AFFINITY environment variable is used by Intel, GOMP_CPU_AFFINITY
+ * by the GNU compilers (Intel also honors it well). If any of the variables
+ * is set, we should honor it and disable the internal pinning.
+ * When using Intel OpenMP, we will disable affinity if the user did not set it
+ * manually through one of the aforementioned environment variables.
+ *
+ * Note that the Intel OpenMP affinity disabling will only take effect if this
+ * function is called before the OpenMP library gets initialized, which happens
+ * when the first call is made into a compilation unit that contains OpenMP
+ * pragmas.
+ *
+ * If this function returns `false`, the caller is responsible to disable the
+ * pinning, show the message from \p *message to the user, and free the memory
+ * allocated for \p *message.
+ * If the return value is `true`, \p *message is NULL.
*/
-void gmx_omp_check_thread_affinity(FILE *fplog, const t_commrec *cr,
- gmx_hw_opt_t *hw_opt);
+gmx_bool gmx_omp_check_thread_affinity(char **message);
/*! \brief
* Pause for use in a spin-wait loop.
* Implements functions in path.h.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
- * \ingroup module_fileio
+ * \ingroup module_utility
*/
#include "path.h"
#endif
#endif
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/stringutil.h"
namespace
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
- * \ingroup module_fileio
+ * \ingroup module_utility
*/
-#ifndef GMX_FILEIO_PATH_H
-#define GMX_FILEIO_PATH_H
+#ifndef GMX_UTILITY_PATH_H
+#define GMX_UTILITY_PATH_H
#include <string>
#include <utility>
#include <dmalloc.h>
#endif
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
+#include "gromacs/utility/fatalerror.h"
#ifdef PRINT_ALLOC_KB
#include "gromacs/utility/gmxmpi.h"
#endif
#include <config.h>
#endif
+#include <stdlib.h>
+
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "vec.h"
#include "vcm.h"
#include "mdebin.h"
#include "md_support.h"
#include "md_logging.h"
#include "network.h"
-#include "xvgr.h"
#include "physics.h"
#include "names.h"
#include "force.h"
#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/filenm.h"
+#include "gromacs/utility/fatalerror.h"
int gmx_mdrun(int argc, char *argv[])
{
#include "typedefs.h"
#include "types/commrec.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "vec.h"
#include "macros.h"
-#include "main.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "index.h"
#include "physics.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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 "types/membedt.h"
+#include "gromacs/fileio/filenm.h"
#ifdef __cplusplus
extern "C" {
#include <config.h>
#endif
-#include "gromacs/utility/smalloc.h"
#include "types/commrec.h"
#include "network.h"
#include "calcgrid.h"
#include "md_logging.h"
#include "pme_loadbal.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
/* Parameters and setting for one PP-PME setup */
typedef struct {
real rcut_coulomb; /* Coulomb cut-off */
#include "vec.h"
#include "names.h"
#include "domdec.h"
+#include "main.h"
#include "gromacs/random/random.h"
#define PROBABILITYCUTOFF 100
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "copyrite.h"
#include "force.h"
#include "mdrun.h"
#include "gmx_detect_hardware.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/gmxpreprocess/calc_verletbuf.h"
-#include "gmx_fatal_collective.h"
#include "membed.h"
#include "macros.h"
#include "gmx_thread_affinity.h"
#include "inputrec.h"
+#include "main.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/mdlib/nbnxn_consts.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/gmxomp.h"
#include "gromacs/swap/swapcoords.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/pulling/pull.h"
}
}
- /* Check for externally set OpenMP affinity and turn off internal
- * pinning if any is found. We need to do this check early to tell
- * thread-MPI whether it should do pinning when spawning threads.
- * TODO: the above no longer holds, we should move these checks down
- */
- gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
-
/* Check and update the hardware options for internal consistency */
check_and_update_hw_opt_1(hw_opt, SIMMASTER(cr));
+ /* Early check for externally set process affinity. */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
if (SIMMASTER(cr))
{
-#ifdef GMX_THREAD_MPI
- /* Early check for externally set process affinity.
- * With thread-MPI this is needed as pinning might get turned off,
- * which needs to be known before starting thread-MPI.
- * With thread-MPI hw_opt is processed here on the master rank
- * and passed to the other ranks later, so we only do this on master.
- */
- gmx_check_thread_affinity_set(fplog,
- NULL,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-#endif
#ifdef GMX_THREAD_MPI
if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
# include <config.h>
#endif
-#include "testutils/integrationtests.h"
-#include "testutils/testoptions.h"
-#include "testutils/cmdlinetest.h"
-#include "gromacs/options/options.h"
-#include "gromacs/options/basicoptions.h"
-#include "gromacs/utility/file.h"
-#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/types/simple.h"
+
#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/file.h"
+
#include "programs/mdrun/mdrun_main.h"
+#include "testutils/integrationtests.h"
+#include "testutils/testoptions.h"
+#include "testutils/cmdlinetest.h"
+
namespace gmx
{
namespace test
#include <gtest/gtest.h>
-#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/fileio/path.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
-#include "../mdrun_main.h"
+#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
#include <algorithm>
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "x11.h"
#include "xutil.h"
#include <config.h>
#endif
+#include <stdlib.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h> // for fork()
#endif
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
#include "x11.h"
#include "xdlghi.h"
#include "xmb.h"
#include "names.h"
#include "nmol.h"
#include "manager.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define MBFLAGS /* MB_APPLMODAL | */ MB_DONTSHOW
#include <config.h>
#endif
+#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <ctype.h>
+
+#include "fgrid.h"
+
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "fgrid.h"
-#include "gromacs/fileio/futil.h"
static const char *type[] = {
"button", "radiobuttons", "groupbox", "checkbox",
#include <algorithm>
-#include "sysstuff.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "index.h"
#include "xdlghi.h"
#include "dialogs.h"
#include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
{
#include <config.h>
#endif
-#include "sysstuff.h"
+#include <stdlib.h>
+
#include "macros.h"
#include "xutil.h"
#include "Xstuff.h"
#endif
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h> // for usleep()
#endif
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "macros.h"
#include "vec.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/math/utilities.h"
#endif
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
+
#include "macros.h"
#include "xutil.h"
#include "buttons.h"
#include "gromacs/fileio/writeps.h"
#include "gromacs/math/3dview.h"
+#include "gromacs/utility/smalloc.h"
#define MSIZE 4
#endif
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
+
#include "macros.h"
#include "xutil.h"
-#include "gromacs/math/3dview.h"
-#include "gmx_fatal.h"
#include "buttons.h"
#include "manager.h"
#include "nmol.h"
#include "txtdump.h"
#include "pbc.h"
+#include "gromacs/math/3dview.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
#define MSIZE 4
static bool MWCallBack(t_x11 *x11, XEvent *event, Window /*w*/, void *data)
#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
+
#include "typedefs.h"
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "Xstuff.h"
#include "x11.h"
#include "xutil.h"
#include "xdlg.h"
#include "xmb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*****************************
*
* Helpful routines
#include <config.h>
#endif
+#include <stdlib.h>
#include <string.h>
#include <algorithm>
-#include "gmx_fatal.h"
-#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "xutil.h"
#include "xdlghi.h"
#include "fgrid.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
t_dlgitem **CreateRadioButtonGroup(t_x11 *x11, char *szTitle,
t_id GroupID, int nrb, t_id rb[],
int nSelect,
#include <algorithm>
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "Xstuff.h"
#include "xdlgitem.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
#define BUFSIZE 16
static t_dlgitem *newitem(void)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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 "xutil.h"
#include "xdlg.h"
#include "xmb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs.bm"
#include "stop.bm"
#include "info.bm"
#include <libxml/parser.h>
#include <libxml/xmlmemory.h>
-#include "gromacs/fileio/path.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/testasserts.h"
#include <gtest/gtest.h>
-#include "gromacs/fileio/path.h"
#include "gromacs/options/options.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "testutils/testoptions.h"
--suppress=variableScope
--suppress=unnecessaryForwardDeclaration
--suppress=invalidscanf:src/gromacs/fileio/matio.cpp
- --suppress=invalidscanf:src/gromacs/gmxlib/xvgr.cpp
+ --suppress=invalidscanf:src/gromacs/fileio/xvgr.cpp
--suppress=invalidscanf:src/gromacs/gmxpreprocess/pdb2top.cpp
--suppress=*:src/gromacs/selection/scanner.cpp)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff