Commit 7fd449a0 authored by Berk Onat's avatar Berk Onat
Browse files

Initial commit for NAMD parser

parents
# NAMD Parser
[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [NAMD](http://www.ks.uiuc.edu/Research/namd/)
## Version 0.0.1
This is the parser for NAMD Molecular Dynamics (namd2) in [NAMD](http://www.ks.uiuc.edu/Research/namd/).
The official version lives at:
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-namd.git
You can browse it at:
https://gitlab.rzg.mpg.de/nomad-lab/parser-namd
It relies on having the nomad-meta-info and the python-common repositories one level higher.
The simplest way to have this is to check out nomad-lab-base recursively:
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
This parser will be in the directory parsers/namd of this repository.
## Running and Testing the Parser
### Requirements
The required python packages can be installed with (see [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common)):
pip install -r nomad-lab-base/python-common/requirements.txt
### Usage
NAMD md (namd2 executable) log output files can be parsed with:
python NAMDParser.py [path/toFile]
### Test Files
Example log output files of NAMD can be found in the directory test/examples.
More details about the calculations and files will be explained in this README file.
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.1 virtualenv at /labEnv3" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/.idea/parser-amber.iml" filepath="$PROJECT_DIR$/.idea/parser-amber.iml" />
</modules>
</component>
</project>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TestRunnerService">
<option name="projectConfiguration" value="Nosetests" />
<option name="PROJECT_TEST_RUNNER" value="Nosetests" />
</component>
</module>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ChangeListManager">
<list default="true" id="7426a5df-0b63-4709-ab28-0c6e68476f74" name="Default" comment="" />
<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
<option name="TRACKING_ENABLED" value="true" />
<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
<option name="LAST_RESOLUTION" value="IGNORE" />
</component>
<component name="ExecutionTargetManager" SELECTED_TARGET="default_target" />
<component name="FileEditorManager">
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300" />
</component>
<component name="ProjectFrameBounds">
<option name="x" value="303" />
<option name="y" value="66" />
<option name="width" value="1602" />
<option name="height" value="1164" />
</component>
<component name="ProjectView">
<navigator currentView="ProjectPane" proportions="" version="1">
<flattenPackages />
<showMembers />
<showModules />
<showLibraryContents />
<hideEmptyPackages />
<abbreviatePackageNames />
<autoscrollToSource />
<autoscrollFromSource />
<sortByType />
<manualOrder />
<foldersAlwaysOnTop value="true" />
</navigator>
<panes>
<pane id="Scratches" />
<pane id="ProjectPane">
<subPane>
<PATH>
<PATH_ELEMENT>
<option name="myItemId" value="parser-amber" />
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
</PATH_ELEMENT>
<PATH_ELEMENT>
<option name="myItemId" value="parser-amber" />
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
</PATH_ELEMENT>
</PATH>
</subPane>
</pane>
<pane id="Scope" />
</panes>
</component>
<component name="PropertiesComponent">
<property name="last_opened_file_path" value="$PROJECT_DIR$" />
</component>
<component name="RunDashboard">
<option name="ruleStates">
<list>
<RuleState>
<option name="name" value="ConfigurationTypeDashboardGroupingRule" />
</RuleState>
<RuleState>
<option name="name" value="StatusDashboardGroupingRule" />
</RuleState>
</list>
</option>
</component>
<component name="RunManager">
<configuration default="true" type="PythonConfigurationType" factoryName="Python">
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs>
<env name="PYTHONUNBUFFERED" value="1" />
</envs>
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="parser-amber" />
<option name="SCRIPT_NAME" value="" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="false" />
<option name="EMULATE_TERMINAL" value="false" />
<method />
</configuration>
<configuration default="true" type="Tox" factoryName="Tox">
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="parser-amber" />
<method />
</configuration>
<configuration default="true" type="tests" factoryName="Doctests">
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="parser-amber" />
<option name="SCRIPT_NAME" value="" />
<option name="CLASS_NAME" value="" />
<option name="METHOD_NAME" value="" />
<option name="FOLDER_NAME" value="" />
<option name="TEST_TYPE" value="TEST_SCRIPT" />
<option name="PATTERN" value="" />
<option name="USE_PATTERN" value="false" />
<method />
</configuration>
<configuration default="true" type="tests" factoryName="Nosetests">
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="parser-amber" />
<option name="_new_regexPattern" value="&quot;&quot;" />
<option name="_new_additionalArguments" value="&quot;&quot;" />
<option name="_new_target" value="&quot;.&quot;" />
<option name="_new_targetType" value="&quot;PATH&quot;" />
<method />
</configuration>
</component>
<component name="ShelveChangesManager" show_recycled="false">
<option name="remove_strategy" value="false" />
</component>
<component name="TaskManager">
<task active="true" id="Default" summary="Default task">
<changelist id="7426a5df-0b63-4709-ab28-0c6e68476f74" name="Default" comment="" />
<created>1497006387415</created>
<option name="number" value="Default" />
<option name="presentableId" value="Default" />
<updated>1497006387415</updated>
</task>
<servers />
</component>
<component name="ToolWindowManager">
<frame x="303" y="66" width="1602" height="1164" extended-state="0" />
<layout>
<window_info id="Project" active="true" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.2496879" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
<window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
<window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32968035" sideWeight="0.5" order="7" side_tool="true" content_ui="tabs" />
<window_info id="Run" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
<window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="false" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
<window_info id="Python Console" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
<window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
<window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
<window_info id="Debug" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
<window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
<window_info id="Data View" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
<window_info id="Cvs" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
<window_info id="Message" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
<window_info id="Commander" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
<window_info id="Inspection" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="5" side_tool="false" content_ui="tabs" />
<window_info id="Hierarchy" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="2" side_tool="false" content_ui="combo" />
<window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
<window_info id="Ant Build" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
</layout>
</component>
<component name="VcsContentAnnotationSettings">
<option name="myLimit" value="2678400000" />
</component>
<component name="VcsManagerConfiguration">
<ignored-roots>
<path value="$PROJECT_DIR$/../.." />
</ignored-roots>
</component>
<component name="XDebuggerManager">
<breakpoint-manager />
<watches-manager />
</component>
<component name="editorHistoryManager">
<entry file="file://$PROJECT_DIR$/AMBERParser.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="0">
<caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
<folding>
<element signature="e#0#24#0" expanded="true" />
</folding>
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/AMBERParser.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="15">
<caret line="42" column="61" lean-forward="false" selection-start-line="42" selection-start-column="61" selection-end-line="42" selection-end-column="61" />
<folding>
<element signature="e#0#24#0" expanded="true" />
</folding>
</state>
</provider>
</entry>
</component>
</project>
\ No newline at end of file
import logging
import os
PARSERNAME = "NAMD"
PROGRAMNAME = "namd"
PARSERVERSION = "0.0.1"
PARSERMETANAME = PARSERNAME.lower()
PARSERTAG = 'x_' + PARSERMETANAME
PARSER_INFO_DEFAULT = {
'name' : PARSERMETANAME+'-parser',
'version': PARSERVERSION
}
META_INFO_PATH = os.path.normpath(os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../../../nomad-meta-info/meta_info/nomad_meta_info/"+PARSERMETANAME+".nomadmetainfo.json"))
LOGGER = logging.getLogger("nomad."+PROGRAMNAME+"Parser")
def set_excludeList(self):
"""Sets the exclude list for x_
Returns:
the list of names
"""
excludelist = [
PARSERTAG+'_mdin_verbatim_writeout',
PARSERTAG+'_dumm_text',
PARSERTAG+'_dummy',
PARSERTAG+'_mdin_wt'
]
excludelist.extend([PARSERTAG+'_mdin_file_%s' % fileNL.lower() for fileNL in self.fileDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % cntrlNL.lower() for cntrlNL in self.cntrlDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % ewaldNL.lower() for ewaldNL in self.ewaldDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % qmmmNL.lower() for qmmmNL in self.qmmmDict.keys()])
return excludelist
def set_includeList():
"""Sets the include list for x_
Returns:
the list of names
"""
includelist = []
return includelist
This diff is collapsed.
This diff is collapsed.
import sys
import os
import os.path
basedir = os.path.dirname(os.path.abspath(__file__))
commondir = os.path.normpath(os.path.join(basedir,"../../../../python-common/common/python"))
if not commondir in sys.path:
sys.path.insert(0, commondir)
package eu.nomad_lab.parsers
import eu.nomad_lab
import eu.nomad_lab.DefaultPythonInterpreter
import org.{ json4s => jn }
import eu.{ nomad_lab => lab }
import scala.collection.breakOut
object NAMDParser extends SimpleExternalParserGenerator(
name = "NAMDParser",
parserInfo = jn.JObject(
("name" -> jn.JString("NAMDParser")) ::
("parserId" -> jn.JString("NAMDParser" + lab.NAMDVersionInfo.version)) ::
("versionInfo" -> jn.JObject(
("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
case (k, v) => k -> jn.JString(v.toString)
}(breakOut): List[(String, jn.JString)])) ::
(lab.NAMDVersionInfo.toMap.map {
case (key, value) =>
(key -> jn.JString(value.toString))
}(breakOut): List[(String, jn.JString)])
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/gromacs/parser/parser-namd/NAMDParser.py",
"${mainFilePath}"),
resList = Seq(
"parser-namd/NAMDParser.py",
"parser-namd/NAMDDictionary.py",
"parser-namd/NAMDCommon.py",
"parser-namd/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/namd.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-namd" -> "parsers/namd/parser/parser-namd",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
"python" -> "python-common/common/python/nomadcore"
) ++ DefaultPythonInterpreter.commonDirMapping(),
metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.gromacs)
)
package eu.nomad_lab.parsers
import org.specs2.mutable.Specification
object NAMDParserTests extends Specification {
"NAMDParserTest" >> {
"[tiny with 507 atoms] test with json-events" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json-events") must_== ParseResult.ParseSuccess
}
"[tiny with 507 atoms] test with json" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json") must_== ParseResult.ParseSuccess
}
"[apoa1-trajectory with 92224 atoms] test with json-events" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json-events") must_== ParseResult.ParseSuccess
}
"[apoa1-trajectory with 92224 atoms] test with json" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json") must_== ParseResult.ParseSuccess
}
}
}
# Tests:
### Source of Tests:
The tests are taken from NAMD (version 2.12) examples in [NAMD](http://www.ks.uiuc.edu/Research/namd/utilities/).
### Example Tests:
#### ApoA1 benchmark
92224 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/)
#### tiny benchmark
507 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/tiny/)
#### Interactive BPTI benchmark
882 atoms, small [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/bpti_imd/)
#### ER-GRE benchmark
36573 atoms, spherical [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/er-gre/)
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
(FFTW-2.1.3 (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 179 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 132 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 66 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 132 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 55 0) (54 537 1 0 4428 1 1 143 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 190 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 143 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 106.961377282 0 0 0 106.961377282 0 0 0 76.4009837728 0 0 0
This diff is collapsed.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment