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Commit doxy files. 

git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6131 e5b18d87-469d-4833-9cc0-8cdfa06e9491
This commit is contained in:
Jeongnim Kim 2013-12-18 01:04:52 +00:00
parent 9c7fb4d06f
commit 5847f344ad
12 changed files with 115 additions and 69 deletions
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20
docs/DoxygenLayout.xml
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@ -3,16 +3,6 @@
<!-- Navigation index tabs for HTML output -->
<navindex>
<tab type="mainpage" visible="yes" title=""/>
<tab type="user" url="http://qmcpack.cmscc.org" title="Wiki"/>
<tab type="user" url="../ug/index.html" title="User guide" intro="userguide,xml">
<tab type="pages" visible="no" title="" intro=""/>
</tab>
<tab type="user" url="../dev/index.html" title="Developers" intro="help for developers">
<tab type="pages" visible="no" title="" intro=""/>
</tab>
<tab type="user" url="../tutorials/index.html" title="Tutorials" intro="tutorials">
<tab type="pages" visible="no" title="Tutorials" intro=""/>
</tab>
<!--
<tab type="user" url="http://users.nccs.gov/~jnkim/qmcpack/ug/index.html" title="Documentation" intro="userguide, developers guide etc"/>
<tab type="pages" visible="yes" title="Others" intro=""/>
@ -33,6 +23,16 @@
<tab type="globals" visible="yes" title="" intro=""/>
</tab>
<tab type="examples" visible="yes" title="" intro=""/>
<tab type="user" url="http://qmcpack.cmscc.org" title="Wiki"/>
<tab type="user" url="../ug/index.html" title="User guide" intro="userguide,xml">
<tab type="pages" visible="no" title="" intro=""/>
</tab>
<tab type="user" url="../dev/index.html" title="Developers" intro="help for developers">
<tab type="pages" visible="no" title="" intro=""/>
</tab>
<tab type="user" url="../tutorials/index.html" title="Tutorials" intro="tutorials">
<tab type="pages" visible="no" title="Tutorials" intro=""/>
</tab>
</navindex>
<!-- Layout definition for a class page -->

97
docs/dev.tag
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@ -1,5 +1,62 @@
<?xml version='1.0' encoding='UTF-8' standalone='yes' ?>
<tagfile>
<compound kind="page">
<name>glue201312</name>
<title>QMC Glue Meeting</title>
<filename>glue201312</filename>
<docanchor file="glue201312" title="Planning">plan</docanchor>
<docanchor file="glue201312" title="INCITE allocations">incite2014</docanchor>
<docanchor file="glue201312" title="QMC school in 2014">school14</docanchor>
<docanchor file="glue201312" title="Science Discussion">app</docanchor>
<docanchor file="glue201312" title="Code development">code</docanchor>
<docanchor file="glue201312" title="Known bugs and problems">bugs</docanchor>
<docanchor file="glue201312" title="Tool development">tool</docanchor>
<docanchor file="glue201312" title="Database">data</docanchor>
</compound>
<compound kind="page">
<name>incite2013</name>
<title>QMC Glue Incite Project</title>
<filename>incite2013</filename>
<docanchor file="incite2013" title="At OLCF">olcf</docanchor>
<docanchor file="incite2013" title="How to apply the user acoount">olcf_user</docanchor>
<docanchor file="incite2013" title="at ALCF">alcf</docanchor>
</compound>
<compound kind="page">
<name>dev_update</name>
<title>Update</title>
<filename>dev_update</filename>
<docanchor file="dev_update" title="New/updated input elements">newinp</docanchor>
<docanchor file="dev_update" title="Setting samples">sa</docanchor>
<docanchor file="dev_update" title="Running DMC with reconfiguraton">sb</docanchor>
<docanchor file="dev_update" title="Defining single-particle orbital sets">sc</docanchor>
</compound>
<compound kind="page">
<name>validation</name>
<title>Validation DataBase</title>
<filename>validation</filename>
<docanchor file="validation" title="Validation types">valid_intro</docanchor>
<docanchor file="validation" title="How to manage the tests">valid_method</docanchor>
<docanchor file="validation" title="Validation suite by Jaron">valid_jk</docanchor>
<docanchor file="validation" title="Candidate systems">valid_sys</docanchor>
<docanchor file="validation" title="Tests provided by Luke">luketests</docanchor>
<docanchor file="validation" title="non-orthorhombic-wfn-test">luke1</docanchor>
<docanchor file="validation" title="real-vs-complex-test">luke2</docanchor>
<docanchor file="validation" title="cubic-wfn-test">luke3</docanchor>
<docanchor file="validation" title="wavefunction-tiling">luke4</docanchor>
<docanchor file="validation" title="all-electron-test">luke5</docanchor>
<docanchor file="validation" title="mechanicstest">luke6</docanchor>
<docanchor file="validation" title="All-electron multideterminant H2O">h2o_msd</docanchor>
</compound>
<compound kind="page">
<name>dev_todo</name>
<title>ToDo</title>
<filename>dev_todo</filename>
<docanchor file="dev_todo" title="Wavefunction">todo_psi</docanchor>
<docanchor file="dev_todo" title="Hamiltonians">todo_ham</docanchor>
<docanchor file="dev_todo" title="Drivers">todo_qmc</docanchor>
<docanchor file="dev_todo" title="Workflow and tools">todo_tool</docanchor>
<docanchor file="dev_todo" title="Computer Science Development">todo_comp</docanchor>
</compound>
<compound kind="page">
<name>dev_basic</name>
<title>Developing QMCPACK</title>
@ -19,46 +76,6 @@
<title>Trial Wave Functions</title>
<filename>dev_psi</filename>
</compound>
<compound kind="page">
<name>dev_update</name>
<title>Update</title>
<filename>dev_update</filename>
<docanchor file="dev_update" title="Code development">code</docanchor>
<docanchor file="dev_update" title="Known bugs and problems">bugs</docanchor>
<docanchor file="dev_update" title="Tool development">tool</docanchor>
<docanchor file="dev_update" title="Database">data</docanchor>
<docanchor file="dev_update" title="New/updated input elements">newinp</docanchor>
<docanchor file="validation" title="Candidate systems">sa</docanchor>
<docanchor file="dev_update" title="Running DMC with reconfiguraton">sb</docanchor>
<docanchor file="dev_update" title="Defining single-particle orbital sets">sc</docanchor>
<docanchor file="dev_update" title="ADIOS checkpointing">sd</docanchor>
<docanchor file="dev_update" title="Trace">se</docanchor>
</compound>
<compound kind="page">
<name>validation</name>
<title>Validation DataBase</title>
<filename>validation</filename>
<docanchor file="validation" title="Candidate systems">sa</docanchor>
<docanchor file="validation" title="Tests provided by Luke">luketests</docanchor>
<docanchor file="validation" title="non-orthorhombic-wfn-test">luke1</docanchor>
<docanchor file="validation" title="real-vs-complex-test">luke2</docanchor>
<docanchor file="validation" title="cubic-wfn-test">luke3</docanchor>
<docanchor file="validation" title="wavefunction-tiling">luke4</docanchor>
<docanchor file="validation" title="all-electron-test">luke5</docanchor>
<docanchor file="validation" title="mechanicstest">luke6</docanchor>
<docanchor file="validation" title="All-electron multideterminant H2O">h2o_msd</docanchor>
<docanchor file="validation" title="How to manage the tests">valid_method</docanchor>
</compound>
<compound kind="page">
<name>dev_todo</name>
<title>ToDo</title>
<filename>dev_todo</filename>
<docanchor file="dev_todo" title="Wavefunction">todo_psi</docanchor>
<docanchor file="dev_todo" title="Hamiltonians">todo_ham</docanchor>
<docanchor file="dev_todo" title="Drivers">todo_qmc</docanchor>
<docanchor file="dev_todo" title="Workflow and tools">todo_tool</docanchor>
<docanchor file="dev_todo" title="Computer Science Development">todo_comp</docanchor>
</compound>
<compound kind="page">
<name>dev_jastrow</name>
<title>Jastrow functions</title>

4
docs/dev_layout.xml
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@ -5,9 +5,7 @@
<tab type="user" url="../doxy/index.html" title="Main Page"/>
<tab type="user" url="http://qmcpack.cmscc.org" title="Wiki"/>
<tab type="user" visiable="yes" url="../ug/index.html" title="User guide" intro="userguide,xml"/>
<tab type="mainpage" visiable="yes" url="index.html" title="Developers" intro="help for developers">
<tab type="pages" visible="yes" title="" intro=""/>
</tab>
<tab type="mainpage" visiable="yes" url="index.html" title="Developers" intro="help for developers"/>
<tab type="user" url="../tutorials/index.html" title="Tutorials" intro="tutorials"/>
</navindex>

2
docs/index.doc
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@ -24,6 +24,8 @@ quantum monte carlo simulations of real materials on gpu clusters,” Computing
in Science and Engineering, vol. 14, p. 40, 2012.
- QMCPACK, http://qmcpack.cmscc.org/
\subpage qmc_bib : bibtex
Different parts of the code are written by different people, whose names are
usually signed at the top of each file. If you are interested in participating
in QMCPACK development, contact Jeongnim Kim jeongnim.kim@gmail.com. QMCPACK

12
docs/qmcpack.cfg
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@ -4,7 +4,7 @@ DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = QMCPACK
PROJECT_NUMBER = 1.0
PROJECT_BRIEF =
PROJECT_LOGO =
PROJECT_LOGO = images/qmcpack_logo2.png
OUTPUT_DIRECTORY = output
CREATE_SUBDIRS = YES
OUTPUT_LANGUAGE = English
@ -461,6 +461,7 @@ INPUT = config.h \
../src/QMCDrivers \
../src/QMCApp \
index.doc \
bib.dox \
history.doc
# This tag can be used to specify the character encoding of the source files
@ -587,7 +588,8 @@ EXCLUDE_PATTERNS = */Experimental/* \
*/PseudGen/* \
*/Spline3D/* \
*/He* \
*/HFD*
*/HFD* \
*/BMakeFunc*
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
@ -1585,7 +1587,7 @@ DOT_FONTPATH =
# indirect inheritance relations. Setting this tag to YES will force the
# CLASS_DIAGRAMS tag to NO.
CLASS_GRAPH = YES
CLASS_GRAPH = NO
# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
@ -1639,7 +1641,7 @@ INCLUDED_BY_GRAPH = YES
# the time of a run. So in most cases it will be better to enable call graphs
# for selected functions only using the \callgraph command.
CALL_GRAPH = YES
CALL_GRAPH = NO
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
# doxygen will generate a caller dependency graph for every global function
@ -1676,7 +1678,7 @@ DOT_IMAGE_FORMAT = png
# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
# visible. Older versions of IE do not have SVG support.
INTERACTIVE_SVG = NO
INTERACTIVE_SVG = YES
# The tag DOT_PATH can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.

5
docs/qmcpack.css
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@ -111,7 +111,7 @@ div.navtab {
margin-right: 15px;
}
/* @group Link Styling */
/* @group Link Styling #3D578C; */
a {
color: #3D578C;
@ -119,8 +119,9 @@ a {
text-decoration: none;
}
/* color: #4665A2; */
.contents a:visited {
color: #4665A2;
color: #a25546;
}
a:hover {

4
docs/tut.cfg
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@ -7,7 +7,8 @@ CREATE_SUBDIRS = NO
INPUT = tutorials/index.dox \
tutorials/FSU20120111.jbm.dox \
tutorials/N2MSD.mam.dox
tutorials/N2MSD.mam.dox \
tutorials/qmc-solids-workflow-ls.dox
OUTPUT_LANGUAGE = English
TAB_SIZE = 2
MARKDOWN_SUPPORT = YES
@ -17,6 +18,7 @@ INPUT_ENCODING = UTF-8
FILE_PATTERNS = *.h *.cpp *.doc
RECURSIVE = YES
IMAGE_PATH = images $(DOXYGEN_IMAGE_PATH)
PROJECT_LOGO = images/qmcpack_logo2.png
#---------------------------------------------------------------------------
# configuration options related to the HTML output

4
docs/tut_layout.xml
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@ -6,9 +6,7 @@
<tab type="user" url="http://qmcpack.cmscc.org" title="Wiki"/>
<tab type="user" url="../ug/index.html" title="User guide" intro="userguide,xml"/>
<tab type="user" url="../dev/index.html" title="Developers" intro="help for developers"/>
<tab type="mainpage" url="index.html" title="Tutorials" intro="tutorials">
<tab type="pages" visible="yes" title="Tutorials" intro=""/>
</tab>
<tab type="mainpage" url="index.html" title="Tutorials" intro="tutorials"/>
</navindex>
<!-- Layout definition for a class page -->

28
docs/tutorials.tag
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@ -38,6 +38,34 @@
<docanchor file="n2msd_p" title="Beyond RHF/UHF">advS</docanchor>
<docanchor file="n2msd_p">qcout</docanchor>
</compound>
<compound kind="page">
<name>solid_luke</name>
<title>QMC workflow for solids</title>
<filename>solid_luke</filename>
<docanchor file="solid_luke" title="Initial DFT Calculations">initial-dft</docanchor>
<docanchor file="solid_luke" title="Pseudopotentials">pp</docanchor>
<docanchor file="solid_luke" title="Creating and testing wavefunctions for QMCPACK">spline-wfns</docanchor>
<docanchor file="solid_luke" title="Extracting Wavefunctions at Particular k-points">kext</docanchor>
<docanchor file="solid_luke" title="Optimizing Jastrow Factors within QMC">opts</docanchor>
<docanchor file="solid_luke">OptFig</docanchor>
<docanchor file="solid_luke" title="Testing Convergence of the Splines in QMCPACK">spline_cov</docanchor>
<docanchor file="solid_luke">SplConvFig</docanchor>
<docanchor file="solid_luke" title="Performing DMC Calculations">dmc_s</docanchor>
<docanchor file="solid_luke">dmc-transient-figure</docanchor>
<docanchor file="solid_luke">dmc-fullfigure</docanchor>
<docanchor file="solid_luke">dmc-tstep-conv</docanchor>
<docanchor file="solid_luke" title="Production Calculations">prod</docanchor>
<docanchor file="solid_luke" title="Controlling Finite Size Effects">fs_s</docanchor>
<docanchor file="solid_luke" title="One-Body Finite Size Effects and Twist Averaging">twist_s</docanchor>
<docanchor file="solid_luke">dmc-ta-conv</docanchor>
<docanchor file="solid_luke" title="Two-Body Finite Size Effects">tb_s</docanchor>
<docanchor file="solid_luke" title="Creating and Using Supercells">supercells</docanchor>
<docanchor file="solid_luke" title="Two-Body Finite Size Corrections">twfs_s</docanchor>
<docanchor file="solid_luke" title="Putting it all Together">all_s</docanchor>
<docanchor file="solid_luke">dmc-fs-conv</docanchor>
<docanchor file="solid_luke" title="Conclusion">con_s</docanchor>
<docanchor file="solid_luke" title="Acknowledgment">ack_s</docanchor>
</compound>
<compound kind="page">
<name>index</name>
<title>Tutorials</title>

2
docs/tutorials/N2MSD.mam.dox
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@ -15,7 +15,7 @@ wavefunctions)
After the build is completed, the converter for Gaussian-base QC code can be found
in the build directory:
<c>bin/convert4qmc</c>
\c bin/convert4qmc
The general usage of the converter and its features are described below:

2
docs/ug.cfg
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@ -51,7 +51,7 @@ PROJECT_BRIEF =
# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
# to the output directory.
PROJECT_LOGO =
PROJECT_LOGO = images/qmcpack_logo2.png
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is

4
docs/ug_layout.xml
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@ -4,9 +4,7 @@
<navindex>
<tab type="user" url="../doxy/index.html" title="Main Page"/>
<tab type="user" url="http://qmcpack.cmscc.org" title="Wiki"/>
<tab type="mainpage" visiable="yes" url="index.html" title="User guide" intro="userguide,xml">
<tab type="pages" visible="yes" title="" intro=""/>
</tab>
<tab type="mainpage" visiable="yes" url="index.html" title="User guide" intro="userguide,xml"/>
<tab type="user" url="../dev/index.html" title="Developers" intro="help for developers"/>
<tab type="user" url="../tutorials/index.html" title="Tutorials" intro="tutorials"/>
</navindex>