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Commit 4fccce3e authored by peastman's avatar peastman
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Fixes to user guide

parent 0e4555a8
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docs-source/CMakeLists.txt
View file @ 4fccce3e
......@@ -84,15 +84,19 @@ ENDIF(DOXYGEN_EXECUTABLE)
SET(SPHINX_BUILD_DIR "${CMAKE_BINARY_DIR}/sphinx-docs/")
FILE(MAKE_DIRECTORY "${SPHINX_BUILD_DIR}")
FILE(GLOB_RECURSE USER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/usersguide/*)
FILE(GLOB_RECURSE DEVELOPER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/developerguide/*)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
DEPENDS ${USER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating PDF user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
DEPENDS ${DEVELOPER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating PDF developer guide"
)
......@@ -103,14 +107,16 @@ ADD_CUSTOM_TARGET(sphinxpdf
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
DEPENDS ${USER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating PDF user guide"
COMMENT "Generating HTML user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
DEPENDS ${DEVELOPER_GUIDE_FILES}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating PDF developer guide"
COMMENT "Generating HTML developer guide"
)
ADD_CUSTOM_TARGET(sphinxhtml
DEPENDS "${SPHINX_BUILD_DIR}/userguide/html/index.html" "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
......
docs-source/sphinx/autonumber.py
View file @ 4fccce3e
......@@ -43,6 +43,7 @@ def doctree_resolved(app, doctree, docname):
chapter = sectionNumbers[chapter.attributes['ids'][0]][0]
if chapter != lastChapter:
index = {}
nextNumber = 1
newNode = Text('%s %d-%d' % (category, chapter, nextNumber))
lastChapter = chapter
else:
......
docs-source/usersguide/application.rst
View file @ 4fccce3e
......@@ -58,7 +58,7 @@ and tell it to install the command line tools. With Xcode 4.2 and earlier, the
command line tools are automatically installed when you install Xcode.)
3. (Optional) If you have an Nvidia GPU and want to use the CUDA platform,
download CUDA 5.5 from https://developer.nvidia.com/cuda-downloads. Be sure to
download CUDA 6.0 from https://developer.nvidia.com/cuda-downloads. Be sure to
install both the drivers and toolkit.
4. (Optional) If you plan to use the CPU platform, it is recommended that you
......@@ -100,7 +100,7 @@ location, you can set OPENMM_CUDA_COMPILER to tell OpenMM where to find it. For
example,
::
export OPENMM_CUDA_COMPILER=/opt/CUDA/cuda-5.5/bin/nvcc
export OPENMM_CUDA_COMPILER=/opt/CUDA/cuda-6.0/bin/nvcc
7. Verify your installation by running the “testInstallation.py” script found in
the “examples” folder of your OpenMM installation. To run it, cd to the
......@@ -132,7 +132,7 @@ into a console window.
3. (Optional) If you want to run OpenMM on a GPU, install CUDA and/or OpenCL.
* If you have an Nvidia GPU, download CUDA 5.5 from
* If you have an Nvidia GPU, download CUDA 6.0 from
https://developer.nvidia.com/cuda-downloads. Be sure to install both the
drivers and toolkit. OpenCL is included with the CUDA drivers.
* If you have an AMD GPU, download the latest version of the Catalyst driver
......@@ -179,7 +179,7 @@ location, you can set OPENMM_CUDA_COMPILER to tell OpenMM where to find it. For
example,
::
export OPENMM_CUDA_COMPILER=/opt/CUDA/cuda-5.5/bin/nvcc
export OPENMM_CUDA_COMPILER=/opt/CUDA/cuda-6.0/bin/nvcc
7. Verify your installation by running the “testInstallation.py” script found in
the “examples” folder of your OpenMM installation. To run it, cd to the
......@@ -214,7 +214,7 @@ and ignore it.)
4. (Optional) If you want to run OpenMM on a GPU, install CUDA and/or OpenCL.
* If you have an Nvidia GPU, download CUDA 5.5 from
* If you have an Nvidia GPU, download CUDA 6.0 from
https://developer.nvidia.com/cuda-downloads. Be sure to install both the
drivers and toolkit. For 64-bit machines, you should install the 64-bit driver,
but download the 32-bit version of the toolkit since the OpenMM binary is
......@@ -651,20 +651,20 @@ For the main force field, OpenMM provides the following options:
.. tabularcolumns:: |l|L|
===================== ================================================================================
============================= ================================================================================
File Force Field
===================== ================================================================================
amber96.xml AMBER96\ :cite:`Kollman1997`
amber99sb.xml AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
amber03.xml AMBER03\ :cite:`Duan2003`
amber10.xml AMBER10
amoeba2009.xml AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
============================= ================================================================================
:code:`amber96.xml` AMBER96\ :cite:`Kollman1997`
:code:`amber99sb.xml` AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
:code:`amber99sbildn.xml` AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
:code:`amber99sbnmr.xml` AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
:code:`amber03.xml` AMBER03\ :cite:`Duan2003`
:code:`amber10.xml` AMBER10
:code:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead.
amoeba2013.xml AMOEBA 2013\ :cite:`Shi2013`
charmm_polar_2013.xml CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
===================== ================================================================================
:code:`amoeba2013.xml` AMOEBA 2013\ :cite:`Shi2013`
:code:`charmm_polar_2013.xml` CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
============================= ================================================================================
The AMBER files do not include parameters for water molecules. This allows you
......@@ -674,17 +674,17 @@ files:
.. tabularcolumns:: |l|L|
=========== ============================================
=================== ============================================
File Water Model
=========== ============================================
tip3p.xml TIP3P water model\ :cite:`Jorgensen1983`
tip3pfb.xml TIP3P-FB water model\ :cite:`Wang2014`
tip4pew.xml TIP4P-Ew water model\ :cite:`Horn2004`
tip4pfb.xml TIP4P-FB water model\ :cite:`Wang2014`
tip5p.xml TIP5P water model\ :cite:`Mahoney2000`
spce.xml SPC/E water model\ :cite:`Berendsen1987`
swm4ndp.xml SWM4-NDP water model\ :cite:`Lamoureux2006`
=========== ============================================
=================== ============================================
:code:`tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983`
:code:`tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014`
:code:`tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004`
:code:`tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014`
:code:`tip5p.xml` TIP5P water model\ :cite:`Mahoney2000`
:code:`spce.xml` SPC/E water model\ :cite:`Berendsen1987`
:code:`swm4ndp.xml` SWM4-NDP water model\ :cite:`Lamoureux2006`
=================== ============================================
For the polarizable force fields (AMOEBA and CHARMM), only one explicit water model
......@@ -697,16 +697,16 @@ the following files:
.. tabularcolumns:: |l|L|
================= =================================================================================================
========================= =================================================================================================
File Implicit Solvation Model
================= =================================================================================================
amber96_obc.xml GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
amber99_obc.xml GBSA-OBC solvation model for use with AMBER99 force fields
amber03_obc.xml GBSA-OBC solvation model for use with AMBER03 force field
amber10_obc.xml GBSA-OBC solvation model for use with AMBER10 force field
amoeba2009_gk.xml Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
amoeba2013_gk.xml Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
================= =================================================================================================
========================= =================================================================================================
:code:`amber96_obc.xml` GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
:code:`amber99_obc.xml` GBSA-OBC solvation model for use with AMBER99 force fields
:code:`amber03_obc.xml` GBSA-OBC solvation model for use with AMBER03 force field
:code:`amber10_obc.xml` GBSA-OBC solvation model for use with AMBER10 force field
:code:`amoeba2009_gk.xml` Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
:code:`amoeba2013_gk.xml` Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
========================= =================================================================================================
For example, to use the GBSA-OBC solvation model with the Amber99SB force field,
......@@ -739,17 +739,17 @@ allowed values for :code:`implicitSolvent`\ :
.. tabularcolumns:: |l|L|
===== ==================================================================================================================================
============= ==================================================================================================================================
Value Meaning
===== ==================================================================================================================================
None No implicit solvent is used.
HCT Hawkins-Cramer-Truhlar GBSA model\ :cite:`Hawkins1995` (corresponds to igb=1 in AMBER)
OBC1 Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ I parameters (corresponds to igb=2 in AMBER).
OBC2 Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ II parameters (corresponds to igb=5 in AMBER).
============= ==================================================================================================================================
:code:`None` No implicit solvent is used.
:code:`HCT` Hawkins-Cramer-Truhlar GBSA model\ :cite:`Hawkins1995` (corresponds to igb=1 in AMBER)
:code:`OBC1` Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ I parameters (corresponds to igb=2 in AMBER).
:code:`OBC2` Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ II parameters (corresponds to igb=5 in AMBER).
This is the same model used by the GBSA-OBC files described in section :ref:`force-fields`.
GBn GBn solvation model\ :cite:`Mongan2007` (corresponds to igb=7 in AMBER).
GBn2 GBn2 solvation model\ :cite:`Nguyen2013` (corresponds to igb=8 in AMBER).
===== ==================================================================================================================================
:code:`GBn` GBn solvation model\ :cite:`Mongan2007` (corresponds to igb=7 in AMBER).
:code:`GBn2` GBn2 solvation model\ :cite:`Nguyen2013` (corresponds to igb=8 in AMBER).
============= ==================================================================================================================================
You can further control the solvation model in a few ways. First, you can
......@@ -785,15 +785,15 @@ The :code:`nonbondedMethod` parameter can have any of the following values:
.. tabularcolumns:: |l|L|
================= ===========================================================================================================================================================================================================================================
========================= ===========================================================================================================================================================================================================================================
Value Meaning
================= ===========================================================================================================================================================================================================================================
NoCutoff No cutoff is applied.
CutoffNonPeriodic The reaction field method is used to eliminate all interactions beyond a cutoff distance. Not valid for AMOEBA.
CutoffPeriodic The reaction field method is used to eliminate all interactions beyond a cutoff distance. Periodic boundary conditions are applied, so each atom interacts only with the nearest periodic copy of every other atom. Not valid for AMOEBA.
Ewald Periodic boundary conditions are applied. Ewald summation is used to compute long range interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
PME Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions.
================= ===========================================================================================================================================================================================================================================
========================= ===========================================================================================================================================================================================================================================
:code:`NoCutoff` No cutoff is applied.
:code:`CutoffNonPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Not valid for AMOEBA.
:code:`CutoffPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Periodic boundary conditions are applied, so each atom interacts only with the nearest periodic copy of every other atom. Not valid for AMOEBA.
:code:`Ewald` Periodic boundary conditions are applied. Ewald summation is used to compute long range interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
:code:`PME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions.
========================= ===========================================================================================================================================================================================================================================
When using any method other than :code:`NoCutoff`\ , you should also specify a
......@@ -902,14 +902,14 @@ The :code:`constraints` parameter can have any of the following values:
.. tabularcolumns:: |l|L|
======== =============================================================================================================================================
================ =============================================================================================================================================
Value Meaning
======== =============================================================================================================================================
None No constraints are applied. This is the default value.
HBonds The lengths of all bonds that involve a hydrogen atom are constrained.
AllBonds The lengths of all bonds are constrained.
HAngles The lengths of all bonds are constrained. In addition, all angles of the form H-X-H or H-O-X (where X is an arbitrary atom) are constrained.
======== =============================================================================================================================================
================ =============================================================================================================================================
:code:`None` No constraints are applied. This is the default value.
:code:`HBonds` The lengths of all bonds that involve a hydrogen atom are constrained.
:code:`AllBonds` The lengths of all bonds are constrained.
:code:`HAngles` The lengths of all bonds are constrained. In addition, all angles of the form H-X-H or H-O-X (where X is an arbitrary atom) are constrained.
================ =============================================================================================================================================
The main reason to use constraints is that it allows one to use a larger
......@@ -2426,9 +2426,10 @@ with the following signature to parse the XML tag and create the generator:
:code:`element` is the XML tag (an xml.etree.ElementTree.Element object) and
:code:`forcefield` is the ForceField being created. This method should
create a generator and add it to the ForceField:
::
generator = MyForceGenerator()
forcefield._forces.append(generator)
generator = MyForceGenerator()
forcefield._forces.append(generator)
It then should parse the information contained in the XML tag and configure the
generator based on it.
......
docs-source/usersguide/library.rst
View file @ 4fccce3e
......@@ -20,11 +20,11 @@ high level interface for running simulations. This layer is targeted at
computational biologists or other people who want to run simulations, and who
may or may not be programmers.
Part I of this guide focused on the application layer and described how to run
The first part of this guide focused on the application layer and described how to run
simulations with it. We now turn to the lower level libraries. We will assume
you are a programmer, that you are writing your own applications, and that you
want to add simulation features to those applications. Part II of this guide
describes how to do that with OpenMM.
want to add simulation features to those applications. The following chapters
describe how to do that with OpenMM.
How to get started
==================
......@@ -42,7 +42,8 @@ License
========
Two different licenses are used for different parts of OpenMM. The public API,
the low level API, and the reference platform are all distributed under the MIT
the low level API, the reference platform, the CPU platform, and the application
layer are all distributed under the MIT
license. This is a very permissive license which allows them to be used in
almost any way, requiring only that you retain the copyright notice and
disclaimer when distributing them.
......@@ -425,12 +426,18 @@ Get the OpenMM source code
You will also need the OpenMM source code before building OpenMM from source.
To download and unpack OpenMM source code:
#. Browse to https://simtk.org/home/openmm/.
#. Browse to https://simtk.org/home/openmm.
#. Click the "Downloads" link in the navigation bar on the left side.
#. Download OpenMM<Version>-Source.zip, choosing the latest version.
#. Unpack the zip file. Note the location where you unpacked the OpenMM source
code.
Alternatively, if you want the most recent development version of the code rather
than the version corresponding to a particular release, you can get it from
https://github.com/SimTk/openmm. Be aware that the development code is constantly
changing, may contain bugs, and should never be used for production work. If
you want a stable, well tested version of OpenMM, you should download the source
code for the latest release as described above.
Other Required Software
=======================
......@@ -540,10 +547,10 @@ There are several variables that can be adjusted in the CMake interface:
install OpenMM.
Configure (press “\ :code:`c`\ ”) again. Adjust any variables that cause an
Configure (press “c”) again. Adjust any variables that cause an
error.
Continue to configure (press “\ :code:`c`\ ”) until no starred/red CMake
Continue to configure (press “c”) until no starred/red CMake
variables are displayed. Congratulations, you have completed the configuration
step.
......@@ -566,7 +573,7 @@ Windows
Mac and Linux
=============
* Press :code:`g` to generate the Makefile.
* Press “g” to generate the Makefile.
* If CMake does not exit automatically, press “q” to exit.
......@@ -1321,8 +1328,10 @@ to change the build environment.
double stepSizeInFs,
std::string& platformName);
static void myStepWithOpenMM(MyOpenMMData*, int numSteps);
static void myGetOpenMMState(MyOpenMMData*, bool
wantEnergy,double& time, double& energy,
static void myGetOpenMMState(MyOpenMMData*,
bool wantEnergy,
double& time,
double& energy,
MyAtomInfo atoms[]);
static void myTerminateOpenMM(MyOpenMMData*);
......
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