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Commit 51b7f9e2 authored by Robert McGibbon's avatar Robert McGibbon
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Merge master

parents 85bfd73c be0387b6
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.travis.yml
View file @ 51b7f9e2
......@@ -73,6 +73,7 @@ matrix:
CUDA=false
CC=clang
CXX=clang++
DOCS_DEPLOY=true
CMAKE_FLAGS=""
- sudo: false
......@@ -98,11 +99,11 @@ before_install:
# but this is a fast way to get an apparently functional precompiled
# build of swig that's more modern than what's in apt.
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2;
wget https://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
mkdir $HOME/swig;
tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig;
tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
export PATH=$HOME/swig/bin:$PATH;
export SWIG_LIB=$HOME/swig/share/swig/3.0.2;
export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
fi
- if [[ "$CUDA" == "true" ]]; then
......@@ -140,3 +141,25 @@ script:
- if [ -s Testing/Temporary/LastTestsFailed.log ]; then
ctest -I FailedTests.log;
fi
- if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
pip install sphinx numpydoc;
make DoxygenApiDocs PythonApiDocs;
mkdir -p api-docs;
mv api-python api-docs;
mv api-c++ api-docs;
fi
deploy:
- provider: s3
access_key_id:
secure: "AjE3nuj6kVuf21mOf0aZydW/3S/uCWsaoXC/huRxkxrmsNlnHBNGHZ9N48san1IxZAQM5pyaf7Yo9gkHur9obgq+e3lNgGvPp2mfkNXtLYcLJ46JF4kYliAtutjLWskrLg25Gu3xzF4EQkqSe0Le/oWldWWbTgvvH+KRq/vTHzI="
secret_access_key:
secure: "ISDQNSG2t0666PULtffo4wsKLFdu622EzuZxmiTxvLkjQGQlqm5+qn1Gd5UMLk7Ts2E0psdnmSrf6LVVCfrrQO/hcZHiJw3ZslMPDBBlRr8Epwdldn98ULhVoyQKtjXjCPzroa2UZCl1RFs4Nwb/VdDlI490XV0Lp4Woj1AT8tY="
bucket: "docs.openmm.org"
skip_cleanup: true
region: us-west-1
local_dir: api-docs/
upload_dir: development
on:
branch: master
condition: '! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true"'
CMakeLists.txt
View file @ 51b7f9e2
......@@ -65,6 +65,11 @@ ELSE(WIN32)
ENDIF(NOT OPENMM_INSTALL_PREFIX)
ENDIF(WIN32)
IF(WIN32)
ADD_DEFINITIONS(-DWIN32)
ENDIF(WIN32)
# Include CPU-Features for Android
IF (ANDROID)
INCLUDE_DIRECTORIES(${ANDROID_NDK}/sources/cpufeatures)
......@@ -119,7 +124,7 @@ IF (APPLE AND (NOT PNACL))
SET (CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "The processor architectures to build for" FORCE)
ENDIF (NOT CMAKE_OSX_ARCHITECTURES)
IF (NOT CMAKE_OSX_SYSROOT)
EXECUTE_PROCESS(COMMAND "xcrun" "--show-sdk-path" OUTPUT_VARIABLE XCRUN_OSX_SYSROOT RESULT_VARIABLE XCRUN_OSX_SYSROOT_STATUS)
EXECUTE_PROCESS(COMMAND "xcrun" "--show-sdk-path" OUTPUT_VARIABLE XCRUN_OSX_SYSROOT RESULT_VARIABLE XCRUN_OSX_SYSROOT_STATUS OUTPUT_STRIP_TRAILING_WHITESPACE)
IF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)
SET (CMAKE_OSX_SYSROOT "${XCRUN_OSX_SYSROOT}" CACHE STRING "SDK Path" FORCE)
ENDIF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)
......
appveyor.yml
View file @ 51b7f9e2
......@@ -20,7 +20,7 @@ install:
- "set PATH=C:\\fftw;%PATH%"
# Download and install some OpenMM build dependencies (doxygen, swig)
- choco install -y doxygen.portable swig
- choco install -y doxygen.portable swig > null
# Set CMake options
- ps: $env:CMAKE_FLAGS='-DOPENMM_BUILD_PME_PLUGIN=ON -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib -DFFTW_INCLUDES=C:/fftw -DCMAKE_BUILD_TYPE=Release -DOPENMM_BUILD_EXAMPLES=OFF -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG"'
......
docs-source/usersguide/application.rst
View file @ 51b7f9e2
......@@ -1125,6 +1125,13 @@ perform integration on a modified potential energy surface to allow much faster
sampling of conformations. For details on how to use them, consult the API
documentation.
Compound Integrator
-------------------
The :class:`CompoundIntegrator` class is useful for cases where you want to use
multiple integration algorithms within a single simulation. It allows you to
create multiple integrators, then switch back and forth between them. For
details on how to use it, consult the API documentation.
Temperature Coupling
====================
......
libraries/pthreads/include/pthread.h
View file @ 51b7f9e2
......@@ -121,6 +121,9 @@
#endif
#if _MSC_VER >= 1900
#include <ctime>
#else
/* Windows doesn't have this, so declare it ourselves. */
struct timespec
{
......@@ -128,6 +131,7 @@ struct timespec
long long tv_sec;
long long tv_nsec;
};
#endif
typedef struct _pthread_cleanup _pthread_cleanup;
struct _pthread_cleanup
......
openmmapi/include/OpenMM.h
View file @ 51b7f9e2
......@@ -36,6 +36,7 @@
#include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/CompoundIntegrator.h"
#include "openmm/CustomBondForce.h"
#include "openmm/CustomCentroidBondForce.h"
#include "openmm/CustomCompoundBondForce.h"
......
openmmapi/include/openmm/CMAPTorsionForce.h
View file @ 51b7f9e2
......@@ -85,8 +85,8 @@ public:
* Get the energy values of a map.
*
* @param index the index of the map for which to get energy values
* @param size the size of the map along each dimension
* @param energy the energy values for the map. This must be of length size*size.
* @param[out] size the size of the map along each dimension
* @param[out] energy the energy values for the map. This must be of length size*size.
* The element energy[i+size*j] contains the energy when the first
* torsion angle equals i*2*PI/size and the second torsion angle
* equals j*2*PI/size.
......@@ -122,15 +122,15 @@ public:
* Get the force field parameters for a CMAP torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param map the index of the map to use for this term
* @param a1 the index of the first particle forming the first torsion
* @param a2 the index of the second particle forming the first torsion
* @param a3 the index of the third particle forming the first torsion
* @param a4 the index of the fourth particle forming the first torsion
* @param b1 the index of the first particle forming the second torsion
* @param b2 the index of the second particle forming the second torsion
* @param b3 the index of the third particle forming the second torsion
* @param b4 the index of the fourth particle forming the second torsion
* @param[out] map the index of the map to use for this term
* @param[out] a1 the index of the first particle forming the first torsion
* @param[out] a2 the index of the second particle forming the first torsion
* @param[out] a3 the index of the third particle forming the first torsion
* @param[out] a4 the index of the fourth particle forming the first torsion
* @param[out] b1 the index of the first particle forming the second torsion
* @param[out] b2 the index of the second particle forming the second torsion
* @param[out] b3 the index of the third particle forming the second torsion
* @param[out] b4 the index of the fourth particle forming the second torsion
*/
void getTorsionParameters(int index, int& map, int& a1, int& a2, int& a3, int& a4, int& b1, int& b2, int& b3, int& b4) const;
/**
......
openmmapi/include/openmm/CompoundIntegrator.h 0 → 100644
View file @ 51b7f9e2
#ifndef OPENMM_COMPOUNDINTEGRATOR_H_
#define OPENMM_COMPOUNDINTEGRATOR_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "Integrator.h"
#include "openmm/Kernel.h"
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* This class allows you to use multiple integration algorithms within a single simulation,
* switching back and forth between them. To use it, create whatever other Integrators
* you need, then add all of them to a CustomIntegrator:
*
* <tt><pre>
* CompoundIntegrator compoundIntegrator;
* compoundIntegrator.addIntegrator(new VerletIntegrator(0.001));
* compoundIntegrator.addIntegrator(new LangevinIntegrator(300.0, 1.0, 0.001));
* </pre></tt>
*
* Next create a Context, specifying the CompoundIntegrator as the Integrator to use for
* the Context:
*
* <tt><pre>
* Context context(system, compoundIntegrator);
* </pre></tt>
*
* Finally, call setCurrentIntegrator() to set which Integrator is active. That one will
* be used for all calls to step() until the next time you change it.
*
* <tt><pre>
* compoundIntegrator.setCurrentIntegrator(0);
* compoundIntegrator.step(1000); // Take 1000 steps of Verlet dynamics
* compoundIntegrator.setCurrentIntegrator(1);
* compoundIntegrator.step(1000); // Take 1000 steps of Langevin dynamics
* </pre></tt>
*
* When switching between integrators, it is important to make sure they are compatible with
* each other, and that they will interpret the positions and velocities in the same way.
* Remember that leapfrog style integrators assume the positions and velocities are offset
* from each other by half a time step. When switching between a leapfrog and non-leapfrog
* integrator, you must first adjust the velocities to avoid introducing error. This is also
* true when switching between two leapfrog integrators that use different step sizes,
* since they will interpret the velocities as corresponding to different times.
*/
class OPENMM_EXPORT CompoundIntegrator : public Integrator {
public:
/**
* Create a CompoundIntegrator.
*/
explicit CompoundIntegrator();
~CompoundIntegrator();
/**
* Get the number of Integrators that have been added to this CompoundIntegrator.
*/
int getNumIntegrators() const;
/**
* Add an Integrator to this CompoundIntegrator. The Integrator object should have
* been created on the heap with the "new" operator. The CompoundIntegrator takes over
* ownership of it, and deletes it when the CompoundIntegrator itself is deleted.
* All Integrators must be added before the Context is created.
*
* @param integrator the Integrator to add
* @return the index of the Integrator that was added
*/
int addIntegrator(Integrator* integrator);
/**
* Get a reference to one of the Integrators that have been added to this CompoundIntegrator.
*
* @param index the index of the Integrator to get
*/
Integrator& getIntegrator(int index);
/**
* Get a const reference to one of the Integrators that have been added to this CompoundIntegrator.
*
* @param index the index of the Integrator to get
*/
const Integrator& getIntegrator(int index) const;
/**
* Get the index of the current Integrator.
*/
int getCurrentIntegrator() const;
/**
* Set the current Integrator.
*
* @param index the index of the Integrator to use
*/
void setCurrentIntegrator(int index);
/**
* Get the size of each time step, in picoseconds. This method calls getStepSize() on
* whichever Integrator has been set as current.
*
* @return the step size, measured in ps
*/
double getStepSize() const;
/**
* Set the size of each time step, in picoseconds. This method calls setStepSize() on
* whichever Integrator has been set as current.
*
* @param size the step size, measured in ps
*/
void setStepSize(double size);
/**
* Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
* This method calls getConstraintTolerance() on whichever Integrator has been set as current.
*/
double getConstraintTolerance() const;
/**
* Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
* This method calls setConstraintTolerance() on whichever Integrator has been set as current.
*/
void setConstraintTolerance(double tol);
/**
* Advance a simulation through time by taking a series of time steps. This method
* calls step() on whichever Integrator has been set as current.
*
* @param steps the number of time steps to take
*/
void step(int steps);
protected:
/**
* This will be called by the Context when it is created. It informs the Integrator
* of what context it will be integrating, and gives it a chance to do any necessary initialization.
* It will also get called again if the application calls reinitialize() on the Context.
*
* The implementation calls initialize() on each Integrator that has been added to this CompoundIntegrator.
*/
void initialize(ContextImpl& context);
/**
* This will be called by the Context when it is destroyed to let the Integrator do any necessary
* cleanup. It will also get called again if the application calls reinitialize() on the Context.
*
* The implementation calls cleanup() on each Integrator that has been added to this CompoundIntegrator.
*/
void cleanup();
/**
* Get the names of all Kernels used by this Integrator.
*
* The implementation returns the union of all kernel names required by all Integrators that have been added.
*/
std::vector<std::string> getKernelNames();
/**
* Compute the kinetic energy of the system at the current time.
*
* The implementation calls computeKineticEnergy() on whichever Integrator has been set as current.
*/
double computeKineticEnergy();
private:
int currentIntegrator;
std::vector<Integrator*> integrators;
};
} // namespace OpenMM
#endif /*OPENMM_COMPOUNDINTEGRATOR_H_*/
openmmapi/include/openmm/Context.h
View file @ 51b7f9e2
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -165,6 +165,11 @@ public:
* @param randomSeed the random number seed to use when selecting velocities
*/
void setVelocitiesToTemperature(double temperature, int randomSeed=osrngseed());
/**
* Get all adjustable parameters that have been defined by Force objects in the System, along
* with their current values.
*/
const std::map<std::string, double>& getParameters() const;
/**
* Get the value of an adjustable parameter defined by a Force object in the System.
*
......
openmmapi/include/openmm/CustomAngleForce.h
View file @ 51b7f9e2
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -176,10 +176,10 @@ public:
* Get the force field parameters for an angle term.
*
* @param index the index of the angle for which to get parameters
* @param particle1 the index of the first particle connected by the angle
* @param particle2 the index of the second particle connected by the angle
* @param particle3 the index of the third particle connected by the angle
* @param parameters the list of parameters for the angle
* @param[out] particle1 the index of the first particle connected by the angle
* @param[out] particle2 the index of the second particle connected by the angle
* @param[out] particle3 the index of the third particle connected by the angle
* @param[out] parameters the list of parameters for the angle
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomBondForce.h
View file @ 51b7f9e2
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -175,9 +175,9 @@ public:
* Get the force field parameters for a bond term.
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param parameters the list of parameters for the bond
* @param[out] particle1 the index of the first particle connected by the bond
* @param[out] particle2 the index of the second particle connected by the bond
* @param[out] parameters the list of parameters for the bond
*/
void getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomCentroidBondForce.h
View file @ 51b7f9e2
......@@ -226,7 +226,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -242,8 +242,8 @@ public:
* Get the properties of a group.
*
* @param index the index of the group to get
* @param particles the indices of the particles in the group
* @param weights the weight used for each particle when computing the center position.
* @param[out] particles the indices of the particles in the group
* @param[out] weights the weight used for each particle when computing the center position.
* If no weights were specified, this vector will be empty indicating that particle
* masses should be used as weights.
*/
......@@ -269,8 +269,8 @@ public:
* Get the properties of a bond.
*
* @param index the index of the bond to get
* @param groups the indices of the groups in the bond
* @param parameters the list of per-bond parameter values for the bond
* @param[out] groups the indices of the groups in the bond
* @param[out] parameters the list of per-bond parameter values for the bond
*/
void getBondParameters(int index, std::vector<int>& groups, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ 51b7f9e2
......@@ -209,7 +209,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -224,8 +224,8 @@ public:
* Get the properties of a bond.
*
* @param index the index of the bond to get
* @param particles the indices of the particles in the bond
* @param parameters the list of per-bond parameter values for the bond
* @param[out] particles the indices of the particles in the bond
* @param[out] parameters the list of per-bond parameter values for the bond
*/
void getBondParameters(int index, std::vector<int>& particles, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomExternalForce.h
View file @ 51b7f9e2
......@@ -170,7 +170,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -185,8 +185,8 @@ public:
* Get the force field parameters for a force field term.
*
* @param index the index of the particle term for which to get parameters
* @param particle the index of the particle this term is applied to
* @param parameters the list of parameters for the force field term
* @param[out] particle the index of the particle this term is applied to
* @param[out] parameters the list of parameters for the force field term
*/
void getParticleParameters(int index, int& particle, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomGBForce.h
View file @ 51b7f9e2
......@@ -309,7 +309,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -324,7 +324,7 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param[out] parameters the list of parameters for the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters) const;
/**
......@@ -355,8 +355,8 @@ public:
* Get the properties of a computed value.
*
* @param index the index of the computed value for which to get parameters
* @param name the name of the value
* @param expression an algebraic expression to evaluate when calculating the computed value. If the
* @param[out] name the name of the value
* @param[out] expression an algebraic expression to evaluate when calculating the computed value. If the
* ComputationType is SingleParticle, the expression is evaluated independently
* for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
* parameters and previous computed values for that particle. If the ComputationType is ParticlePair
......@@ -366,7 +366,7 @@ public:
* the per-particle parameters and previous computed values for each of them.
* Append "1" to a variable name to indicate the parameter for the particle whose
* value is being calculated, and "2" to indicate the particle it is interacting with.
* @param type the method to use for computing this value
* @param[out] type the method to use for computing this value
*/
void getComputedValueParameters(int index, std::string& name, std::string& expression, ComputationType& type) const;
/**
......@@ -407,7 +407,7 @@ public:
* Get the properties of a term to the energy computation.
*
* @param index the index of the term for which to get parameters
* @param expression an algebraic expression to evaluate when calculating the energy. If the
* @param[out] expression an algebraic expression to evaluate when calculating the energy. If the
* ComputationType is SingleParticle, the expression is evaluated once
* for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
* parameters and computed values for that particle. If the ComputationType is ParticlePair or
......@@ -417,7 +417,7 @@ public:
* the per-particle parameters and computed values for each of them.
* Append "1" to a variable name to indicate the parameter for the first particle
* in the pair and "2" to indicate the second particle in the pair.
* @param type the method to use for computing this value
* @param[out] type the method to use for computing this value
*/
void getEnergyTermParameters(int index, std::string& expression, ComputationType& type) const;
/**
......@@ -449,8 +449,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......
openmmapi/include/openmm/CustomHbondForce.h
View file @ 51b7f9e2
......@@ -282,7 +282,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -301,12 +301,12 @@ public:
* Get the properties of a donor group.
*
* @param index the index of the donor group to get
* @param d1 the index of the first particle for this donor group
* @param d2 the index of the second particle for this donor group. If the group only
* @param[out] d1 the index of the first particle for this donor group
* @param[out] d2 the index of the second particle for this donor group. If the group only
* includes one particle, this will be -1.
* @param d3 the index of the third particle for this donor group. If the group includes
* @param[out] d3 the index of the third particle for this donor group. If the group includes
* less than three particles, this will be -1.
* @param parameters the list of per-donor parameter values for the donor
* @param[out] parameters the list of per-donor parameter values for the donor
*/
void getDonorParameters(int index, int& d1, int& d2, int& d3, std::vector<double>& parameters) const;
/**
......@@ -337,12 +337,12 @@ public:
* Get the properties of an acceptor group.
*
* @param index the index of the acceptor group to get
* @param a1 the index of the first particle for this acceptor group
* @param a2 the index of the second particle for this acceptor group. If the group only
* @param[out] a1 the index of the first particle for this acceptor group
* @param[out] a2 the index of the second particle for this acceptor group. If the group only
* includes one particle, this will be -1.
* @param a3 the index of the third particle for this acceptor group. If the group includes
* @param[out] a3 the index of the third particle for this acceptor group. If the group includes
* less than three particles, this will be -1.
* @param parameters the list of per-acceptor parameter values for the acceptor
* @param[out] parameters the list of per-acceptor parameter values for the acceptor
*/
void getAcceptorParameters(int index, int& a1, int& a2, int& a3, std::vector<double>& parameters) const;
/**
......@@ -369,16 +369,16 @@ public:
* Get the donor and acceptor in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get donor and acceptor indices
* @param particle1 the index of the donor
* @param particle2 the index of the acceptor
* @param[out] particle1 the index of the donor
* @param[out] particle2 the index of the acceptor
*/
void getExclusionParticles(int index, int& donor, int& acceptor) const;
/**
* Get the donor and acceptor in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get donor and acceptor indices
* @param particle1 the index of the donor
* @param particle2 the index of the acceptor
* @param donor the index of the donor
* @param acceptor the index of the acceptor
*/
void setExclusionParticles(int index, int donor, int acceptor);
/**
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 51b7f9e2
......@@ -371,7 +371,7 @@ public:
* Get the value of a per-DOF variable, specified by name.
*
* @param name the name of the variable to get
* @param values the values of the variable for all degrees of freedom
* @param[out] values the values of the variable for all degrees of freedom
* are stored into this
*/
void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
......@@ -446,7 +446,7 @@ public:
/**
* Add a step which begins a new "if" block.
*
* @param expression a mathematical expression involving a comparison operator
* @param condition a mathematical expression involving a comparison operator
* and global variables. All steps between this one and
* the end of the block are executed only if the condition
* is true.
......@@ -457,7 +457,7 @@ public:
/**
* Add a step which begins a new "while" block.
*
* @param expression a mathematical expression involving a comparison operator
* @param condition a mathematical expression involving a comparison operator
* and global variables. All steps between this one and
* the end of the block are executed repeatedly as long as
* the condition remains true.
......@@ -476,12 +476,13 @@ public:
* Get the details of a computation step that has been added to the integration algorithm.
*
* @param index the index of the computation step to get
* @param type on exit, the type of computation this step performs
* @param variable on exit, the variable into which this step stores its result. If this
* step does not store a result in a variable, this will be an
* empty string.
* @param expression on exit, the expression this step evaluates. If this step does not
* evaluate an expression, this will be an empty string.
* @param[out] type the type of computation this step performs
* @param[out] variable the variable into which this step stores its
* result. If this step does not store a result in
* a variable, this will be an empty string.
* @param[out] expression the expression this step evaluates. If
* this step does not evaluate an expression, this
* will be an empty string.
*/
void getComputationStep(int index, ComputationType& type, std::string& variable, std::string& expression) const;
/**
......
openmmapi/include/openmm/CustomManyParticleForce.h
View file @ 51b7f9e2
......@@ -337,7 +337,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -353,8 +353,8 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param type the type of the specified particle
* @param[out] parameters the list of parameters for the specified particle
* @param[out] type the type of the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters, int& type) const;
/**
......@@ -379,8 +379,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......@@ -406,7 +406,7 @@ public:
* regardless of the type of the specified particle.
*
* @param index the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
* @param types the allowed types for the specified particle
* @param[out] types the allowed types for the specified particle
*/
void getTypeFilter(int index, std::set<int>& types) const;
/**
......
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 51b7f9e2
......@@ -318,7 +318,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -333,7 +333,7 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param[out] parameters the list of parameters for the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters) const;
/**
......@@ -357,8 +357,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......@@ -441,8 +441,8 @@ public:
* Get the parameters for an interaction group.
*
* @param index the index of the interaction group for which to get parameters
* @param set1 the first set of particles forming the interaction group
* @param set2 the second set of particles forming the interaction group
* @param[out] set1 the first set of particles forming the interaction group
* @param[out] set2 the second set of particles forming the interaction group
*/
void getInteractionGroupParameters(int index, std::set<int>& set1, std::set<int>& set2) const;
/**
......
openmmapi/include/openmm/CustomTorsionForce.h
View file @ 51b7f9e2
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -177,11 +177,11 @@ public:
* Get the force field parameters for a torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle connected by the torsion
* @param particle2 the index of the second particle connected by the torsion
* @param particle3 the index of the third particle connected by the torsion
* @param particle4 the index of the fourth particle connected by the torsion
* @param parameters the list of parameters for the torsion
* @param[out] particle1 the index of the first particle connected by the torsion
* @param[out] particle2 the index of the second particle connected by the torsion
* @param[out] particle3 the index of the third particle connected by the torsion
* @param[out] particle4 the index of the fourth particle connected by the torsion
* @param[out] parameters the list of parameters for the torsion
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, std::vector<double>& parameters) const;
/**
......
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