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Unverified Commit b3be7aec authored by Andy Simmonett's avatar Andy Simmonett
Browse files

Clean up NHC interface and fix bug in swig generator

parent 75104c41
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Showing with 104 additions and 78 deletions
openmmapi/include/openmm/NoseHooverIntegrator.h
View file @ b3be7aec
......@@ -58,15 +58,15 @@ public:
/**
* Create a NoseHooverIntegrator.
*
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param temperature the target temperature for the system (in Kelvin).
* @param collisionFrequency the frequency of the interaction with the heat bath (in inverse picoseconds).
* @param stepSize the step size with which to integrate the system (in picoseconds)
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
explicit NoseHooverIntegrator(double temperature, int collisionFrequnency, double stepSize,
explicit NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
virtual ~NoseHooverIntegrator();
......@@ -81,7 +81,7 @@ public:
*
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param chainLength the number of beads in the Nose-Hoover chain
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
......@@ -94,6 +94,7 @@ public:
* provided and the thermostat will only control members of that list. Additionally a list of pairs of
* connected atoms may be provided; in this case both the center of mass absolute motion of each pair is
* controlled as well as their motion relative to each other, which is independently thermostated.
* If both the list of thermostated particles and thermostated pairs are empty all particles will be thermostated.
*
* @param thermostatedParticles list of particle ids to be thermostated.
* @param thermostatedPairs a list of pairs of connected atoms whose absolute center of mass motion
......@@ -215,9 +216,9 @@ protected:
*/
void initialize(ContextImpl& context);
/**
* Goes through the list of requested thermostat data and creates the thermostat chains.
* Goes through the list of thermostats, sets the number of DOFs, and checks for errors in the thermostats.
*/
void createThermostats(const System& system);
void initializeThermostats(const System& system);
/**
* 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.
......@@ -232,25 +233,6 @@ protected:
*/
virtual double computeKineticEnergy();
struct ThermostatData {
std::vector<int> thermostatedParticles;
std::vector< std::pair< int, int> > thermostatedPairs;
double temperature;
double relativeTemperature;
double collisionFrequency;
double relativeCollisionFrequency;
int chainLength;
int numMTS;
int numYoshidaSuzuki;
ThermostatData(const std::vector<int>&particles, const std::vector<std::pair<int, int>> &pairs, double temp,
double relTemp, double freq, double relFreq, int length, int MTS, int YS) :
thermostatedParticles(particles), thermostatedPairs(pairs), temperature(temp),
relativeTemperature(relTemp), collisionFrequency(freq), relativeCollisionFrequency(relFreq),
chainLength(length), numMTS(MTS), numYoshidaSuzuki(YS) {}
};
std::vector<ThermostatData> thermostatData;
std::vector<NoseHooverChain> noseHooverChains;
bool forcesAreValid;
Kernel vvKernel, nhcKernel;
......
openmmapi/src/NoseHooverIntegrator.cpp
View file @ b3be7aec
......@@ -53,11 +53,11 @@ NoseHooverIntegrator::NoseHooverIntegrator(double stepSize):
setStepSize(stepSize);
setConstraintTolerance(1e-5);
}
NoseHooverIntegrator::NoseHooverIntegrator(double temperature, int collisionFrequnency, double stepSize,
NoseHooverIntegrator::NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
int chainLength, int numMTS, int numYoshidaSuzuki) : forcesAreValid(false) {
setStepSize(stepSize);
setConstraintTolerance(1e-5);
addThermostat(temperature, collisionFrequnency, chainLength, numMTS, numYoshidaSuzuki);
addThermostat(temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}
NoseHooverIntegrator::~NoseHooverIntegrator() {}
......@@ -79,40 +79,45 @@ int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermos
double temperature, double collisionFrequency,
double relativeTemperature, double relativeCollisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) {
auto data = ThermostatData(thermostatedParticles, thermostatedPairs, temperature,
relativeTemperature, collisionFrequency,
relativeCollisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
thermostatData.push_back(data);
return thermostatData.size() - 1;
int chainID = noseHooverChains.size();
int nDOF = 0; // is set in initializeThermostats()
noseHooverChains.emplace_back(temperature, relativeTemperature,
collisionFrequency, relativeCollisionFrequency,
nDOF, chainLength, numMTS,
numYoshidaSuzuki, chainID,
thermostatedParticles, thermostatedPairs);
return chainID;
}
void NoseHooverIntegrator::createThermostats(const System &system) {
void NoseHooverIntegrator::initializeThermostats(const System &system) {
for (const auto &thermostat : thermostatData) {
for (auto &thermostat : noseHooverChains) {
const auto &thermostatedParticles = thermostat.getThermostatedAtoms();
const auto &thermostatedPairs = thermostat.getThermostatedPairs();
// figure out the number of DOFs
int nDOF = 3*(thermostat.thermostatedParticles.size() + thermostat.thermostatedPairs.size());
int nDOF = 3*(thermostatedParticles.size() + thermostatedPairs.size());
for (int constraintNum = 0; constraintNum < system.getNumConstraints(); constraintNum++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(constraintNum, particle1, particle2, distance);
bool particle1_in_thermostatedParticles = ((std::find(thermostat.thermostatedParticles.begin(),
thermostat.thermostatedParticles.end(), particle1)
!= thermostat.thermostatedParticles.end())) ||
(std::find_if(thermostat.thermostatedPairs.begin(),
thermostat.thermostatedPairs.end(),
bool particle1_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
thermostatedParticles.end(), particle1)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(),
thermostatedPairs.end(),
[&particle1](const std::pair<int, int>& pair){
return pair.first == particle1 || pair.second == particle1;})
!= thermostat.thermostatedPairs.end());
bool particle2_in_thermostatedParticles = ((std::find(thermostat.thermostatedParticles.begin(),
thermostat.thermostatedParticles.end(), particle2)
!= thermostat.thermostatedParticles.end())) ||
(std::find_if(thermostat.thermostatedPairs.begin(),
thermostat.thermostatedPairs.end(),
!= thermostatedPairs.end());
bool particle2_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
thermostatedParticles.end(), particle2)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(),
thermostatedPairs.end(),
[&particle2](const std::pair<int, int>& pair){
return pair.first == particle2 || pair.second == particle2;})
!= thermostat.thermostatedPairs.end());
!= thermostatedPairs.end());
if ((system.getParticleMass(particle1) > 0) && (system.getParticleMass(particle2) > 0)){
if ((particle1_in_thermostatedParticles && !particle2_in_thermostatedParticles) ||
(!particle1_in_thermostatedParticles && particle2_in_thermostatedParticles)){
......@@ -127,21 +132,14 @@ void NoseHooverIntegrator::createThermostats(const System &system) {
// remove 3 degrees of freedom from thermostats that act on absolute motions
int numForces = system.getNumForces();
if (thermostat.thermostatedPairs.size() == 0){
if (thermostatedPairs.size() == 0){
for (int forceNum = 0; forceNum < numForces; ++forceNum) {
if (dynamic_cast<const CMMotionRemover*>(&system.getForce(forceNum))) nDOF -= 3;
}
}
// create and add new chain
int chainID = noseHooverChains.size();
auto chain = NoseHooverChain(thermostat.temperature, thermostat.relativeTemperature,
thermostat.collisionFrequency, thermostat.relativeCollisionFrequency,
nDOF, thermostat.chainLength, thermostat.numMTS,
thermostat.numYoshidaSuzuki, chainID,
thermostat.thermostatedParticles, thermostat.thermostatedPairs);
noseHooverChains.push_back(chain);
// set number of DoFs for chain
thermostat.setDefaultNumDegreesOfFreedom(nDOF);
}
......@@ -271,9 +269,10 @@ void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
// check for drude particles and build the Nose-Hoover Chains
const System& system = context->getSystem();
for (auto& thermostat: thermostatData){
for (auto& thermostat: noseHooverChains){
// if there are no thermostated particles or pairs in the lists this is a regular thermostat for the whole (non-Drude) system
if ( (thermostat.thermostatedParticles.size() == 0) && (thermostat.thermostatedPairs.size() == 0) ){
if ( (thermostat.getThermostatedAtoms().size() == 0) && (thermostat.getThermostatedPairs().size() == 0) ){
std::vector<int> thermostatedParticles;
for(int particle = 0; particle < system.getNumParticles(); ++particle) {
double mass = system.getParticleMass(particle);
if ( (mass > 0) && (mass < 0.8) ){
......@@ -281,13 +280,14 @@ void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
"The thermostat you are about to use will not treat these particles as Drude particles!" << std::endl;
}
if(system.getParticleMass(particle) > 0) {
thermostat.thermostatedParticles.push_back(particle);
thermostatedParticles.push_back(particle);
}
}
thermostat.setThermostatedAtoms(thermostatedParticles);
}
}
createThermostats(system);
initializeThermostats(system);
}
void NoseHooverIntegrator::cleanup() {
......
plugins/drude/openmmapi/include/OpenMMDrude.h
View file @ b3be7aec
......@@ -35,6 +35,6 @@
#include "openmm/DrudeForce.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include "openmm/DrudeSCFIntegrator.h"
#include "openmm/DrudeNIntegrator.h"
#include "openmm/DrudeNoseHooverIntegrator.h"
#endif /*OPENMM_DRUDE_H_*/
plugins/drude/openmmapi/include/openmm/DrudeNoseHooverIntegrator.h
View file @ b3be7aec
......@@ -54,10 +54,10 @@ public:
/**
* Create a DrudeNoseHooverIntegrator.
*
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the system's interaction with the heat bath (in 1/ps).
* @param drudeTemperature the target temperature for the Drude particles, relative to their parent atom.
* @param drudeCollisionFrequency the frequency of the drude particles' interaction with the heat bath (in 1/ps).
* @param temperature the target temperature for the system (in Kelvin).
* @param collisionFrequency the frequency of the system's interaction with the heat bath (in inverse picoseconds).
* @param drudeTemperature the target temperature for the Drude particles, relative to their parent atom (in Kelvin).
* @param drudeCollisionFrequency the frequency of the drude particles' interaction with the heat bath (in inverse picoseconds).
* @param stepSize the step size with which to integrator the system (in picoseconds)
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
......
plugins/drude/openmmapi/src/DrudeNoseHooverIntegrator.cpp
View file @ b3be7aec
......@@ -94,8 +94,8 @@ void DrudeNoseHooverIntegrator::initialize(ContextImpl& contextRef) {
std::cout << "Warning: Did not find a center-of-mass motion remover in the system. "
"This is problematic when using Drude." << std::endl;
}
for (auto& thermostat: thermostatData){
if ( (thermostat.thermostatedParticles.size() == 0) && (thermostat.thermostatedPairs.size() == 0) ){
for (auto& thermostat: noseHooverChains){
if ( (thermostat.getThermostatedAtoms().size() == 0) && (thermostat.getThermostatedPairs().size() == 0) ){
std::set<int> realParticlesSet;
vector<int> realParticles, drudeParticles, drudeParents;
vector<std::pair<int, int>> drudePairs;
......@@ -108,13 +108,14 @@ void DrudeNoseHooverIntegrator::initialize(ContextImpl& contextRef) {
drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
realParticlesSet.erase(p);
realParticlesSet.erase(p1);
thermostat.thermostatedPairs.push_back({p,p1});
drudePairs.push_back({p,p1});
}
for(const auto &p : realParticlesSet) thermostat.thermostatedParticles.push_back(p);
thermostat.setThermostatedPairs(drudePairs);
thermostat.setThermostatedAtoms(std::vector<int>(realParticlesSet.begin(), realParticlesSet.end()));
}
}
createThermostats(system);
initializeThermostats(system);
}
double DrudeNoseHooverIntegrator::computeDrudeKineticEnergy() {
......
wrappers/python/src/swig_doxygen/swigInputBuilder.py
View file @ b3be7aec
......@@ -21,6 +21,9 @@ except ImportError:
INDENT = " "
docTags = {'emphasis':'i', 'bold':'b', 'itemizedlist':'ul', 'listitem':'li', 'preformatted':'pre', 'computeroutput':'tt', 'subscript':'sub'}
def is_method_abstract(argstring):
return argstring.split(")")[-1].find("=0") >= 0
def striphtmltags(s):
"""Strip a couple html tags used inside docstrings in the C++ source
to produce something more easily read as plain text.
......@@ -511,7 +514,7 @@ class SwigInputBuilder:
mArgsstring = getText("argsstring", memberNode)
if self.fOutPythonprepend and \
len(paramList) and \
mArgsstring.find('=0') < 0:
not is_method_abstract(mArgsstring):
text = '''
%pythonprepend OpenMM::{shortClassName}::{methName}{mArgsstring} %{{{{{{0}}
%}}}}'''.format(shortClassName=shortClassName, methName=methName, mArgsstring=mArgsstring)
......@@ -529,6 +532,7 @@ class SwigInputBuilder:
% self.__class__.__name__)
raise Exception(s)'''.format(argName=argName)
# Convert input arguments to the proper units, if specified.
if key not in methodsWithOutputArgs:
if key in self.configModule.UNITS:
......@@ -563,9 +567,10 @@ class SwigInputBuilder:
# write pythonappend blocks
if self.fOutPythonappend \
and mArgsstring.find('=0') < 0:
and not is_method_abstract(mArgsstring):
key = (shortClassName, methName)
#print "key %s %s \n" % (shortClassName, methName)
#sys.stdout.write("key %s %s \n" % (shortClassName, methName))
addText=''
returnType = getText("type", memberNode)
......@@ -619,8 +624,15 @@ class SwigInputBuilder:
pType = getText('type', pNode)
except IndexError:
pType = getText('type/ref', pNode)
# parse default arguments
try:
defaultValue = getText('defval', pNode)
except:
defaultValue = ""
if defaultValue != "":
defaultValue = "=%s" %defaultValue
pName = getText('declname', pNode)
self.fOutPythonappend.write("%s%s %s" % (sepChar, pType, pName))
self.fOutPythonappend.write("%s%s %s%s" % (sepChar, pType, pName, defaultValue))
sepChar=', '
if pType.find('&')>=0 and \
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ b3be7aec
......@@ -217,6 +217,9 @@ UNITS = {
("*", "getTabulatedFunction") : (None, ()),
("*", "getUseDispersionCorrection") : (None, ()),
("*", "getTemperature") : ("unit.kelvin", ()),
("*", "getRelativeTemperature") : ("unit.kelvin", ()),
("*", "getCollisionFrequency") : ( "1/unit.picosecond", ()),
("*", "getRelativeCollisionFrequency") : ( "1/unit.picosecond", ()),
("*", "getUseDispersionCorrection") : (None, ()),
("*", "getWeight") : (None, ()),
("*", "getWeight12") : (None, ()),
......@@ -343,9 +346,11 @@ UNITS = {
("HippoNonbondedForce", "getInducedDipoles") : ( None, ()),
("HippoNonbondedForce", "getLabFramePermanentDipoles") : ( None, ()),
("Context", "getParameter") : (None, ()),
("Context", "getParameters") : (None, ()),
("Context", "getMolecules") : (None, ()),
("Context", "getState") : (None, (None, None, None)),
("CMAPTorsionForce", "getMapParameters") : (None, (None, 'unit.kilojoule_per_mole')),
("CMAPTorsionForce", "getTorsionParameters") : (None, ()),
("CMMotionRemover", "getFrequency") : (None, ()),
......@@ -466,17 +471,28 @@ UNITS = {
("System", "getVirtualSite") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeTemperature") : ("unit.kelvin", ()),
("DrudeLangevinIntegrator", "getMaxDrudeDistance") : ("unit.nanometer", ()),
("MonteCarloMembraneBarostat", "MonteCarloMembraneBarostat") : (None, ("unit.bar", "unit.bar*unit.nanometer", "unit.kelvin", None, None, None)),
("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
("NoseHooverChain", "getThermostatedPairs") : (None, ()),
("NoseHooverChain", "getThermostatedAtoms") : (None, ()),
("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : (None, ()),
("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
("RPMDIntegrator", "getContractions") : (None, ()),
("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),
("RPMDIntegrator", "getState"): (None,(None, None, None, None)),
("RMSDForce", "getReferencePositions") : ("unit.nanometer", ()),
("RMSDForce", "getParticles") : (None, ()),
#("NoseHooverChain", "getThermostatedPairs") : (None, ()),
#("NoseHooverChain", "getThermostatedAtoms") : (None, ()),
#("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : (None, ()),
#("NoseHooverIntegrator", "NoseHooverIntegrator") : (None, ("unit.kelvin", "1/unit.picosecond", "unit,picosecond", None, None, None)),
("NoseHooverIntegrator", "setTemperature") : (None, ("unit.kelvin", None)),
("NoseHooverIntegrator", "setRelativeTemperature") : (None, ("unit.kelvin", None) ),
("NoseHooverIntegrator", "setCollisionFrequency") : (None, ("1/unit.picosecond", None)),
("NoseHooverIntegrator", "setRelativeCollisionFrequency") : (None, ("1/unit.picosecond", None)),
("NoseHooverIntegrator", "computeHeatBathEnergy") : ( "unit.kilojoules_per_mole", ()),
("NoseHooverIntegrator", "addThermostat"): (None, ("unit.kelvin", "1/unit.picosecond", None, None, None)),
("NoseHooverIntegrator", "addSubsystemThermostat"):
(None, (None, None, "unit.kelvin", "1/unit.picosecond", "unit.kelvin", "1/unit.picosecond", None, None, None))
}
wrappers/python/tests/TestAPIUnits.py
View file @ b3be7aec
......@@ -1165,6 +1165,21 @@ class TestAPIUnits(unittest.TestCase):
self.assertAlmostEqualUnit(integrator.getFriction(), 0.1/microsecond)
self.assertEqual(integrator.getStepSize(), 1*femtosecond)
def testNoseHooverIntegrator(self):
""" Tests the NoseHooverIntegrator API features """
integrator = NoseHooverIntegrator(300, 0.1, 1)
self.assertEqual(integrator.getTemperature(0), 300*kelvin)
self.assertEqual(integrator.getCollisionFrequency(), 0.1/picosecond)
self.assertEqual(integrator.getStepSize(), 1*picosecond)
integrator = NoseHooverIntegrator(300*kelvin, 0.1/microsecond, 1*femtosecond)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertAlmostEqualUnit(integrator.getCollisionFrequency(), 0.1/microsecond)
self.assertEqual(integrator.getStepSize(), 1*femtosecond)
integrator = NoseHooverIntegrator(1*femtosecond)
self.assertEqual(integrator.getStepSize(), 1*femtosecond)
def testAndersenThermostat(self):
""" Tests the AndersenThermostat API features """
force = AndersenThermostat(300*kelvin, 1/microsecond)
......
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