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Changes for 8.1.2 (#4578)

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* Revert #3521; see #4405 (#4410)

* Fixed memory leak (#4461)

* Avoid overflow in large XTC files (#4485)

* Avoid overflow in large XTC files

* Also cast box indices to size_t

* Fixed error when using both CustomNonbondedForce and LennardJonesForce (#4508)

* Allow multiple registrations of the same atom type if definitions identical (#4531)

* Allow multiple registrations of the same atom type if definitions identical

* Different short-circuiting logic

* Update version number to 8.1.2

---------

Co-authored-by: Daniel R. Roe <daniel.r.roe@gmail.com>
Co-authored-by: Raul <raulppelaez@gmail.com>
Co-authored-by: Matt Thompson <mattwthompson@protonmail.com>
This commit is contained in:
Peter Eastman
2024-07-02 11:12:51 -07:00
committed by GitHub
parent ec797acabe
commit 440a9c7ae5
5 changed files with 34 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
CMakeLists.txt
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@@ -165,7 +165,7 @@ ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
SET(OPENMM_LIBRARY_NAME OpenMM)
SET(OPENMM_MAJOR_VERSION 8)
SET(OPENMM_MINOR_VERSION 1)
SET(OPENMM_BUILD_VERSION 1)
SET(OPENMM_BUILD_VERSION 2)
ADD_DEFINITIONS(-DOPENMM_LIBRARY_NAME=${OPENMM_LIBRARY_NAME}
-DOPENMM_MAJOR_VERSION=${OPENMM_MAJOR_VERSION}

9
openmmapi/src/ATMForceImpl.cpp
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@@ -9,7 +9,7 @@
* https://github.com/Gallicchio-Lab/openmm-atmmetaforce-plugin *
* with support from the National Science Foundation CAREER 1750511 *
* *
* Portions copyright (c) 2021-2023 by the Authors *
* Portions copyright (c) 2021-2024 by the Authors *
* Authors: Emilio Gallicchio *
* Contributors: Peter Eastman *
* *
@@ -56,7 +56,8 @@
using namespace OpenMM;
using namespace std;
ATMForceImpl::ATMForceImpl(const ATMForce& owner) : owner(owner), innerIntegrator0(1.0), innerIntegrator1(1.0) {
ATMForceImpl::ATMForceImpl(const ATMForce& owner) : owner(owner), innerIntegrator0(1.0), innerIntegrator1(1.0),
innerContext0(NULL), innerContext1(NULL) {
Lepton::ParsedExpression expr = Lepton::Parser::parse(owner.getEnergyFunction()).optimize();
energyExpression = expr.createCompiledExpression();
u0DerivExpression = expr.differentiate("u0").createCompiledExpression();
@@ -81,6 +82,10 @@ ATMForceImpl::ATMForceImpl(const ATMForce& owner) : owner(owner), innerIntegrato
}
ATMForceImpl::~ATMForceImpl() {
if (innerContext0 != NULL)
delete innerContext0;
if (innerContext1 != NULL)
delete innerContext1;
}
void ATMForceImpl::copySystem(ContextImpl& context, const OpenMM::System& system, OpenMM::System& innerSystem) {

2
wrappers/python/openmm/app/dcdfile.py
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@@ -92,7 +92,7 @@ class DCDFile(object):
raise ValueError('Cannot append to a DCD file that contains a different number of atoms')
else:
header = struct.pack('<i4c9if', 84, b'C', b'O', b'R', b'D', 0, firstStep, interval, 0, 0, 0, 0, 0, 0, dt)
header += struct.pack('<13i', boxFlag, 0, 0, 0, 0, 0, 0, 0, 0, 21, 84, 164, 2)
header += struct.pack('<13i', boxFlag, 0, 0, 0, 0, 0, 0, 0, 0, 24, 84, 164, 2)
header += struct.pack('<80s', b'Created by OpenMM')
header += struct.pack('<80s', b'Created '+time.asctime(time.localtime(time.time())).encode('ascii'))
header += struct.pack('<4i', 164, 4, len(list(topology.atoms())), 4)

11
wrappers/python/openmm/app/forcefield.py
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@@ -6,7 +6,7 @@ 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) 2012-2022 Stanford University and the Authors.
Portions copyright (c) 2012-2024 Stanford University and the Authors.
Authors: Peter Eastman, Mark Friedrichs
Contributors:
@@ -436,6 +436,10 @@ class ForceField(object):
"""Register a new atom type."""
name = parameters['name']
if name in self._atomTypes:
# allow multiple registrations of the same atom type provided the definitions are identical
existing = self._atomTypes[name]
if existing.atomClass == parameters['class'] and existing.mass == float(parameters['mass']) and existing.element.symbol == parameters['element']:
return
raise ValueError('Found multiple definitions for atom type: '+name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
@@ -3010,8 +3014,9 @@ class CustomNonbondedGenerator(object):
# Create the exclusions.
bondIndices = _findBondsForExclusions(data, sys)
nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)
for f in sys.getForces():
if isinstance(f, mm.CustomNonbondedForce) and f.getEnergyFunction() == self.energy:
f.createExclusionsFromBonds(bondIndices, self.bondCutoff)
parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement

32
wrappers/python/openmm/app/internal/xtc_utils/src/xtc.cpp
View File

@@ -123,20 +123,21 @@ void xtc_read(std::string filename, float* coords_arr, float* box_arr, float* ti
throw std::runtime_error("xtc_read(): natoms is 0\n");
}
XDRFILE_RAII xd(filename, "r");
int fidx = 0;
size_t fidx = 0;
size_t nframes_long = nframes;
XTCFrame frame(natoms);
while (exdrOK == frame.readNextFrame(xd)) {
time_arr[fidx] = frame.time;
step_arr[fidx] = frame.step;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
box_arr[fidx + (3 * i + j) * nframes] = frame.box[i][j];
box_arr[fidx + (3 * i + j) * nframes_long] = frame.box[i][j];
}
}
for (int aidx = 0; aidx < natoms; aidx++) {
int xidx = Xf(aidx, fidx, nframes);
int yidx = Yf(xidx, nframes);
int zidx = Zf(yidx, nframes);
for (size_t aidx = 0; aidx < natoms; aidx++) {
size_t xidx = Xf(aidx, fidx, nframes_long);
size_t yidx = Yf(xidx, nframes_long);
size_t zidx = Zf(yidx, nframes_long);
coords_arr[xidx] = frame.positions[3 * aidx + 0];
coords_arr[yidx] = frame.positions[3 * aidx + 1];
coords_arr[zidx] = frame.positions[3 * aidx + 2];
@@ -145,9 +146,9 @@ void xtc_read(std::string filename, float* coords_arr, float* box_arr, float* ti
}
}
static void box_from_array(matrix& matrix_box, float* box, int frame, int nframes) {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
static void box_from_array(matrix& matrix_box, float* box, size_t frame, size_t nframes) {
for (size_t i = 0; i < 3; i++) {
for (size_t j = 0; j < 3; j++) {
matrix_box[i][j] = box[(3 * i + j) * nframes + frame];
}
}
@@ -156,12 +157,13 @@ static void box_from_array(matrix& matrix_box, float* box, int frame, int nframe
void xtc_write(std::string filename, int natoms, int nframes, int* step, float* timex, float* pos, float* box) {
XDRFILE_RAII xd(filename, "a");
XTCFrame frame(natoms);
for (int f = 0; f < nframes; f++) {
box_from_array(frame.box, box, f, nframes);
for (int i = 0; i < natoms; i++) {
int xidx = Xf(i, f, nframes);
int yidx = Yf(xidx, nframes);
int zidx = Zf(yidx, nframes);
size_t nframes_long = nframes;
for (size_t f = 0; f < nframes; f++) {
box_from_array(frame.box, box, f, nframes_long);
for (size_t i = 0; i < natoms; i++) {
size_t xidx = Xf(i, f, nframes_long);
size_t yidx = Yf(xidx, nframes_long);
size_t zidx = Zf(yidx, nframes_long);
frame.positions[3 * i + 0] = pos[xidx];
frame.positions[3 * i + 1] = pos[yidx];
frame.positions[3 * i + 2] = pos[zidx];