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Nan aware dihedrals (#166)
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* initial fixes

* fix

* disable IDX testing for now

* try?

* try neg

* try gcc?

* try again
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@hmacdope
hmacdope authored Oct 13, 2024
1 parent d435868 commit 8cf5dac
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Showing 6 changed files with 294 additions and 200 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/make_and_test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ jobs:
- name: Build
# Execute the build. You can specify a specific target with "--target <NAME>"
run: python setup.py build -- -DCMAKE_VERBOSE_MAKEFILE=ON
run: python setup.py build -- -DCMAKE_VERBOSE_MAKEFILE=ON -DHAVE_STD_REGEX=ON -DRUN_HAVE_STD_REGEX=1

- name: Test
# Execute tests defined by the CMake configuration.
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3 changes: 2 additions & 1 deletion devtools/conda_envs/distopia_macos-latest.yaml
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Expand Up @@ -11,5 +11,6 @@ dependencies:
- ninja
- pytest
- scikit-build
- compilers
- clang <=15.0
- clangxx <=15.0
- libxcrypt
7 changes: 6 additions & 1 deletion libdistopia/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -41,10 +41,14 @@ Include(GoogleTest)
add_subdirectory("googletest")
enable_testing()
include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR})
include_directories(${gmock_SOURCE_DIR}/include ${gmock_SOURCE_DIR})


add_executable(test)
target_sources(test PRIVATE "test/test.cpp")
target_link_libraries(test PUBLIC gtest gtest_main)
target_link_libraries(test PUBLIC gmock gmock_main)

target_link_libraries(test PUBLIC libdistopia)
target_include_directories(test PUBLIC ${CMAKE_SOURCE_DIR})
gtest_discover_tests(test WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
Expand All @@ -58,6 +62,7 @@ target_include_directories(targets PUBLIC ${CMAKE_SOURCE_DIR})
add_executable(test_mda_match)
target_sources(test_mda_match PRIVATE "test/test_mda_match.cpp")
target_link_libraries(test_mda_match PUBLIC gtest gtest_main)
target_link_libraries(test PUBLIC gmock gmock_main)
target_link_libraries(test_mda_match PUBLIC libdistopia)
target_include_directories(test_mda_match PUBLIC ${CMAKE_SOURCE_DIR})
gtest_discover_tests(test_mda_match WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
Expand All @@ -70,4 +75,4 @@ if(APPLE)
else()
set_target_properties(libdistopia PROPERTIES INSTALL_RPATH "\$ORIGIN")
endif()
install(TARGETS libdistopia DESTINATION distopia)
install(TARGETS libdistopia DESTINATION distopia)
92 changes: 87 additions & 5 deletions libdistopia/src/distopia.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -488,11 +488,17 @@ namespace distopia {
y = hn::MulAdd(xp_y, rbc_y, y);
y = hn::MulAdd(xp_z, rbc_z, y);



y = y / vb_norm;

return hn::Neg(hn::Atan2(d, y, x));
// find where x and y are both zero, and set result to NAN
auto mask = hn::And(hn::Eq(x, hn::Zero(d)), hn::Eq(y, hn::Zero(d)));

auto res = hn::Neg(hn::Atan2(d, y, x));
// apply mask to set NAN where x and y are both zero
auto fin = hn::IfThenElse(mask, hn::Set(d, NAN), res);

return fin;
}

template <typename T, typename B>
Expand Down Expand Up @@ -1607,74 +1613,132 @@ namespace distopia {
}
HWY_DLLEXPORT template <> void CalcBondsNoBoxIdx(const float *coords, const int *a_idx, const int *b_idx,
int n, float *out) {

if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcBondsNoBoxIdxSingle(coords, a_idx, b_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsNoBoxIdxSingle)(coords, a_idx, b_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcBondsNoBoxIdx(const double *coords, const int *a_idx, const int *b_idx,
int n, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcBondsNoBoxIdxDouble(coords, a_idx, b_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsNoBoxIdxDouble)(coords, a_idx, b_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcBondsOrthoIdx(const float *coords, const int *a_idx, const int *b_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcBondsOrthoIdxSingle(coords, a_idx, b_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsOrthoIdxSingle)(coords, a_idx, b_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcBondsOrthoIdx(const double *coords, const int *a_idx, const int *b_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcBondsOrthoIdxDouble(coords, a_idx, b_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsOrthoIdxDouble)(coords, a_idx, b_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcBondsTriclinicIdx(const float *coords, const int *a_idx, const int *b_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcBondsTriclinicIdxSingle(coords, a_idx, b_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsTriclinicIdxSingle)(coords, a_idx, b_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcBondsTriclinicIdx(const double *coords, const int *a_idx, const int *b_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcBondsTriclinicIdxDouble(coords, a_idx, b_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcBondsTriclinicIdxDouble)(coords, a_idx, b_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcAnglesNoBoxIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcAnglesNoBoxIdxSingle(coords, a_idx, b_idx, c_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesNoBoxIdxSingle)(coords, a_idx, b_idx, c_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcAnglesNoBoxIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcAnglesNoBoxIdxDouble(coords, a_idx, b_idx, c_idx, n, out);
}
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcAnglesNoBoxIdxDouble(coords, a_idx, b_idx, c_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesNoBoxIdxDouble)(coords, a_idx, b_idx, c_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcAnglesOrthoIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcAnglesOrthoIdxSingle(coords, a_idx, b_idx, c_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesOrthoIdxSingle)(coords, a_idx, b_idx, c_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcAnglesOrthoIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcAnglesOrthoIdxDouble(coords, a_idx, b_idx, c_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesOrthoIdxDouble)(coords, a_idx, b_idx, c_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcAnglesTriclinicIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcAnglesTriclinicIdxSingle(coords, a_idx, b_idx, c_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesTriclinicIdxSingle)(coords, a_idx, b_idx, c_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcAnglesTriclinicIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcAnglesTriclinicIdxDouble(coords, a_idx, b_idx, c_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcAnglesTriclinicIdxDouble)(coords, a_idx, b_idx, c_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsNoBoxIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcDihedralsNoBoxIdxSingle(coords, a_idx, b_idx, c_idx, d_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsNoBoxIdxSingle)(coords, a_idx, b_idx, c_idx, d_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsNoBoxIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDihedralsNoBoxIdxDouble(coords, a_idx, b_idx, c_idx, d_idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsNoBoxIdxDouble)(coords, a_idx, b_idx, c_idx, d_idx, n, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsOrthoIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcDihedralsOrthoIdxSingle(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsOrthoIdxSingle)(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsOrthoIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDihedralsOrthoIdxDouble(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsOrthoIdxDouble)(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsTriclinicIdx(const float *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcDihedralsTriclinicIdxSingle(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsTriclinicIdxSingle)(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcDihedralsTriclinicIdx(const double *coords, const int *a_idx, const int *b_idx, const int *c_idx, const int *d_idx,
int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDihedralsTriclinicIdxDouble(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDihedralsTriclinicIdxDouble)(coords, a_idx, b_idx, c_idx, d_idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcDistanceArrayNoBoxIdx(const float *coords, const int *a_idx, const int *b_idx, int na, int nb, float *out) {
Expand All @@ -1684,7 +1748,7 @@ namespace distopia {
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayNoBoxIdxSingle)(coords, a_idx, b_idx, na, nb, out);
}
HWY_DLLEXPORT template <> void CalcDistanceArrayNoBoxIdx(const double *coords, const int *a_idx, const int *b_idx, int na, int nb, double *out) {
if (nb < GetNFloatLanes()) {
if (nb < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDistanceArrayNoBoxIdxDouble(coords, a_idx, b_idx, na, nb, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayNoBoxIdxDouble)(coords, a_idx, b_idx, na, nb, out);
Expand All @@ -1696,7 +1760,7 @@ namespace distopia {
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayOrthoIdxSingle)(coords, a_idx, b_idx, na, nb, box, out);
}
HWY_DLLEXPORT template <> void CalcDistanceArrayOrthoIdx(const double *coords, const int *a_idx, const int *b_idx, int na, int nb, const double *box, double *out) {
if (nb < GetNFloatLanes()) {
if (nb < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDistanceArrayOrthoIdxDouble(coords, a_idx, b_idx, na, nb, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayOrthoIdxDouble)(coords, a_idx, b_idx, na, nb, box, out);
Expand All @@ -1708,27 +1772,45 @@ namespace distopia {
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayTriclinicIdxSingle)(coords, a_idx, b_idx, na, nb, box, out);
}
HWY_DLLEXPORT template <> void CalcDistanceArrayTriclinicIdx(const double *coords, const int *a_idx, const int *b_idx, int na, int nb, const double *box, double *out) {
if (nb < GetNFloatLanes()) {
if (nb < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcDistanceArrayTriclinicIdxDouble(coords, a_idx, b_idx, na, nb, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcDistanceArrayTriclinicIdxDouble)(coords, a_idx, b_idx, na, nb, box, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayNoBoxIdx(const float *coords, const int *idx, int n, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayNoBoxIdxSingle(coords, idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayNoBoxIdxSingle)(coords, idx, n, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayNoBoxIdx(const double *coords, const int *idx, int n, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayNoBoxIdxDouble(coords, idx, n, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayNoBoxIdxDouble)(coords, idx, n, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayOrthoIdx(const float *coords, const int *idx, int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayOrthoIdxSingle(coords, idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayOrthoIdxSingle)(coords, idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayOrthoIdx(const double *coords, const int *idx, int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayOrthoIdxDouble(coords, idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayOrthoIdxDouble)(coords, idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayTriclinicIdx(const float *coords, const int *idx, int n, const float *box, float *out) {
if (n < GetNFloatLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayTriclinicIdxSingle(coords, idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayTriclinicIdxSingle)(coords, idx, n, box, out);
}
HWY_DLLEXPORT template <> void CalcSelfDistanceArrayTriclinicIdx(const double *coords, const int *idx, int n, const double *box, double *out) {
if (n < GetNDoubleLanes()) {
return distopia::N_SCALAR::CalcSelfDistanceArrayTriclinicIdxDouble(coords, idx, n, box, out);
}
return HWY_DYNAMIC_DISPATCH(CalcSelfDistanceArrayTriclinicIdxDouble)(coords, idx, n, box, out);
}

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