Merge pull request #11 from prisms-center/2.0a3

bpuchala · web-flow · commit 47e0af63d0d1 · 2023-10-25T23:46:37.000-04:00
Merge 2.0a3
diff --git a/.github/workflows/test-linux-build.yml b/.github/workflows/test-linux-build.yml
@@ -40,7 +40,7 @@ jobs:
         uses: actions/cache/restore@v3
         with:
           path: CASMcode_crystallography/dist
-          key: ${{ runner.os }}-libcasm-xtal-v2-0a2
+          key: ${{ runner.os }}-libcasm-xtal-v2-0a5
 
       - name: Install CASM dependencies
         run: |
diff --git a/.github/workflows/test-linux-cxx-only.yml b/.github/workflows/test-linux-cxx-only.yml
@@ -40,7 +40,7 @@ jobs:
         uses: actions/cache/restore@v3
         with:
           path: CASMcode_crystallography/dist
-          key: ${{ runner.os }}-libcasm-xtal-v2-0a2
+          key: ${{ runner.os }}-libcasm-xtal-v2-0a5
 
       - name: Install CASM dependencies
         run: |
diff --git a/.github/workflows/test-linux-dependencies.yml b/.github/workflows/test-linux-dependencies.yml
@@ -58,15 +58,15 @@ jobs:
         uses: actions/cache/restore@v3
         with:
           path: CASMcode_crystallography/dist
-          key: ${{ runner.os }}-libcasm-xtal-v2-0a2
+          key: ${{ runner.os }}-libcasm-xtal-v2-0a5
 
       - name: checkout libcasm-xtal
         if: steps.cache-libcasm-xtal-restore.outputs.cache-hit != 'true'
         uses: actions/checkout@v3
         with:
           repository: prisms-center/CASMcode_crystallography
           path: CASMcode_crystallography
-          ref: v2.0a2
+          ref: v2.0a5
 
       - name: make xtal
         if: steps.cache-libcasm-xtal-restore.outputs.cache-hit != 'true'
diff --git a/.github/workflows/test-linux.yml b/.github/workflows/test-linux.yml
@@ -40,7 +40,7 @@ jobs:
         uses: actions/cache/restore@v3
         with:
           path: CASMcode_crystallography/dist
-          key: ${{ runner.os }}-libcasm-xtal-v2-0a2
+          key: ${{ runner.os }}-libcasm-xtal-v2-0a5
 
       - name: Install CASM dependencies
         run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,17 @@ All notable changes to `libcasm-clexulator` will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.0a3] - 2023-10-25
+
+### Fixed
+
+- Fixed error messages for conversion of local DoF to the standard basis
+- Fixed DiffClexParamPack traits namespace
+
+### Added
+
+- Tests for correct treatment of local DoF basis with dim=0 on some sublattices
+
 
 ## [2.0a2] - 2023-09-28
 
diff --git a/build_requirements.txt b/build_requirements.txt
@@ -5,4 +5,4 @@ cmake>=3.20
 ninja
 pybind11>=2.6
 libcasm-global>=2.0.2
-libcasm-xtal>=2.0a2
+libcasm-xtal>=2.0a5
diff --git a/include/casm/clexulator/ConfigDoFValuesTools.hh b/include/casm/clexulator/ConfigDoFValuesTools.hh
@@ -141,9 +141,23 @@ template <typename DoFSetType>
 Eigen::MatrixXd local_to_standard_values(
     Eigen::MatrixXd const &dof_values, Index N_sublat, Index N_volume,
     std::vector<DoFSetType> const &dof_info) {
+  Index N_sites = N_volume * N_sublat;
   Index rows = dof_info.front().basis().rows();
-  Eigen::MatrixXd standard_values(rows, dof_values.cols());
+  if (dof_values.rows() != max_dim(dof_info) || dof_values.cols() != N_sites) {
+    std::stringstream msg;
+    msg << "Invalid dof values input size in "
+           "local_to_standard_values: "
+        << "Expected rows=" << max_dim(dof_info)
+        << ", received rows=" << dof_values.rows()
+        << ", expected cols=" << N_sites
+        << ", received cols=" << dof_values.cols();
+    throw std::runtime_error(msg.str());
+  }
+  Eigen::MatrixXd standard_values = Eigen::MatrixXd::Zero(rows, N_sites);
   for (Index b = 0; b < N_sublat; ++b) {
+    if (dof_info[b].dim() == 0) {
+      continue;
+    }
     standard_values.block(0, b * N_volume, rows, N_volume) =
         dof_info[b].basis() *
         sublattice_block(dof_values, b, N_volume).topRows(dof_info[b].dim());
@@ -161,18 +175,22 @@ Eigen::MatrixXd local_from_standard_values(
       standard_values.cols() != N_sites) {
     std::stringstream msg;
     msg << "Invalid standard values input size in "
-           "local_dof_values_from_standard_basis: "
+           "local_from_standard_value: "
         << "Expected rows=" << dof_info.front().basis().rows()
         << ", received rows=" << standard_values.rows()
         << ", expected cols=" << N_sites
         << ", received cols=" << standard_values.cols();
     throw std::runtime_error(msg.str());
   }
   Eigen::MatrixXd result = Eigen::MatrixXd::Zero(max_dim(dof_info), N_sites);
-  for (Index b = 0; b < N_sublat; ++b)
+  for (Index b = 0; b < N_sublat; ++b) {
+    if (dof_info[b].dim() == 0) {
+      continue;
+    }
     sublattice_block(result, b, N_volume).topRows(dof_info[b].dim()) =
         dof_info[b].inv_basis() *
         sublattice_block(standard_values, b, N_volume);
+  }
   return result;
 }
 
diff --git a/include/casm/clexulator/DiffClexParamPack.hh b/include/casm/clexulator/DiffClexParamPack.hh
@@ -484,15 +484,6 @@ class DiffClexParamHessKey : public DiffClexParamKey {
 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-template <>
-struct traits<DiffClexParamPack::EvalMode> {
-  static const std::string name;
-
-  static const std::multimap<DiffClexParamPack::EvalMode,
-                             std::vector<std::string> >
-      strval;
-};
-
 template <>
 struct ValAccess<double> {
   using size_type = DiffClexParamPack::size_type;
@@ -672,6 +663,15 @@ inline DiffClexParamPack::Key DiffClexParamPack::allocate(
 
 }  // namespace clexulator
 
+template <>
+struct traits<clexulator::DiffClexParamPack::EvalMode> {
+  static const std::string name;
+
+  static const std::multimap<clexulator::DiffClexParamPack::EvalMode,
+                             std::vector<std::string> >
+      strval;
+};
+
 inline std::ostream &operator<<(
     std::ostream &sout, const clexulator::DiffClexParamPack::EvalMode &val) {
   sout << to_string<clexulator::DiffClexParamPack::EvalMode>(val);
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,13 +7,13 @@ requires = [
     "ninja",
     "pybind11>=2.6",
     "libcasm-global>=2.0.2",
-    "libcasm-xtal>=2.0a2",
+    "libcasm-xtal>=2.0a5",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "libcasm-clexulator"
-version = "2.0a2"
+version = "2.0a3"
 authors = [
   { name="CASM developers", email="casm-developers@lists.engr.ucsb.edu" },
 ]
@@ -30,7 +30,7 @@ classifiers = [
 ]
 dependencies = [
     "libcasm-global>=2.0.2",
-    "libcasm-xtal>=2.0a2",
+    "libcasm-xtal>=2.0a5",
     "numpy",
 ]
 
diff --git a/python/doc/conf.py b/python/doc/conf.py
@@ -97,7 +97,7 @@
 # The short X.Y version.
 version = "2.0"
 # The full version, including alpha/beta/rc tags.
-release = "2.0a2"
+release = "2.0a3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/python/pyproject.toml b/python/pyproject.toml
@@ -5,6 +5,6 @@ requires = [
     "wheel",
     "pybind11>=2.8.0",
     "libcasm-global>=2.0.2",
-    "libcasm-xtal>=2.0a2",
+    "libcasm-xtal>=2.0a5",
 ]
 build-backend = "setuptools.build_meta"
diff --git a/python/setup.py b/python/setup.py
@@ -1,6 +1,6 @@
 import os
 
-__version__ = "2.0a2"
+__version__ = "2.0a3"
 
 # Available at setup time due to pyproject.toml
 from pybind11.setup_helpers import Pybind11Extension, build_ext
@@ -83,7 +83,7 @@
     install_requires=[
         "pybind11",
         "libcasm-global>=2.0.2",
-        "libcasm-xtal>=2.0a2",
+        "libcasm-xtal>=2.0a5",
     ],
     ext_modules=ext_modules,
     cmdclass={"build_ext": build_ext},
diff --git a/python/src/clexulator.cpp b/python/src/clexulator.cpp
@@ -1895,7 +1895,7 @@ PYBIND11_MODULE(_clexulator, m) {
       .def_readonly("dof_key", &clexulator::DoFSpace::dof_key, R"pbdoc(
           str : The DoF type for this DoFSpace.
           )pbdoc")
-      .def_readonly("is_global", &clexulator::DoFSpace::dof_key, R"pbdoc(
+      .def_readonly("is_global", &clexulator::DoFSpace::is_global, R"pbdoc(
           bool : True if the DoF type is a global DoF, False otherwise.
           )pbdoc")
       .def_readonly("prim", &clexulator::DoFSpace::prim, R"pbdoc(
diff --git a/python/tests/clexulator/conftest.py b/python/tests/clexulator/conftest.py
diff --git a/python/tests/clexulator/test_config_dof_values.py b/python/tests/clexulator/test_config_dof_values.py
diff --git a/setup.py b/setup.py

Original file line number	Diff line number	Diff line change
`@@ -7,13 +7,13 @@ requires = [`
`7`	`7`	`"ninja",`
`8`	`8`	`"pybind11>=2.6",`
`9`	`9`	`"libcasm-global>=2.0.2",`
`10`		`- "libcasm-xtal>=2.0a2",`
	`10`	`+ "libcasm-xtal>=2.0a5",`
`11`	`11`	`]`
`12`	`12`	`build-backend = "setuptools.build_meta"`
`13`	`13`
`14`	`14`	`[project]`
`15`	`15`	`name = "libcasm-clexulator"`
`16`		`-version = "2.0a2"`
	`16`	`+version = "2.0a3"`
`17`	`17`	`authors = [`
`18`	`18`	`{ name="CASM developers", email="[email protected]" },`
`19`	`19`	`]`
`@@ -30,7 +30,7 @@ classifiers = [`
`30`	`30`	`]`
`31`	`31`	`dependencies = [`
`32`	`32`	`"libcasm-global>=2.0.2",`
`33`		`- "libcasm-xtal>=2.0a2",`
	`33`	`+ "libcasm-xtal>=2.0a5",`
`34`	`34`	`"numpy",`
`35`	`35`	`]`
`36`	`36`