Merge branch 'tempering_update' of github.com:mlund/faunus into tempe…

…ring_update

.github/workflows/cmake.yml

@@ -12,14 +12,14 @@ jobs:
     # well on Windows or Mac.  You can convert this to a matrix build if you need
     # cross-platform coverage.
     # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     steps:
-
-    - name: Set up Clang
-      uses: egor-tensin/setup-clang@v1
-      with:
-        version: latest
+    - name: Install newer Clang
+      run: |
+        wget https://apt.llvm.org/llvm.sh
+        chmod +x ./llvm.sh
+        sudo ./llvm.sh 17
 
     - uses: actions/checkout@v2
 
@@ -36,13 +36,20 @@ jobs:
       # Note the current convention is to use the -S and -B options here to specify source 
       # and build directories, but this is only available with CMake 3.13 and higher.  
       # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DENABLE_OPENMP=on -DENABLE_PYTHON=off -DENABLE_TBB=off
+      # Force libc++ due to https://github.com/actions/runner-images/issues/8659
+      run: |
+        export CXX=clang++-17
+        export CC=clang-17
+        cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DENABLE_OPENMP=on -DENABLE_PYTHON=off -DENABLE_TBB=off -DCMAKE_C_COMPILER=clang-17 -DCMAKE_CXX_COMPILER=clang++-17
 
     - name: Build
       working-directory: ${{github.workspace}}/build
       shell: bash
       # Execute the build.  You can specify a specific target with "--target <NAME>"
-      run: cmake --build . --config $BUILD_TYPE --target faunus -j 2
+      run: |
+        export CXX=clang++-17
+        export CC=clang-17
+        cmake --build . --config $BUILD_TYPE --target faunus -j 2
 
     - name: Test
       working-directory: ${{github.workspace}}/build

.gitignore

@@ -9,7 +9,7 @@ include/
 examples/
 _deps/
 sids/
-
+docs/html/
 unittests.log
 a.out
 

.readthedocs.yml → .readthedocs.yaml

@@ -1,12 +1,17 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 version: 2
+
+# Set the version of Python and other tools you might need
+build:
+    os: ubuntu-22.04
+    tools:
+        python: "3.11"
 sphinx:
     configuration: docs/conf.py
 
 formats: [htmlzip,pdf]
 python:
-    version: 3.7
     install:
         - requirements: docs/requirements.txt
 

cmake/ExternalTools.cmake

@@ -5,19 +5,19 @@ include(FetchContent)
 # CPM Packages
 ###############
 
-CPMAddPackage("gh:gabime/spdlog@1.11.0")
+CPMAddPackage("gh:gabime/spdlog@1.12.0")
 CPMAddPackage("gh:ericniebler/range-v3#0.12.0")
 CPMAddPackage("gh:docopt/docopt.cpp#v0.6.3")
-CPMAddPackage("gh:doctest/doctest#v2.4.9")
-CPMAddPackage("gh:mateidavid/zstr#v1.0.6")
-CPMAddPackage("gh:martinus/nanobench#v4.3.9")
-CPMAddPackage("gh:pybind/pybind11#v2.10.1")
+CPMAddPackage("gh:doctest/doctest#v2.4.11")
+CPMAddPackage("gh:mateidavid/zstr#v1.0.7")
+CPMAddPackage("gh:martinus/nanobench#v4.3.11")
+CPMAddPackage("gh:pybind/pybind11#v2.11.1")
 CPMAddPackage("gh:imneme/pcg-cpp#ffd522e7188bef30a00c74dc7eb9de5faff90092")
 CPMAddPackage("gh:ArashPartow/exprtk#93a9f44f99b910bfe07cd1e933371e83cea3841c")
 
 CPMAddPackage(
     NAME mpl GITHUB_REPOSITORY rabauke/mpl DOWNLOAD_ONLY YES
-    GIT_TAG ff9512fc61195b6c7e643e234789b0b937d28ee3
+    GIT_TAG v0.3.0
 )
 
 CPMAddPackage(

docs/CMakeLists.txt

@@ -8,11 +8,10 @@ if (HAS_JSONSCHEMA EQUAL 1)
     message("python: missing `jsonschema` package is highly recommended")
 endif()
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel_yaml as yaml" RESULT_VARIABLE HAS_YAML1 ERROR_QUIET)
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel.yaml as yaml" RESULT_VARIABLE HAS_YAML2 ERROR_QUIET)
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import yaml" RESULT_VARIABLE HAS_YAML3 ERROR_QUIET)
-if ((HAS_YAML1 EQUAL 1) AND (HAS_YAML2 EQUAL 1) AND (HAS_YAML3 EQUAL 1))
-    message("python: missing `ruamel_yaml` (preferred) or `yaml` packages are highly recommended")
+execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel.yaml as yaml" RESULT_VARIABLE HAS_YAML1 ERROR_QUIET)
+execute_process(COMMAND ${Python_EXECUTABLE} -c "import yaml" RESULT_VARIABLE HAS_YAML2 ERROR_QUIET)
+if ((HAS_YAML1 EQUAL 1) AND (HAS_YAML2 EQUAL 1))
+    message("python: missing `ruamel.yaml` (preferred) or `yaml` packages are highly recommended")
 endif()
 
 find_program(PANDOC pandoc)

docs/_docs/analysis.md

@@ -341,6 +341,29 @@ with gzip.open('distances.mtx.gz', 'rt') as f:
         print(np.sort(counts)) # cluster size distribution
 ~~~
 
+### Surface Area
+
+Calculates surface areas using different sample policies
+that selects by:
+
+1. atoms types (`atomic`)
+2. molecule types (`molecular`)
+3. atom types in specific molecules (`atoms_in_molecule`)
+
+In addition to the optional `file` streaming, a histogram of observed areas
+is filed to disk, `sasa_histogram.dat`.
+
+`sasa`         | Description
+-------------- | ---------------------------
+`nstep`        | Interval between samples
+`nskip=0`      | Number of initial steps excluded from the analysis
+`policy`       | Sample policy: `atomic`, `molecular`, `atoms_in_molecule`
+`molecule`     | Molecule name to sample if `molecular` or `atoms_in_molecule` policies
+`atom`         | Atom name to sample if `atomic` policy
+`atomlist`     | List of atom names if `atoms_in_molecule` policy
+`file`         | Optionally stream area for each `nstep` to file (`.dat|.dat.gz`)
+`radius=1.4`   | Probe radius (Å)
+
 ## Charge Properties
 
 ### Molecular Multipoles
@@ -352,6 +375,7 @@ Calculates average molecular multipolar moments and their fluctuations.
 `nstep`        | Interval between samples.
 
 The output from the multipole analysis gives the following:
+
 `multipole`    | Description
 -------------- | ----------------------
  `C`           | Capacitance, eV⁻¹  
@@ -360,34 +384,34 @@ The output from the multipole analysis gives the following:
  `μ`           | Dipole moment, eÅ 
  `μ2`          | Squared dipole moment, (eÅ)²
 
- The capacitance, $C$, is defined accordingly: 
+ The capacitance, `C`, is defined accordingly: 
 
  $$ 
- c = < z² > - < z >² 
+ C = \langle z^2 \rangle - \langle z \rangle^2 
  $$
 
- Where $Z$ is defined as the average charge/valency: 
+ Where `Z` is defined as the average charge/valency: 
 
  $$ 
- < z > = < \sum_i z_i > 
+ Z = \langle \sum_i z_i \rangle 
  $$
 
- This gives that $Z2$ is just the squared average charge/valency:
+ This gives that `Z2` is just the squared average charge/valency:
 
  $$
- < z² > = < \sum_i z²_i >
+ \text{Z2} = \langle \sum_i z^2_i \rangle
  $$
 
- Continuing, the dipole moment, $μ$ , is defined as:
+ Continuing, the dipole moment, `μ`, is defined as:
 
  $$
- μ  =  < \mu > = < | \sum_i z_i (r_i - r_{cm}) | >
+ \mu  =  \langle | \sum_i z_i (r_i - r_{cm}) | \rangle
  $$
 
- Lastly, the $μ2$ is defined as the mean squared dipole moment:
+ Lastly, the `μ2` is defined as the mean squared dipole moment:
 
  $$
- μ2 = < \mu² >
+ \mu^2 = \langle \mu^2 \rangle
  $$
 
 ### Multipole Moments
@@ -457,7 +481,7 @@ $$
 $$
 
 $$
-    u_{\text{ion-quad}} =  \frac{ q_a \boldsymbol{R}^T \boldsymbol{Q}_b \boldsymbol{R} }{R^5}-\frac{q_a \mbox{tr}(\boldsymbol{Q}_b) }{R^3}+ ...
+    u_{\text{ion-quad}} =  \frac{ q_a \boldsymbol{R}^T \boldsymbol{Q}_b \boldsymbol{R} }{R^5}-\frac{q_a \text{tr}(\boldsymbol{Q}_b) }{R^3}+ ...
 $$
 
 $$
@@ -505,6 +529,7 @@ atomic species can be saved.
 `nstep`               | Interval between samples
 `nskip=0`             | Number of initial steps excluded from the analysis
 `epsr`                | Dielectric constant
+`file=potential`      | Filename prefix for output files
 `type`                | Coulomb type, `plain` etc. -- see energies
 `structure`           | Either a _filename_ (pqr, aam, gro etc) or a _list_ of positions
 `policy=fixed`        | Policy used to augment positions before each sample event, see below
@@ -619,6 +644,8 @@ All units in $k\_BT$.
 -------------- | -------------------------------------------
 `file`         | Output filename (`.dat`, `.csv`, `.dat.gz`)
 `nstep`        | Interval between samples
+`nskip=0`      | Number of initial steps excluded from the analysis
+`save_min_conf=false` | Dump minimum energy configuration to `PQR` file
 
 
 ### Penalty function

docs/_docs/install.md

@@ -59,7 +59,7 @@ but compile on most unix operating systems, including the Windows Subsystem for
 - CMake 3.24+
 - C++20 compiler (clang, g++, intel ixpc, ...)
 - Python 3.7+ with the following packages:
-  - `jinja2`, `ruamel_yaml` or `yaml`
+  - `jinja2`, `ruamel.yaml` or `yaml`
 
 The following are optional:
 

docs/_docs/moves.md

@@ -393,6 +393,9 @@ _Warning:_ Untested for cylinders, slits.
 
 ## Gibbs Ensemble (unstable)
 
+_Note: this is marked unstable or experimental, meaning that it is still being tested and
+may see significant changes over time._
+
 [Gibbs ensemble](https://dx.doi.org/10/cvzgw9)
 can be used to investigate phase transitions by _matter_ and _volume_ exchange between two cells.
 The `examples/gibbs-ensemble/` directory contains a Jupyter Notebook with a worked example of a simple Lennard-Jones system.

docs/conf.py

@@ -27,7 +27,11 @@ def getCurrentYear():
 author = 'Mikael Lund'
 source_suffix = ['.rst', '.md']
 master_doc = 'index'
-extensions = ['recommonmark', 'sphinx_markdown_tables', 'sphinx.ext.autosectionlabel']
+extensions = [
+        'recommonmark',
+        'sphinx_markdown_tables',
+        'sphinx.ext.autosectionlabel',
+        'sphinx_rtd_theme']
+html_theme = "sphinx_rtd_theme"
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
 autosectionlabel_prefix_document = True