Merge pull request #37 from rsdefever/update/cassandra-source

Switch to github release and conda release for AZP testing

azure-pipelines.yml

@@ -39,7 +39,7 @@ jobs:
     - bash: echo "##vso[task.prependpath]$CONDA/bin"
       displayName: Add Conda to path
 
-    - bash : echo "##vso[task.prependpath]$(Build.SourcesDirectory)/mosdef_cassandra/tests/files/Cassandra_V1.2/bin"
+    - bash : echo "##vso[task.prependpath]$(Build.SourcesDirectory)/Cassandra-1.2.2/bin"
       displayName: Add Cassandra to path
 
     # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
@@ -56,35 +56,22 @@ jobs:
       condition: eq( variables['Agent.OS'], 'Linux' )
 
     - bash: |
-        brew install gcc@8
-        brew upgrade gcc@8
-        gfortran-8 --version
+        brew install gcc
+        brew upgrade gcc
+        gfortran --version
       displayName: Install gfortran macOS
       condition: eq( variables['Agent.OS'], 'Darwin' )
 
     - bash: |
-        cd mosdef_cassandra/tests/files/
-        tar -xzvf Cassandra_V1.2.tar.gz
-        cd Cassandra_V1.2/Src
+        wget https://github.com/MaginnGroup/Cassandra/archive/v1.2.2.tar.gz
+        tar -xzvf v1.2.2.tar.gz
+        cd Cassandra-1.2.2/Src
         make -f Makefile.gfortran
         mkdir ../bin
         cp cassandra_gfortran.exe ../bin/.
         cp ../Scripts/Frag_Library_Setup/library_setup.py ../bin/.
-        cd ../../../../../
+        cd ../../
       displayName: Build Cassandra Linux
-      condition: eq( variables['Agent.OS'], 'Linux' )
-
-    - bash: |
-        cd mosdef_cassandra/tests/files/
-        tar -xzvf Cassandra_V1.2.tar.gz
-        cd Cassandra_V1.2/Src
-        make -f Makefile.gfortran FC=gfortran-8
-        mkdir ../bin
-        cp cassandra_gfortran.exe ../bin/.
-        cp ../Scripts/Frag_Library_Setup/library_setup.py ../bin/.
-        cd ../../../../../
-      displayName: Build Cassandra macOS
-      condition: eq( variables['Agent.OS'], 'Darwin' )
 
     - bash: |
         echo Working directory:
@@ -154,7 +141,7 @@ jobs:
         imageName: 'macOS-10.14'
         python.version: 3.7
       Python36macOS:
-        imageName: 'macOS-10.14'
+        imageName: 'macOS-latest'
         python.version: 3.6
 
   pool:
@@ -164,68 +151,12 @@ jobs:
     - bash: echo "##vso[task.prependpath]$CONDA/bin"
       displayName: Add Conda to path
 
-    - bash : echo "##vso[task.prependpath]$(Build.SourcesDirectory)/mosdef_cassandra/tests/files/Cassandra_V1.2/bin"
-      displayName: Add Cassandra to path
-
     # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
     # We need to take ownership if we want to update conda or install packages globally
     - bash: sudo chown -R $USER $CONDA
       displayName: Take ownership of conda installation
       condition: eq( variables['Agent.OS'], 'Darwin' )
 
-    - bash: |
-        sudo apt-get update
-        sudo apt-get install gfortran
-        gfortran --version
-      displayName: Install gfortran Linux
-      condition: eq( variables['Agent.OS'], 'Linux' )
-
-    - bash: |
-        brew install gcc@8
-        brew upgrade gcc@8
-        gfortran-8 --version
-      displayName: Install gfortran macOS
-      condition: eq( variables['Agent.OS'], 'Darwin' )
-
-    - bash: |
-        cd mosdef_cassandra/tests/files/
-        tar -xzvf Cassandra_V1.2.tar.gz
-        cd Cassandra_V1.2/Src
-        make -f Makefile.gfortran
-        mkdir ../bin
-        cp cassandra_gfortran.exe ../bin/.
-        cp ../Scripts/Frag_Library_Setup/library_setup.py ../bin/.
-        cd ../../../../../
-      displayName: Build Cassandra Linux
-      condition: eq( variables['Agent.OS'], 'Linux' )
-
-    - bash: |
-        cd mosdef_cassandra/tests/files/
-        tar -xzvf Cassandra_V1.2.tar.gz
-        cd Cassandra_V1.2/Src
-        make -f Makefile.gfortran FC=gfortran-8
-        mkdir ../bin
-        cp cassandra_gfortran.exe ../bin/.
-        cp ../Scripts/Frag_Library_Setup/library_setup.py ../bin/.
-        cd ../../../../../
-      displayName: Build Cassandra macOS
-      condition: eq( variables['Agent.OS'], 'Darwin' )
-
-    - bash: |
-        echo Working directory:
-        pwd
-        echo ls:
-        ls
-        echo PATH:
-        echo "$PATH"
-        echo CASSANDRA:
-        which cassandra_gfortran.exe
-        echo PYTHON2
-        which python2
-        echo LIBRARY_SETUP:
-        which library_setup.py
-      displayName: Check cassandra install
-
     - bash: |
         conda config --set always_yes yes --set changeps1 no
         conda config --add channels omnia
@@ -241,6 +172,8 @@ jobs:
         source activate test-environment
         echo "PYTHON VERSION:"
         python --version
+        echo "CASSANDRA EXEC:"
+        which cassandra.exe
         python -m pip install --user .
       displayName: clone,install foyer,mbuild; install mosdef_cassandra
 

mosdef_cassandra/examples/gemc.py

@@ -33,7 +33,7 @@ def run_gemc():
 
     thermo_props = [
         "energy_total",
-        "energy_lj",
+        "energy_intervdw",
         "pressure",
         "volume",
         "nmols",

mosdef_cassandra/runners/runners.py

@@ -14,7 +14,7 @@ def run(system, moves, run_type, run_length, temperature, **kwargs):
 
     # Check that the user has the Cassandra binary on their PATH
     # Also need library_setup.py on the PATH and python2
-    py2, fraglib_setup, cassandra = detect_cassandra_binaries()
+    py, fraglib_setup, cassandra = detect_cassandra_binaries()
 
     # Sanity checks
     # TODO: Write more of these
@@ -49,7 +49,7 @@ def run(system, moves, run_type, run_length, temperature, **kwargs):
     # Run fragment generation (again, will be removed...)
     print("Generating fragment libraries...")
     successful_fraglib = _run_fraglib_setup(
-        py2,
+        py,
         fraglib_setup,
         cassandra,
         inp_file,
@@ -71,7 +71,7 @@ def restart(system, moves, run_type, run_length, temperature, **kwargs):
 
     # Check that the user has the Cassandra binary on their PATH
     # Also need library_setup.py on the PATH and python2
-    py2, fraglib_setup, cassandra = detect_cassandra_binaries()
+    py, fraglib_setup, cassandra = detect_cassandra_binaries()
 
     kwargs["restart"] = True
 
@@ -98,21 +98,21 @@ def restart(system, moves, run_type, run_length, temperature, **kwargs):
 
 
 def _run_fraglib_setup(
-    py2, fraglib_setup, cassandra, inp_file, log_file, nspecies
+    py, fraglib_setup, cassandra, inp_file, log_file, nspecies
 ):
     """Builds the fragment libraries required to run Cassandra.
 
-    Requires python2.
+    Requires python.
     """
 
     species_pdb_files = ""
     for isp in range(nspecies):
         species_pdb_files += "species{}.pdb ".format(isp + 1)
 
     fraglib_cmd = (
-        "{py2} {fraglib_setup} {cassandra} {inp_file} "
+        "{py} {fraglib_setup} {cassandra} {inp_file} "
         "{species_pdb_files}".format(
-            py2=py2,
+            py=py,
             fraglib_setup=fraglib_setup,
             cassandra=cassandra,
             inp_file=inp_file,

mosdef_cassandra/tests/test_examples.py

@@ -28,7 +28,7 @@ def test_run_nvt(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed
 
@@ -51,7 +51,7 @@ def test_run_npt(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed
 
@@ -74,7 +74,7 @@ def test_run_gcmc(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed
 
@@ -97,7 +97,7 @@ def test_run_gemc(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed
 
@@ -120,7 +120,7 @@ def test_run_nvt_mixture(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed
 
@@ -143,6 +143,6 @@ def test_run_gcmc_adsorption(self):
 
                 completed = False
                 for line in log_data:
-                    if "Energy of final" in line:
+                    if "Cassandra simulation complete" in line:
                         completed = True
                 assert completed

mosdef_cassandra/tests/test_writers.py

@@ -1399,7 +1399,7 @@ def test_property_info(self, onecomp_system, twobox_system):
         )
 
         assert (
-            "# Property_Info 1\nenergy_total\nenergy_lj\nenergy_elec\nenergy_intra\nenthalpy\npressure\nvolume\nnmols\nmass_density\n"
+            "# Property_Info 1\nenergy_total\nenergy_intra\nenergy_inter\nenthalpy\npressure\nvolume\nnmols\nmass_density\n"
             in inp_data
         )
 
@@ -1413,7 +1413,7 @@ def test_property_info(self, onecomp_system, twobox_system):
         )
 
         assert (
-            "# Property_Info 1\nenergy_total\nenergy_lj\nenergy_elec\nenergy_intra\nenthalpy\npressure\nvolume\nnmols\nmass_density\n\n# Property_Info 2\nenergy_total\nenergy_lj\nenergy_elec\nenergy_intra\nenthalpy\npressure\nvolume\nnmols\nmass_density\n"
+            "# Property_Info 1\nenergy_total\nenergy_intra\nenergy_inter\nenthalpy\npressure\nvolume\nnmols\nmass_density\n\n# Property_Info 2\nenergy_total\nenergy_intra\nenergy_inter\nenthalpy\npressure\nvolume\nnmols\nmass_density\n"
             in inp_data
         )
 

mosdef_cassandra/utils/detect.py

@@ -12,7 +12,7 @@ def detect_cassandra_binaries():
         "cassandra_pgfortran.exe",
     ]
 
-    py2_exec_names = ["python2", "python2.7"]
+    py_exec_names = ["python"]
 
     for name in cassandra_exec_names:
         cassandra = shutil.which(name)
@@ -27,18 +27,18 @@ def detect_cassandra_binaries():
             "'library_setup.py' must be in your PATH"
         )
 
-    for name in py2_exec_names:
-        py2 = shutil.which(name)
-        if py2 is not None:
+    for name in py_exec_names:
+        py = shutil.which(name)
+        if py is not None:
             break
-    if py2 is None:
+    if py is None:
         raise ValueError(
-            "Error detecting python2. library_setup.py requires python2"
+            "Error detecting python. library_setup.py requires python."
         )
 
     print("Using the following executables for Cassandra:")
-    print("Python: {}".format(py2))
+    print("Python: {}".format(py))
     print("library_setup: {}".format(fraglib_setup))
     print("Cassandra: {}".format(cassandra))
 
-    return py2, fraglib_setup, cassandra
+    return py, fraglib_setup, cassandra

mosdef_cassandra/writers/inp_functions.py

@@ -425,9 +425,8 @@ def generate_input(system, moves, run_type, run_length, temperature, **kwargs):
     else:
         properties = [
             "energy_total",
-            "energy_lj",
-            "energy_elec",
             "energy_intra",
+            "energy_inter",
             "enthalpy",
             "pressure",
             "volume",
@@ -1588,11 +1587,24 @@ def get_property_info(properties, nbr_boxes):
 
     valid_properties = [
         "energy_total",
-        "energy_lj",
-        "energy_elec",
         "energy_intra",
+        "energy_bond",
+        "energy_angle",
+        "energy_dihedral",
+        "energy_improper",
+        "energy_intravdw",
+        "energy_intraq",
+        "energy_inter",
+        "energy_intervdw",
+        "energy_lrc",
+        "energy_interq",
+        "energy_recip",
+        "energy_self",
         "enthalpy",
         "pressure",
+        "pressure_xx",
+        "pressure_yy",
+        "pressyre_zz",
         "volume",
         "nmols",
         "density",

requirements-dev.txt

@@ -7,3 +7,4 @@ black
 sphinx
 sphinx_rtd_theme
 pytest
+cassandra >= 1.2.2

requirements-test.txt

@@ -4,3 +4,4 @@ foyer >= 0.7.3
 mbuild >= 0.10.5
 openbabel
 pytest
+cassandra >= 1.2.2

requirements.txt

@@ -2,3 +2,4 @@ numpy
 parmed
 foyer >= 0.7.3
 mbuild >= 0.10.5
+cassandra >= 1.2.2