Merge pull request #3 from d-SEAMS/addCI

CI: Add a basic test

Author: HaoZeke

.github/workflows/build_test.yml

@@ -0,0 +1,29 @@
+name: "Build pyseams and test"
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  build_test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+
+      - name: Build pyseams
+        shell: bash -l {0}
+        run: |
+          micromamba activate pyseamsdev
+          meson setup bbdir
+          meson compile -C bbdir
+
+      - name: Run a test
+        shell: bash -l {0}
+        run: |
+          python -c 'import bbdir.cyoda'

BPring.py

@@ -0,0 +1,50 @@
+import bbdir.cyoda as cyoda
+trajectory ="subprojects/seams-core/input/traj/clathrate-thf.lammpstrj"
+
+#Get the frame
+resCloud = cyoda.readLammpsTrjreduced(
+          filename = trajectory,
+          targetFrame = 1,
+          typeI = 1, #oxygenAtomType
+          isSlice = True,
+          coordLow = [0,0,0],
+          coordHigh = [34.728,0,0],
+)
+
+#Calculate the neighborlist by ID
+nList = cyoda.neighListO(
+    rcutoff = 3.5,
+    yCloud = resCloud,
+    typeI = 1, #oxygenAtomType
+)
+
+#Get the hydrogen-bonded network for the current frame
+hbnList = cyoda.populateHbonds(
+    filename = trajectory,
+    yCloud = resCloud,
+    nList = nList, 
+    targetFrame = 1,
+    Htype = 2, #hydrogen atom type
+)
+
+#Hydrogen-bonded network using indices not IDs
+hbnList =  cyoda.neighbourListByIndex(
+    yCloud = resCloud,
+    nList = hbnList,
+)
+
+#Gets every ring (non-primitives included)
+rings = cyoda.ringNetwork(
+    nList = hbnList,
+    maxDepth = 6,
+)
+
+#Writes out primitive rings for a bulk system
+ring = cyoda.bulkPolygonRingAnalysis(
+    path = "runOne/", #outDir
+    rings = rings,
+    nList = hbnList,
+    yCloud = resCloud,
+    maxDepth = 6,
+    firstFrame = 1,
+)

bulktopoC.py

@@ -0,0 +1,48 @@
+import bbdir.cyoda as cyoda
+trajectory ="subprojects/seams-core/input/traj/cluster-417.lammpstrj"
+
+#Get the frame
+resCloud = cyoda.readLammpsTrjreduced(
+          filename = trajectory,
+          targetFrame = 1302,
+          typeI = 1, #oxygenAtomType
+          isSlice = False,
+          coordLow = [0,0,0],
+          coordHigh = [0,0,0],
+)
+
+#Calculate the neighborlist by ID
+nList = cyoda.neighListO(
+    rcutoff = 3.5,
+    yCloud = resCloud,
+    typeI = 1, #oxygenAtomType
+)
+solCloud = cyoda.PointCloudDouble()
+iceList = []
+clump = cyoda.clusterAnalysis(
+        path = "runOne/", #outDir 
+        iceCloud = solCloud,
+        yCloud = resCloud,
+        nList = nList,
+        iceNeighbourList = iceList,
+        cutoff = 3.5,
+        firstFrame = 1302,
+        bopAnalysis = "q6",
+)
+
+#Gets every ring (non-primitives included)
+rings = cyoda.ringNetwork(
+    nList = iceList,
+    maxDepth = 6,
+)
+
+#Finds DDCs and HCs
+tum3 = cyoda.topoUnitMatchingBulk(
+    path = "runOne/", #outDir
+    rings = rings,
+    iceNeighbourList = iceList,
+    yCloud = solCloud,
+    firstFrame = 1302,
+    printClusters = True,
+    onlyTetrahedral = False,
+)

chillPlus.py

@@ -0,0 +1,100 @@
+import bbdir.cyoda as cyoda
+trajectory ="input/traj/mW_cubic.lammpstrj"
+
+solCloud = cyoda.PointCloudDouble()
+iceList = []
+
+#Get the frame
+resCloud = cyoda.readLammpsTrjO(
+          filename = trajectory,
+          targetFrame = 1,
+          type0 = 1, #oxygenAtomType
+          isSlice = False,
+          coordLow = [0,0,0],
+          coordHigh = [50,0,0],
+)
+
+#Calculate the neighborlist by ID
+nList = cyoda.neighListO(
+    rcutoff = 3.5,
+    yCloud = resCloud,
+    type0 = 1, #oxygenAtomType
+)
+
+#Calculate Cij (cloud,slice)
+resCloud = cyoda.getCorrelPlus(
+    yCloud = resCloud,
+    nList = nList, 
+    isSlice = False, 
+)
+
+#Write out data (cloud,slice,name)
+resCloud =  cyoda.getIceTypePlus(
+    yCloud = resCloud,
+    nList = nList,
+    path = "runOne/",
+    firstFrame = 1,
+    isSlice = False
+    outputFileName = "chillPlus.txt",
+)
+
+#Dump the rescloud which currently has CHILL Plus classifications
+cyoda.writeDump(
+    yCloud = resCloud,
+    path = "runOne/",
+    outFile = "waterChillP.lammpstrj",
+)
+
+#Average Q6 (cloud,slice)
+avgQ6 = cyoda.getq6(
+    yCloud = resCloud,
+    nList = nList,
+    isSlice = False,
+)
+
+#Modification (cloud,q6)
+resCloud = cyoda.reclassifyWater(
+    yCloud = resCloud,
+    q6 = avgQ6,
+)
+
+#Post reclassification writeOut
+cyoda.printIceType(
+    yCloud = resCloud,
+    path = "runOne/",
+    firstFrame = 1,
+    isSlice = False,
+    outputFileName = "chillPlus.txt",
+)
+
+#Dump the rescloud which now has the supaa CHILL Plus Trajectory
+cyoda.writeDump(
+    yCloud = resCloud,
+    path = "runOne/",
+    outFile = "waterSupaaP.lammpstrj",
+)
+
+#Get the largest ice cluster. Here, iceNeighbourList is the neighbour list by index.
+cyoda.clusterAnalysis(
+    path = "runOne/",
+    iceCloud = solCloud,
+    yCloud = resCloud,
+    nList = nList,
+    iceNeighbourList = iceList,
+    cutoff = 3.5,
+    firstFrame = 1,
+    bopAnalysis = "q6",
+)
+
+#Recenter the cluster such that the centroid is at the center of the simulation box
+cyoda.recenterClusterCloud(
+    iceCloud = solCloud,
+    nList = iceList,
+)
+
+#Dump the recentered largest ice cluster
+cyoda.writeDump(
+    yCloud = resCloud,
+    path = "runOne/",
+    outFile = "largestIce.lammpstrj",
+)

environment.yml

@@ -19,4 +19,4 @@ dependencies:
   - eigen==3.4.0
   # Python
   - pdm
-  - pybind11
+  - pybind11

meson.build

@@ -1,6 +1,6 @@
 project('pyseams', 'cpp',
        version: '1.0.1',
-    default_options: ['warning_level=3', 'cpp_std=c++17'])
+    default_options: ['warning_level=1', 'cpp_std=c++14'])
 
 host_system = host_machine.system()
 
@@ -12,14 +12,8 @@ host_system = host_machine.system()
    _incdirs = [] # All the includes
 
 # ---------------------- Library Dependencies
-seams_core_deps = subproject('seams-core', version: '1.0.1').get_variable('_deps')
-seams_core_inc = subproject('seams-core', version: '1.0.1').get_variable('_incdirs')
-seams_core_linkto = subproject('seams-core', version: '1.0.1').get_variable('_linkto')
-ydslib = subproject('seams-core', version: '1.0.1').get_variable('ydslib')
-seams_core_dep = declare_dependency(link_with: [seams_core_linkto, ydslib],
-                                    dependencies: seams_core_deps,
-                                    include_directories: seams_core_inc)
-_deps += seams_core_dep
+ydslib = subproject('seams-core').get_variable('yds_dep')
+_deps += ydslib
 
 # ---------------------- Bindings
 py_mod = import('python')