Now pycv appears to load correcly

plugins/pycv/pythontests/justInit.py

@@ -0,0 +1,10 @@
+import numpy as np
+import plumedCommunications
+
+
+def myInit(_: plumedCommunications.PythonCVInterface):
+    return{"Value": plumedCommunications.defaults.COMPONENT_NODEV,}
+
+def plumedCalculate(action: plumedCommunications.PythonCVInterface):
+    at: np.ndarray = action.getPositions()
+    return at[0][0]+at[0][1]

plugins/pycv/pythontests/justInitDict.py

@@ -0,0 +1,8 @@
+import numpy as np
+import plumedCommunications
+
+plumedInit={"Value": plumedCommunications.defaults.COMPONENT,}
+
+def plumedCalculate(action: plumedCommunications.PythonCVInterface):
+    at: np.ndarray = action.getPositions()
+    return at[0][0]+at[0][1]

plugins/pycv/pythontests/justPrepare.py

@@ -0,0 +1,13 @@
+import numpy as np
+import plumedCommunications
+
+plumedInit={"Value": plumedCommunications.defaults.COMPONENT,}
+
+def plumedPrepare(_: plumedCommunications.PythonCVInterface):
+    toret = {"setAtomRequest": f"1"}
+    return toret
+
+
+def plumedCalculate(action: plumedCommunications.PythonCVInterface):
+    at: np.ndarray = action.getPositions()
+    return at[0][0]+at[0][1]

plugins/pycv/pythontests/justUpdate.py

@@ -0,0 +1,12 @@
+import numpy as np
+import plumedCommunications
+
+plumedInit={"Value": plumedCommunications.defaults.COMPONENT,}
+
+def myUpdate(_: plumedCommunications.PythonCVInterface):
+    print("myUpdate")
+    return {}
+
+def plumedCalculate(action: plumedCommunications.PythonCVInterface):
+    at: np.ndarray = action.getPositions()
+    return at[0][0]+at[0][1]

plugins/pycv/pythontests/test_cv_calls.py

@@ -0,0 +1,122 @@
+import unittest
+import numpy as np
+
+from utilities_for_test import *
+
+import os
+
+THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+
+
+class TestPyCV(unittest.TestCase):
+    def test_INIT(self):
+        with cd(THIS_DIR):
+            os.environ["PLUMED_MAXBACKUP"] = "0"
+            traj, _, num_atoms, box, virial, masses, forces, charges = setUpTraj(
+                "traj.xyz"
+            )
+            plmd = preparePlumed(num_atoms)
+
+            cvPy = create_plumed_var(
+                plmd, "cvPy", "PYCVINTERFACE ATOMS=4 IMPORT=justInit INIT=myInit"
+            )
+
+            plmd.cmd("readInputLine", "PRINT FILE=colvar.out ARG=*")
+
+            step = 0
+
+            plmd.cmd("setStep", step)
+            plmd.cmd("setBox", box)
+            plmd.cmd("setMasses", masses)
+            plmd.cmd("setCharges", charges)
+            plmd.cmd("setPositions", traj[step])
+            plmd.cmd("setForces", forces)
+            plmd.cmd("setVirial", virial)
+            plmd.cmd("calc")
+            np.testing.assert_almost_equal(cvPy, 10.0, decimal=4)
+
+    def test_INITDICT(self):
+        with cd(THIS_DIR):
+            os.environ["PLUMED_MAXBACKUP"] = "0"
+            traj, _, num_atoms, box, virial, masses, forces, charges = setUpTraj(
+                "traj.xyz"
+            )
+            plmd = preparePlumed(num_atoms)
+
+            cvPy = create_plumed_var(
+                plmd, "cvPy", "PYCVINTERFACE ATOMS=4 IMPORT=justInitDict"
+            )
+
+            plmd.cmd("readInputLine", "PRINT FILE=colvar.out ARG=*")
+
+            step = 0
+
+            plmd.cmd("setStep", step)
+            plmd.cmd("setBox", box)
+            plmd.cmd("setMasses", masses)
+            plmd.cmd("setCharges", charges)
+            plmd.cmd("setPositions", traj[step])
+            plmd.cmd("setForces", forces)
+            plmd.cmd("setVirial", virial)
+            plmd.cmd("calc")
+            np.testing.assert_almost_equal(cvPy, 10.0, decimal=4)
+
+    def test_UPDATE(self):
+        with cd(THIS_DIR):
+            os.environ["PLUMED_MAXBACKUP"] = "0"
+            traj, _, num_atoms, box, virial, masses, forces, charges = setUpTraj(
+                "traj.xyz"
+            )
+            plmd = preparePlumed(num_atoms)
+
+            cvPy = create_plumed_var(
+                plmd, "cvPy", "PYCVINTERFACE ATOMS=4 IMPORT=justUpdate UPDATE=myUpdate"
+            )
+
+            plmd.cmd("readInputLine", "PRINT FILE=colvar.out ARG=*")
+
+            step = 0
+
+            plmd.cmd("setStep", step)
+            plmd.cmd("setBox", box)
+            plmd.cmd("setMasses", masses)
+            plmd.cmd("setCharges", charges)
+            plmd.cmd("setPositions", traj[step])
+            plmd.cmd("setForces", forces)
+            plmd.cmd("setVirial", virial)
+            plmd.cmd("calc")
+            np.testing.assert_almost_equal(cvPy, 10.0, decimal=4)
+
+    def test_PREPARE(self):
+        with cd(THIS_DIR):
+            os.environ["PLUMED_MAXBACKUP"] = "0"
+            traj, _, num_atoms, box, virial, masses, forces, charges = setUpTraj(
+                "traj.xyz"
+            )
+            plmd = preparePlumed(num_atoms)
+            #atoms=4 but the module choses 1
+            cvPy = create_plumed_var(
+                plmd, "cvPy", "PYCVINTERFACE ATOMS=4 IMPORT=justPrepare PREPARE=plumedPrepare")
+            plmd.cmd("readInputLine", "PRINT FILE=colvar.out ARG=*")
+            # Open an output file
+
+            step = 0
+
+            plmd.cmd("setStep", step)
+            plmd.cmd("setBox", box)
+            plmd.cmd("setMasses", masses)
+            plmd.cmd("setCharges", charges)
+            plmd.cmd("setPositions", traj[step])
+            plmd.cmd("setForces", forces)
+            plmd.cmd("setVirial", virial)
+            plmd.cmd("calc")
+
+            np.testing.assert_almost_equal(cvPy, 5.0, decimal=4)
+
+
+
+
+if __name__ == "__main__":
+    # Output to four decimal places only
+    np.set_printoptions(precision=4)
+    unittest.main()

plugins/pycv/src/PythonCVInterface.cpp

@@ -643,6 +643,7 @@ void PythonCVInterface::prepare() {
 void PythonCVInterface::update() {
   try {
     if(hasUpdate) {
+      py::gil_scoped_acquire gil;
       py::dict updateDict=pyUpdate(this);
       //See what to do here
     }