added some methods for function arguments

pycv/PlumedPythonEmbeddedModule.cpp

@@ -261,5 +261,16 @@ return toRet;
   ,"Retuns a ndarray with the values of the arguments")
   .def_property_readonly("nargs", &PLMD::pycv::PythonFunction::
                          getNumberOfArguments,"Get the number of arguments")
+  .def("difference", &PLMD::pycv::PythonFunction::
+       difference,"Takes the difference taking into account pbc for argument i",
+       py::arg("i"),py::arg("x"),py::arg("y"))
+  .def("bringBackInPbc", &PLMD::pycv::PythonFunction::
+       bringBackInPbc,"Takes one value and brings it back into the pbc of argument i",
+       py::arg("i"),py::arg("x"))
+  //I cannot find a way of testing:
+  // .def("getProjection", &PLMD::pycv::PythonFunction::
+  //      getProjection,"Get the scalar product between the gradients of two variables",
+  //      py::arg("i"),py::arg("j"))
+  //to be added and tested getNumberOfArguments
   ;
 }

pycv/regtest/pycvfunc/rt-ArgsMethods/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

pycv/regtest/pycvfunc/rt-ArgsMethods/colvar.out.reference

@@ -0,0 +1,10 @@
+#! FIELDS time fPY.py-difference fPY.py-bringBackInPbc dz
+#! SET min_dz 0.0
+#! SET max_dz 1.3
+ 0.000000 0.000000 0.000000 0.000000
+ 1.000000 0.300000 0.000000 0.000000
+ 2.000000 -0.400000 0.600000 0.300000
+ 3.000000 -0.100000 0.900000 0.300000
+ 4.000000 0.200000 1.200000 0.300000
+ 5.000000 0.200000 0.000000 0.000000
+ 6.000000 -0.500000 0.500000 0.300000

pycv/regtest/pycvfunc/rt-ArgsMethods/config

@@ -0,0 +1,3 @@
+
+type=driver
+arg="--plumed plumed.dat --ixyz traj.xyz"

pycv/regtest/pycvfunc/rt-ArgsMethods/plumed.dat

@@ -0,0 +1,15 @@
+LOAD GLOBAL FILE=../../../../PythonCVInterface.so
+
+d12c: DISTANCE ATOMS=1,2 COMPONENTS
+
+dz: COMBINE ARG=d12c.z PERIODIC=0.0,1.3
+
+fPY: ...
+PYFUNCTION
+IMPORT=unitTest
+INIT=initForF
+CALCULATE=function
+ARG=dz
+...
+
+PRINT FILE=colvar.out ARG=fPY.py-difference,fPY.py-bringBackInPbc,dz

pycv/regtest/pycvfunc/rt-ArgsMethods/traj.xyz

@@ -0,0 +1,35 @@
+3
+100 100 100
+X 0 0 0
+X 99 0 0
+X 99 0 50
+3
+100 100 100
+X 0 0 0
+X 0 99 0
+X 0 99 50
+3
+100 100 100
+X 0 0 0
+X 0 0 99
+X 0 0 50
+3
+100 100 100
+X 0 0 0
+X 0 99 99
+X 50 99 50
+3
+100 100 100
+X 0 0 0
+X 99 0 99
+X 98 0 50
+3
+100 100 100
+X 0 0 0
+X 99 99 0
+X 99 98 50
+3
+100 100 100
+X 0 0 0
+X 99 99 99
+X 99 99 50

pycv/regtest/pycvfunc/rt-ArgsMethods/unitTest.py

@@ -0,0 +1,22 @@
+import plumedCommunications as PLMD
+import numpy
+
+log = open("pydist.log", "w")
+
+print("Imported my pydist+.", file=log)
+
+initForF = {
+    "COMPONENTS": {
+        "difference": PLMD.defaults.COMPONENT_NODEV,
+        "bringBackInPbc": PLMD.defaults.COMPONENT_NODEV,
+    }
+}
+
+
+def function(action: PLMD.PythonFunction):
+    arg = action.arguments()
+
+    return {
+        "difference": action.difference(0, action.getStep(), arg[0]),
+        "bringBackInPbc": action.bringBackInPbc(0, arg[0] * action.getStep()),
+    }