more powerful (and somehow correct) test

pycv/regtest/pycvcomm/rt-Coordination/colvar.out.reference

@@ -1,6 +1,6 @@
 #! FIELDS time cvPY coord diff
- 0.000000 1.833292 1.833292 -0.000000
- 1.000000 0.051942 0.051942 -0.000000
- 2.000000 0.004564 0.004564 -0.000000
- 3.000000 0.051942 0.051942 -0.000000
- 4.000000 1.833292 1.833292 -0.000000
+ 0.000000 0.054853 0.054853 -0.000000
+ 1.000000 0.000648 0.000648 0.000000
+ 2.000000 0.000000 0.000000 0.000000
+ 3.000000 0.000648 0.000648 0.000000
+ 4.000000 0.054853 0.054853 -0.000000

pycv/regtest/pycvcomm/rt-Coordination/config

@@ -1,2 +1,10 @@
 type=driver
 arg="--plumed plumed.dat --ixyz traj.xyz"
+
+plumed_regtest_after() {
+  {
+    head -1 deriv | awk '{printf "%s %s %s %s %s-%s\n" , $1, $2,$3,$4,$5,$6 }'
+    #I'm giving some(a LOT OF) space to the floating point precision
+    awk 'function abs(v) {return v < 0 ? -v : v} NR>1{print $1, $2, 0.01 < abs($3-$4) } ' <deriv
+  } >deriv_delta
+}

pycv/regtest/pycvcomm/rt-Coordination/deriv_delta.reference

@@ -0,0 +1,166 @@
+#! FIELDS time parameter cvPY-coord
+0.000000 0 0
+0.000000 1 0
+0.000000 2 0
+0.000000 3 0
+0.000000 4 0
+0.000000 5 0
+0.000000 6 0
+0.000000 7 0
+0.000000 8 0
+0.000000 9 0
+0.000000 10 0
+0.000000 11 0
+0.000000 12 0
+0.000000 13 0
+0.000000 14 0
+0.000000 15 0
+0.000000 16 0
+0.000000 17 0
+0.000000 18 0
+0.000000 19 0
+0.000000 20 0
+0.000000 21 0
+0.000000 22 0
+0.000000 23 0
+0.000000 24 0
+0.000000 25 0
+0.000000 26 0
+0.000000 27 0
+0.000000 28 0
+0.000000 29 0
+0.000000 30 0
+0.000000 31 0
+0.000000 32 0
+1.000000 0 0
+1.000000 1 0
+1.000000 2 0
+1.000000 3 0
+1.000000 4 0
+1.000000 5 0
+1.000000 6 0
+1.000000 7 0
+1.000000 8 0
+1.000000 9 0
+1.000000 10 0
+1.000000 11 0
+1.000000 12 0
+1.000000 13 0
+1.000000 14 0
+1.000000 15 0
+1.000000 16 0
+1.000000 17 0
+1.000000 18 0
+1.000000 19 0
+1.000000 20 0
+1.000000 21 0
+1.000000 22 0
+1.000000 23 0
+1.000000 24 0
+1.000000 25 0
+1.000000 26 0
+1.000000 27 0
+1.000000 28 0
+1.000000 29 0
+1.000000 30 0
+1.000000 31 0
+1.000000 32 0
+2.000000 0 0
+2.000000 1 0
+2.000000 2 0
+2.000000 3 0
+2.000000 4 0
+2.000000 5 0
+2.000000 6 0
+2.000000 7 0
+2.000000 8 0
+2.000000 9 0
+2.000000 10 0
+2.000000 11 0
+2.000000 12 0
+2.000000 13 0
+2.000000 14 0
+2.000000 15 0
+2.000000 16 0
+2.000000 17 0
+2.000000 18 0
+2.000000 19 0
+2.000000 20 0
+2.000000 21 0
+2.000000 22 0
+2.000000 23 0
+2.000000 24 0
+2.000000 25 0
+2.000000 26 0
+2.000000 27 0
+2.000000 28 0
+2.000000 29 0
+2.000000 30 0
+2.000000 31 0
+2.000000 32 0
+3.000000 0 0
+3.000000 1 0
+3.000000 2 0
+3.000000 3 0
+3.000000 4 0
+3.000000 5 0
+3.000000 6 0
+3.000000 7 0
+3.000000 8 0
+3.000000 9 0
+3.000000 10 0
+3.000000 11 0
+3.000000 12 0
+3.000000 13 0
+3.000000 14 0
+3.000000 15 0
+3.000000 16 0
+3.000000 17 0
+3.000000 18 0
+3.000000 19 0
+3.000000 20 0
+3.000000 21 0
+3.000000 22 0
+3.000000 23 0
+3.000000 24 0
+3.000000 25 0
+3.000000 26 0
+3.000000 27 0
+3.000000 28 0
+3.000000 29 0
+3.000000 30 0
+3.000000 31 0
+3.000000 32 0
+4.000000 0 0
+4.000000 1 0
+4.000000 2 0
+4.000000 3 0
+4.000000 4 0
+4.000000 5 0
+4.000000 6 0
+4.000000 7 0
+4.000000 8 0
+4.000000 9 0
+4.000000 10 0
+4.000000 11 0
+4.000000 12 0
+4.000000 13 0
+4.000000 14 0
+4.000000 15 0
+4.000000 16 0
+4.000000 17 0
+4.000000 18 0
+4.000000 19 0
+4.000000 20 0
+4.000000 21 0
+4.000000 22 0
+4.000000 23 0
+4.000000 24 0
+4.000000 25 0
+4.000000 26 0
+4.000000 27 0
+4.000000 28 0
+4.000000 29 0
+4.000000 30 0
+4.000000 31 0
+4.000000 32 0

pycv/regtest/pycvcomm/rt-Coordination/plumed.dat

@@ -2,12 +2,11 @@ LOAD GLOBAL FILE=../../../../PythonCVInterface.so
 
 cvPY: ...
 PYCVINTERFACE 
-GROUPA=1-4
 IMPORT=pyCOORDINATION
 CALCULATE=pyCoord
 ...
 
-coord: COORDINATION GROUPA=1-4 R_0=1.0
+coord: COORDINATION GROUPA=@mdatoms,@mdatoms R_0=0.4
 
 diff: CUSTOM ARG=cvPY,coord FUNC=y-x PERIODIC=NO
 

pycv/regtest/pycvcomm/rt-Coordination/pyCOORDINATION.py

@@ -11,7 +11,7 @@
 N: int = 6
 M: int = 12
 D0: float = 0.0
-R0: float = 1.0
+R0: float = 0.4
 INVR0: float = 1.0 / R0
 DMAX = D0 + R0 * (0.00001 ** (1.0 / (N - M)))
 STRETCH = 1.0
@@ -35,7 +35,7 @@ def switch(d: np.ndarray) -> np.ndarray:
     WhereToCalc = d < DMAX  # & d > D0
     # print(f"{dfunc=}", file=log)
     # not doinf d-D0 for now, so no need for rdist<=0
-    ret[WhereToCalc], dfunc[WhereToCalc] = jaxSwitch(d)
+    ret[WhereToCalc], dfunc[WhereToCalc] = jaxSwitch(d[WhereToCalc])
     return ret, dfunc
 
 
@@ -58,13 +58,20 @@ def pyCoord(action: plumedCommunications.PythonCVInterface):
     assert nl.size() == ((nat - 1) * nat) // 2
     pbc = action.getPbc()
     couples = nl.getClosePairs()
-
+    absoluteIndexes=[]
+    #not so fast, but speed here is not important
+    for i in action.absoluteIndexes:
+        absoluteIndexes.append(i.index)
+    absoluteIndexes=np.array(absoluteIndexes)
+    #sameIndex = np.where(absoluteIndexes[couples[:, 0]]==absoluteIndexes[couples[:, 1]])
+    sameIndex = absoluteIndexes[couples[:, 0]]==absoluteIndexes[couples[:, 1]]
     d = atoms[couples[:, 0]] - atoms[couples[:, 1]]
-    # print(f"before {d}",file=log)
     d = pbc.apply(d)
-    # print(f"after {d}",file=log)
     # from here we are in "pure python"
     dist = np.linalg.norm(d, axis=1)
+
+    dist[sameIndex] += DMAX*2.0
+
     sw, dfunc = switch(dist)
     dev = np.zeros_like(atoms)
 
@@ -81,5 +88,8 @@ def pyCoord(action: plumedCommunications.PythonCVInterface):
 
     return np.sum(sw), dev, virial
 
-
-plumedInit = {"Value": plumedCommunications.defaults.COMPONENT}
+#this tests also the concatenating special keywords
+plumedInit = {
+    "Value": plumedCommunications.defaults.COMPONENT,
+    "GROUPA": "@mdatoms,@mdatoms",
+}