tests: add integration tests for QM/MM

integration_tests/analysis.py

@@ -22,41 +22,47 @@
 *****************************************************************************
 """
 
+from pathlib import Path
+
 import numpy as np
 
 from PQAnalysis.io import read_trajectory, EnergyFileReader
 
 
-def check_pq_output(base_name, folder_name, ref_folder="ref_data"):
+def check_pq_output(
+    base_name,
+    folder_name,
+    ref_folder="ref_data",
+):
 
-    ref_path = "../" + folder_name + "/" + ref_folder + "/"
+    ref_path = Path("..") / folder_name / ref_folder
 
     traj = read_trajectory(base_name + ".xyz")
-    ref_traj = read_trajectory(ref_path + base_name + ".xyz")
+    ref_traj = read_trajectory(str(ref_path / (base_name + ".xyz")))
 
     assert traj.isclose(ref_traj)
 
     traj = read_trajectory(base_name + ".vel", traj_format="vel")
     ref_traj = read_trajectory(
-        ref_path + base_name + ".vel", traj_format="vel")
+        str(ref_path / (base_name + ".vel")), traj_format="vel")
 
     assert traj.isclose(ref_traj)
 
     traj = read_trajectory(base_name + ".force", traj_format="force")
     ref_traj = read_trajectory(
-        ref_path + base_name + ".force", traj_format="force")
+        str(ref_path / (base_name + ".force")), traj_format="force")
 
     assert traj.isclose(ref_traj)
 
     traj = read_trajectory(base_name + ".chrg", traj_format="charge")
     ref_traj = read_trajectory(
-        ref_path + base_name + ".chrg", traj_format="charge")
+        str(ref_path / (base_name + ".chrg")), traj_format="charge")
 
     assert traj.isclose(ref_traj)
 
     reader = EnergyFileReader(base_name + ".en")
     ref_reader = EnergyFileReader(
-        ref_path + base_name + ".en")
+        str(ref_path / (base_name + ".en")))
 
     energy = reader.read()
     ref_energy = ref_reader.read()

integration_tests/qm-mm/exact_smoothing/no_water_model/brute_force/dftb_in.template

@@ -0,0 +1,74 @@
+Geometry = GenFormat {
+<<< "geom.gen"
+}
+
+
+
+Driver =  {}
+
+Hamiltonian = DFTB {
+  charge = __CHARGE__
+  SCC = Yes
+  SCCTolerance = 1.0e-5
+  MaxSccIterations = 100
+  ThirdOrderFull = Yes
+
+  __GUESS__
+
+  HCorrection = Damping { Exponent = 4.00 }
+
+  #HalogenXCorr = Yes
+
+  HubbardDerivs {
+  H  = -0.1857
+  O  = -0.1575
+  K  = -0.0339
+  }
+
+  Dispersion = DftD3 {
+     Damping = BeckeJohnson {
+     a1 = 0.746
+     a2 = 4.191
+     }
+     s6 = 1.0
+     s8 = 3.209
+     }
+
+  MaxAngularMomentum {
+    H  = "s"
+    O  = "p"
+    K  = "p"
+  }
+
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../build/external/slakos/3ob/skfiles/"
+    Separator = "-"
+    Suffix = ".skf"
+    LowerCaseTypeName = No
+  }
+
+  ElectricField = {
+     PointCharges = {
+     CoordsAndCharges [Angstrom] = DirectRead {
+     Records = __N_PC__
+     File = "pointcharges"
+      }
+    }
+  }
+
+
+  Filling = Fermi {
+    Temperature [Kelvin] = 0.0
+  }
+}
+
+Options {}
+
+Analysis = {
+   MullikenAnalysis = Yes
+   PrintForces = Yes
+}
+
+ParserOptions {
+  ParserVersion = 5
+}

integration_tests/qm-mm/exact_smoothing/no_water_model/brute_force/guff.dat

@@ -0,0 +1,38 @@
+# moltype_A;atomtype_A;moltype_B;atomtype_B;rnoncoulomb;guffcoeff[0];guffcoeff[1];guffcoeff[2];guffcoeff[3];guffcoeff[4];guffcoeff[5];guffcoeff[6];guffcoeff[7];guffcoeff[8];guffcoeff[9];guffcoeff[10];guffcoeff[11];guffcoeff[12];guffcoeff[13];guffcoeff[14];guffcoeff[15];guffcoeff[16];guffcoeff[17];guffcoeff[18];guffcoeff[19];guffcoeff[20];guffcoeff[21];guffcoeff[22];
+# First Trial for guff coefficients
+# H2O H2O
+#  Note: physical units MUST be:
+# 
+#  'kcal/mol' for energies
+#  'Angstroem' for distances
+# 
+#   guffcoeff[0] denotes for Coulombic interactions:
+#   conversion factor:  332.0640694675 * q(i) *q(j)
+#                  0            1        2       3         4         5         6        7       8     9    10    11    12     13      14     15    16     17      18     19     20     21   22
+
+################################
+#####   WATER - Moltype 1  ##### 
+################################
+
+# SPC/Fw
+1;0;1;0;-1.0;223.27988030994698;-625.502467657;6.0;629358.4725833069183;12.0;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;    
+1;0;1;1;0.100000;-111.63994015497349;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;               
+1;1;1;1;0.100000;55.819970077486744;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;
+
+
+# SPC/Fw water - K(I)
+# K(I)
+# q(K)=1.0e; rm=3.75Ang;  eps=0.075 kcal/mol
+1;0;2;0;-1.0;-272.29253696335;-417.137145996;6.0;580011.328566;12.0;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;
+1;1;2;0;0.1;136.146268481675;0.0000000000000000000;0.0;0.0000000000000000000;0.0;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;
+
+
+
+# Copied dummy values for K(I) - K(I) interaction
+2;0;2;0;0.1;332.0640694675;70.0000000000000000000;0.0;0.0000000000000000000;0.0;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;0.000000;
+
+
+
+
+
+