updated test module

qforce/initialize.py

@@ -6,7 +6,7 @@
 from colt import Colt
 from calkeeper import CalculationKeeper
 #
-from .schemes import Computations
+from .schemes import Computations_
 from .qm.qm import QM, calculators
 from .forcefield.forcefield import ForceField
 from .dihedral_scan import DihedralScan
@@ -36,7 +36,7 @@ def _extend_user_input(cls, questions):
         questions.generate_block("qm", QM.colt_user_input)
         questions.generate_block("ff", ForceField.colt_user_input)
         questions.generate_block("scan", DihedralScan.colt_user_input)
-        questions.generate_block("addstructs", Computations.colt_user_input)
+        questions.generate_block("addstructs", Computations_.colt_user_input)
         # ff terms
         for name, ffcls in ForceField.implemented_md_software.items():
             questions.generate_block(name, ffcls.get_questions(), block='ff')

qforce/main.py

@@ -44,7 +44,8 @@ def runjob_(config, job, ext_q=None, ext_lj=None):
 
     mol = Molecule(config, job, bondorder, ffcls, ext_q, ext_lj)
     #
-    structs = Computations.from_config(config.addstructs)
+    folder = job.pathways.getdir('addstruct')
+    structs = Computations(config.addstructs, folder)
     structs.register('dihedrals', NoFragmentationDihedralsCreator(mol, job, config))
     structs.register('hessian', HessianCreator(molecule))
     #

qforce/schemes/__init__.py

@@ -1,4 +1,4 @@
-from .computations import Computations
+from .computations import Computations, Computations_
 from .creator import CustomStructureCreator
 #
 from .hessian import HessianCreator

qforce/schemes/computations.py

@@ -7,7 +7,7 @@
 from .additionalstructures import StructuresFromFile
 
 
-class Computations(CustomStructureCreator):
+class Computations_(CustomStructureCreator):
 
     _user_input = """
     energy_element_weights = 15000 :: float
@@ -39,14 +39,14 @@ def __init__(self, folder, energy_ele_weight, gradient_ele_weight, hessian_ele_w
         self._activatable = activatable
 
     @classmethod
-    def from_config(cls, config):
+    def from_config(cls, config, folder):
         activatable = {}
         for name, cls_ in cls.classes.items():
             settings = getattr(config, name)
             activatable[name] = (cls_, settings)
-        return cls(config.energy_element_weights,
+        return cls(folder, config.energy_element_weights,
                    config.gradient_element_weights, config.hessian_element_weights,
-                   config.hessian_weight, config.dihedral_weight, activatable)
+                   config.hessian_weight, config.dihedral_weight, activatable=activatable)
 
     @classmethod
     def _extend_user_input(cls, questions):
@@ -231,3 +231,7 @@ def check_main(self):
 
     def parse_main(self, qm):
         pass
+
+
+def Computations(config, folder):
+    return Computations_.from_config(config, folder)

tests/test.py

@@ -1,7 +1,7 @@
 from copy import deepcopy
 
 from qforce.cli import initialize
-from qforce.main import runjob2
+from qforce.main import runjob_
 from qforce.fit import *
 from scipy.optimize import minimize
 
@@ -357,13 +357,13 @@ def update(values):
 
 
 config = {
-        'file': 'methanol.xyz',
+        'file': 'qchem.xyz',
         'options': 'settings.ini',
         }
 
 config, job = initialize(config)
 
-mol, structs = runjob2(config, job)
+qm_hessian, md_hessian, mol, structs = runjob_(config, job)
 fit = Fitter(mol, equfits=['bond'])