Removed vtens_parts and gpos_parts

yaff/pes/ext.pyx

@@ -47,13 +47,13 @@ from yaff.log import log
 __all__ = [
     'Cell', 'nlist_status_init', 'nlist_build', 'nlist_status_finish',
     'nlist_recompute', 'nlist_inc_r', 'Hammer', 'Switch3', 'PairPot',
-    'PairPotLJ', 'PairPotMM3', 'PairPotGrimme', 'PairPotExpRep', 
-    'PairPotQMDFFRep', 'PairPotLJCross', 'PairPotDampDisp', 
-    'PairPotDisp68BJDamp', 'PairPotEI', 'PairPotEIDip', 
-    'PairPotEiSlater1s1sCorr', 'PairPotEiSlater1sp1spCorr', 
-    'PairPotOlpSlater1s1s','PairPotChargeTransferSlater1s1s', 
-    'compute_ewald_reci', 'compute_ewald_reci_dd',  'compute_ewald_corr_dd', 
-    'compute_ewald_corr', 'dlist_forward', 'dlist_back', 'iclist_forward', 
+    'PairPotLJ', 'PairPotMM3', 'PairPotGrimme', 'PairPotExpRep',
+    'PairPotQMDFFRep', 'PairPotLJCross', 'PairPotDampDisp',
+    'PairPotDisp68BJDamp', 'PairPotEI', 'PairPotEIDip',
+    'PairPotEiSlater1s1sCorr', 'PairPotEiSlater1sp1spCorr',
+    'PairPotOlpSlater1s1s','PairPotChargeTransferSlater1s1s',
+    'compute_ewald_reci', 'compute_ewald_reci_dd',  'compute_ewald_corr_dd',
+    'compute_ewald_corr', 'dlist_forward', 'dlist_back', 'iclist_forward',
     'iclist_back', 'vlist_forward', 'vlist_back', 'compute_grid3d',
 ]
 
@@ -1606,7 +1606,7 @@ cdef class PairPotDisp68BJDamp(PairPot):
         return pair_pot.pair_data_disp68bjdamp_get_bj_b(self._c_pair_pot)
 
     bj_b = property(_get_bj_b)
-    
+
     def _get_global_pars(self):
         '''Global parameters'''
         return [self.c6_scale,self.c8_scale,self.bj_a,self.bj_b]

yaff/pes/ff.py

@@ -192,8 +192,6 @@ def __init__(self, system, parts, nlist=None):
         self.needs_nlist_update = nlist is not None
         for part in parts:
             self.add_part(part)
-        self.gpos_parts = np.zeros((len(parts), system.pos.shape[0], system.pos.shape[1]), float)
-        self.vtens_parts = np.zeros((len(parts), 3, 3), float)
         if log.do_medium:
             with log.section('FFINIT'):
                 log('Force field with %i parts:&%s.' % (
@@ -208,14 +206,6 @@ def add_part(self, part):
         if name in self.__dict__:
             raise ValueError('The part %s occurs twice in the force field.' % name)
         self.__dict__[name] = part
-        # Extend the matrices containing the gpos and vtens parts
-        gpos_parts_new = np.zeros((len(self.parts), self.system.pos.shape[0], self.system.pos.shape[1]), float)
-        vtens_parts_new = np.zeros((len(self.parts), 3, 3), float)
-        for i in xrange(len(self.parts)-1):
-            gpos_parts_new[i,:,:] = self.gpos_parts[i,:,:]
-            vtens_parts_new[i,:,:] = self.vtens_parts[i,:,:]
-        self.gpos_parts = gpos_parts_new.copy()
-        self.vtens_parts = vtens_parts_new.copy()
 
     @classmethod
     def generate(cls, system, parameters, **kwargs):
@@ -272,15 +262,7 @@ def _internal_compute(self, gpos, vtens):
         if self.needs_nlist_update:
             self.nlist.update()
             self.needs_nlist_update = False
-        self.gpos_parts[:] = 0.0
-        self.vtens_parts[:] = 0.0
-        result = 0.0
-        for i, part in enumerate(self.parts):
-            result += part.compute(self.gpos_parts[i,:,:], self.vtens_parts[i,:,:])
-        if gpos is not None:
-            gpos[:] = np.sum(self.gpos_parts, axis=0)
-        if vtens is not None:
-            vtens[:] = np.sum(self.vtens_parts, axis=0)
+        result = sum([part.compute(gpos, vtens) for part in self.parts])
         return result
 
 

yaff/pes/generator.py

@@ -491,7 +491,7 @@ def process_pars(self, pardef, conversions, nffatype, par_info=None):
         '''
         tmp = Generator.process_pars(self, pardef, conversions, nffatype, par_info=par_info)
         par_table = {}
-        
+
         for key, oldpars in tmp.iteritems():
             K = oldpars[0][0]
             r0 = oldpars[0][1]

yaff/pes/test/test_generator.py

@@ -515,7 +515,7 @@ def test_generator_water32_d3bj():
     c8HH = 5.74321564987e+00
     c8HO = 5.01673173654e+00
     c8OO = 3.13071058512e+00
-    
+
     c6_cross = d3bj.pair_pot.c6_cross
     assert c6_cross.shape == (2,2)
     assert abs(c6_cross[0,0] - c6HH) < 1e-10
@@ -536,7 +536,7 @@ def test_generator_water32_d3bj():
     assert abs(gps[1] - 2.0) < 1e-10
     assert abs(gps[2] - 3.0) < 1e-10
     assert abs(gps[3] - 4.0) < 1e-10
-    
+
     R_cross = d3bj.pair_pot.R_cross
     assert R_cross.shape == (2,2)
     assert abs(R_cross[0,0] - np.sqrt(c8HH/c6HH)) < 1e-10
@@ -552,7 +552,7 @@ def test_generator_water32_qmdffrep():
     ff = ForceField.generate(system, fn_pars)
     assert len(ff.parts) == 1
     qmdffrep = ff.part_pair_qmdffrep
-    # check parameters  
+    # check parameters
     A_cross = qmdffrep.pair_pot.amp_cross
     assert A_cross.shape == (2,2)
     print A_cross
@@ -567,8 +567,8 @@ def test_generator_water32_qmdffrep():
     assert abs(B_cross[0,1] - 5.00924416592e+00) < 1e-10
     assert abs(B_cross[1,0] - 5.00924416592e+00) < 1e-10
     assert abs(B_cross[1,1] - 6.34212100945e+00) < 1e-10
-    
-    # check scalings  
+
+    # check scalings
     scalings = qmdffrep.scalings
     assert abs(scalings.scale1 - 0.0) < 1e-10
     assert abs(scalings.scale2 - 0.0) < 1e-10

yaff/sampling/verlet.py

@@ -69,7 +69,6 @@ class VerletIntegrator(Iterative):
         AttributeStateItem('cons_err'),
         AttributeStateItem('ptens'),
         AttributeStateItem('vtens'),
-        AttributeStateItem('vtens_parts'),
         AttributeStateItem('press'),
         DipoleStateItem(),
         DipoleVelStateItem(),
@@ -375,8 +374,6 @@ def compute_properties(self, restart_h5=None):
         for hook in self.hooks:
             if isinstance(hook, VerletHook):
                 self.econs += hook.econs_correction
-        self.gpos_parts = self.ff.gpos_parts
-        self.vtens_parts = self.ff.vtens_parts
         if restart_h5 is not None:
             self.econs = restart_h5['trajectory/econs'][-1]
         else: