rmgpy/rmg/*.py import numpy as np

rmgpy/rmg/input.py

@@ -32,7 +32,7 @@
 import os
 from copy import deepcopy
 
-import numpy
+import numpy as np
 
 from rmgpy import settings
 from rmgpy.exceptions import InputError
@@ -545,16 +545,16 @@ def solvation(solvent):
     rmg.solvent = solvent
 
 
-def model(toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=numpy.inf, toleranceKeepInEdge=0.0,
+def model(toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=np.inf, toleranceKeepInEdge=0.0,
           toleranceInterruptSimulation=1.0,
-          toleranceMoveEdgeReactionToSurface=numpy.inf, toleranceMoveSurfaceSpeciesToCore=numpy.inf,
-          toleranceMoveSurfaceReactionToCore=numpy.inf,
+          toleranceMoveEdgeReactionToSurface=np.inf, toleranceMoveSurfaceSpeciesToCore=np.inf,
+          toleranceMoveSurfaceReactionToCore=np.inf,
           toleranceMoveEdgeReactionToSurfaceInterrupt=None,
           toleranceMoveEdgeReactionToCoreInterrupt=None, maximumEdgeSpecies=1000000, minCoreSizeForPrune=50,
           minSpeciesExistIterationsForPrune=2, filterReactions=False, filterThreshold=1e8,
           ignoreOverallFluxCriterion=False,
           maxNumSpecies=None, maxNumObjsPerIter=1, terminateAtMaxObjects=False,
-          toleranceThermoKeepSpeciesInEdge=numpy.inf, dynamicsTimeScale=(0.0, 'sec'),
+          toleranceThermoKeepSpeciesInEdge=np.inf, dynamicsTimeScale=(0.0, 'sec'),
           toleranceBranchReactionToCore=0.0, branchingIndex=0.5, branchingRatioMax=1.0):
     """
     How to generate the model. `toleranceMoveToCore` must be specified. 

rmgpy/rmg/model.py

@@ -38,7 +38,7 @@
 import logging
 import os
 
-import numpy
+import numpy as np
 
 import rmgpy.data.rmg
 from rmgpy import settings
@@ -211,10 +211,10 @@ def __init__(self, core=None, edge=None, surface=None):
         self.indexSpeciesDict = {}
         self.saveEdgeSpecies = False
         self.iterationNum = 0
-        self.toleranceThermoKeepSpeciesInEdge = numpy.inf
-        self.Gfmax = numpy.inf
-        self.Gmax = numpy.inf
-        self.Gmin = -numpy.inf
+        self.toleranceThermoKeepSpeciesInEdge = np.inf
+        self.Gfmax = np.inf
+        self.Gmax = np.inf
+        self.Gmin = -np.inf
         self.minCoreSizeForPrune = 50
         self.maximumEdgeSpecies = 100000
         self.Tmax = 0
@@ -612,7 +612,7 @@ def enlarge(self, newObject=None, reactEdge=False,
             self.applyThermoToSpecies(procnum)
 
         # Do thermodynamic filtering
-        if not numpy.isinf(self.toleranceThermoKeepSpeciesInEdge) and self.newSpeciesList != []:
+        if not np.isinf(self.toleranceThermoKeepSpeciesInEdge) and self.newSpeciesList != []:
             self.thermoFilterSpecies(self.newSpeciesList)
 
         # Generate kinetics of new reactions
@@ -1125,9 +1125,9 @@ def thermoFilterDown(self, maximumEdgeSpecies, minSpeciesExistIterationsForPrune
             logging.info('Reached maximum number of edge species')
             logging.info('Attempting to remove excess edge species with Thermodynamic filtering')
             spcs = self.edge.species
-            Gfs = numpy.array([spc.thermo.getFreeEnergy(Tmax) for spc in spcs])
+            Gfs = np.array([spc.thermo.getFreeEnergy(Tmax) for spc in spcs])
             Gns = (Gfs - self.Gmax) / (self.Gmax - self.Gmin)
-            inds = numpy.argsort(Gns)  # could actually do this with the Gfs, but want to print the Gn value later
+            inds = np.argsort(Gns)  # could actually do this with the Gfs, but want to print the Gn value later
             inds = inds[::-1]  # get in order of increasing Gf
 
             ind = 0
@@ -1200,7 +1200,7 @@ def prune(self, reactionSystems, toleranceKeepInEdge, toleranceMoveToCore, maxim
 
         # Get the maximum species rates (and network leak rates)
         # across all reaction systems
-        max_edge_species_rate_ratios = numpy.zeros((num_prunable_species), numpy.float64)
+        max_edge_species_rate_ratios = np.zeros((num_prunable_species), np.float64)
         for reactionSystem in reactionSystems:
             for i in range(num_prunable_species):
                 rate_ratio = reactionSystem.maxEdgeSpeciesRateRatios[i]
@@ -1223,7 +1223,7 @@ def prune(self, reactionSystems, toleranceKeepInEdge, toleranceMoveToCore, maxim
                         ineligible_species.append(spec)
 
         # Sort the edge species rates by index
-        indices = numpy.argsort(max_edge_species_rate_ratios)
+        indices = np.argsort(max_edge_species_rate_ratios)
         # Determine which species to prune
         species_to_prune = []
         prune_due_to_rate_counter = 0

rmgpy/rmg/settings.py

@@ -54,7 +54,7 @@
     `maxNumObjPerIter`                              Maximum number of objects that can be sent for enlargement from a single simulation
 ==================================================================================================================================================
 """
-import numpy
+import numpy as np
 
 from rmgpy.quantity import Quantity
 
@@ -64,15 +64,15 @@ class ModelSettings(object):
     class for holding the parameters affecting an RMG run
     """
 
-    def __init__(self, toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=numpy.inf, toleranceKeepInEdge=0.0,
+    def __init__(self, toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=np.inf, toleranceKeepInEdge=0.0,
                  toleranceInterruptSimulation=1.0,
-                 toleranceMoveEdgeReactionToSurface=numpy.inf, toleranceMoveSurfaceSpeciesToCore=numpy.inf,
-                 toleranceMoveSurfaceReactionToCore=numpy.inf,
+                 toleranceMoveEdgeReactionToSurface=np.inf, toleranceMoveSurfaceSpeciesToCore=np.inf,
+                 toleranceMoveSurfaceReactionToCore=np.inf,
                  toleranceMoveEdgeReactionToSurfaceInterrupt=None, toleranceMoveEdgeReactionToCoreInterrupt=None,
                  maximumEdgeSpecies=1000000, minCoreSizeForPrune=50,
                  minSpeciesExistIterationsForPrune=2, filterReactions=False, filterThreshold=1e8,
                  ignoreOverallFluxCriterion=False, maxNumSpecies=None, maxNumObjsPerIter=1,
-                 terminateAtMaxObjects=False, toleranceThermoKeepSpeciesInEdge=numpy.inf,
+                 terminateAtMaxObjects=False, toleranceThermoKeepSpeciesInEdge=np.inf,
                  dynamicsTimeScale=Quantity((0.0, 'sec')),
                  toleranceBranchReactionToCore=0.0, branchingIndex=0.5, branchingRatioMax=1.0):
 
@@ -114,10 +114,10 @@ def __init__(self, toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=num
         if maxNumSpecies:
             self.maxNumSpecies = maxNumSpecies
         else:
-            self.maxNumSpecies = numpy.inf
+            self.maxNumSpecies = np.inf
 
         if maxNumObjsPerIter <= 0:
-            self.maxNumObjsPerIter = numpy.inf
+            self.maxNumObjsPerIter = np.inf
         else:
             self.maxNumObjsPerIter = maxNumObjsPerIter