Merge pull request #241 from leeping/add_two_openmm_test

Code updates to enable TestLiquid_OpenMM

src/liquid.py

@@ -253,7 +253,7 @@ def prepare_temp_directory(self):
 
  def read_data(self):
  # Read the 'data.csv' file. The file should contain guidelines.
- with open(os.path.join(self.tgtdir,'data.csv'),'rU') as f: R0 = list(csv.reader(f))
+ with open(os.path.join(self.tgtdir,'data.csv'),'r') as f: R0 = list(csv.reader(f))
  # All comments are erased.
  R1 = [[sub('#.*$','',word) for word in line] for line in R0 if len(line[0]) > 0 and line[0][0] != "#"]
  # All empty lines are deleted and words are converted to lowercase.
@@ -727,7 +727,6 @@ def get_normal(self, mvals, AGrad=True, AHess=True):
  @return property_results
 
  """
-
  unpack = lp_load('forcebalance.p')
  mvals1 = unpack[1]
  if len(mvals) > 0 and (np.max(np.abs(mvals1 - mvals)) > 1e-3):

src/target.py

@@ -598,7 +598,7 @@ def meta_get(self, mvals, AGrad=False, AHess=False, customdir=None):
  def submit_jobs(self, mvals, AGrad=False, AHess=False):
  return
 
- def stage(self, mvals, AGrad=False, AHess=False, customdir=None, firstIteration=False):
+ def stage(self, mvals, AGrad=False, AHess=False, use_iterdir=True, customdir=None, firstIteration=False):
  """
 
  Stages the directory for the target, and then launches Work Queue processes if any.
@@ -614,7 +614,7 @@ def stage(self, mvals, AGrad=False, AHess=False, customdir=None, firstIteration=
  cwd = os.getcwd()
 
  absgetdir = os.path.join(self.root,self.tempdir)
- if Counter() is not None:
+ if use_iterdir and Counter() is not None:
  ## Not expecting more than ten thousand iterations
  iterdir = "iter_%04i" % Counter()
  absgetdir = os.path.join(absgetdir,iterdir)

src/tests/test_openmmio.py

@@ -23,26 +23,28 @@
 """
 The testing functions for this class are located in test_target.py.
 """
+
 class TestLiquid_OpenMM(TargetTests):
  def setup_method(self, method):
- pytest.skip("Needs optimizing to reduce runtime")
  super(TestLiquid_OpenMM, self).setup_method(method)
+ self.check_grad_fd = False
  # settings specific to this target
  self.options.update({
  'jobtype': 'NEWTON',
  'forcefield': ['dms.xml']})
 
  self.tgt_opt.update({'type':'LIQUID_OPENMM',
- 'name':'dms-liquid'})
+ 'name':'dms-liquid', 'liquid_eq_steps':100, 'liquid_md_steps':200, 'gas_eq_steps':100, 'gas_md_steps':200})
 
  self.ff = forcebalance.forcefield.FF(self.options)
 
  self.ffname = self.options['forcefield'][0][:-3]
  self.filetype = self.options['forcefield'][0][-3:]
- self.mvals = [.5]*self.ff.np
+ self.mvals = np.array([.5]*self.ff.np)
 
  self.target = forcebalance.openmmio.Liquid_OpenMM(self.options, self.tgt_opt, self.ff)
- self.target.stage(self.mvals)
+ self.target.stage(self.mvals, AGrad=True, use_iterdir=False)
+
 
  def teardown_method(self):
  shutil.rmtree('temp')

src/tests/test_target.py

@@ -17,6 +17,7 @@ def setup_method(self, method):
  self.tgt_opt = forcebalance.parser.tgt_opts_defaults.copy()
  self.ff = None # Forcefield this target is fitting
  self.options.update({'root': os.path.join(os.getcwd(), 'files')})
+ self.check_grad_fd = True # Whether to check gradient vs. finite difference. Set to False for liquid targets.
 
  os.chdir(self.options['root'])
 
@@ -25,7 +26,6 @@ def test_get_function(self):
  #os.chdir(self.target.tempdir)
  os.chdir('temp/%s' % self.tgt_opt['name'])
 
-
  self.logger.debug("Evaluating objective function for target...\n")
  objective = self.target.get(self.mvals)
  self.target.indicate()
@@ -76,16 +76,17 @@ def test_get_agrad(self):
  assert G.any() # with AGrad=True, G should not be [0]
  g = numpy.zeros(self.ff.np)
 
- print(">ASSERT objective['G'] approximately matches finite difference calculations\n")
- for p in range(self.ff.np):
- mvals_lo = self.mvals[:]
- mvals_hi = self.mvals[:]
- mvals_lo[p]-=(self.mvals[p]/200.)
- mvals_hi[p]+=(self.mvals[p]/200.)
-
- Xlo = self.target.get(mvals_lo)['X']
- Xhi = self.target.get(mvals_hi)['X']
- g[p] = (Xhi-Xlo)/(self.mvals[p]/100.)
- assert abs(g[p]-G[p]) < X*.01 +1e-7
-
+ if self.check_grad_fd:
+ print(">ASSERT objective['G'] approximately matches finite difference calculations\n")
+ for p in range(self.ff.np):
+ mvals_lo = self.mvals[:]
+ mvals_hi = self.mvals[:]
+ mvals_lo[p]-=(self.mvals[p]/200.)
+ mvals_hi[p]+=(self.mvals[p]/200.)
+
+ Xlo = self.target.get(mvals_lo)['X']
+ Xhi = self.target.get(mvals_hi)['X']
+ g[p] = (Xhi-Xlo)/(self.mvals[p]/100.)
+ assert abs(g[p]-G[p]) < X*.01 +1e-7
+
  os.chdir('../..')