Merge pull request #31 from rinikerlab/build_release_1

test Pull request

.github/workflows/CI.yaml

@@ -19,8 +19,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.6, 3.7]
+        os: [macOS-latest, ubuntu-latest, windows-latest]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
       - uses: actions/checkout@v2
@@ -67,3 +67,4 @@ jobs:
           file: ./coverage.xml
           flags: unittests
           name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+

.gitignore

@@ -114,3 +114,10 @@ ENV/
 ensembler/potentials/look_up_tables
 examples/dev/img
 examples/dev/ttt.ipynb
+
+
+#test results:
+ensembler/tests/tmp_test_*
+
+#jupyter_nB
+**/.ipynb_checkpoints

ensembler/potentials/_basicPotentials.py

@@ -117,7 +117,7 @@ def ene(self, positions: Union[Number, Sized]) -> Union[Number, Sized]:
         return np.squeeze(self._calculate_energies(*np.hsplit(np.array(positions, ndmin=1), self.constants[self.nDim])))
 
     def force(self, positions: Union[Number, Sized]) -> Union[Number, Sized]:
-        return np.squeeze(self._calculate_dVdpos(*np.hsplit(np.array(positions, ndmin=1), self.constants[self.nDim])))
+        return np.squeeze(self._calculate_dVdpos(*np.hsplit(np.array(positions, ndmin=1), self.constants[self.nDim]))).T
 
     # just alternative name
     def dvdpos(self, positions: Union[Number, Sized]) -> Union[Number, Sized]:

ensembler/potentials/biased_potentials/biasOneD.py

@@ -6,9 +6,10 @@
 import numpy as np
 import sympy as sp
 
-from ensembler.potentials.OneD import gaussPotential
+from ensembler.potentials.OneD import gaussPotential, harmonicOscillatorPotential
 from ensembler.potentials._basicPotentials import _potential1DCls
-from ensembler.samplers.stochastic import  langevinIntegrator
+
+from ensembler.samplers.stochastic import langevinIntegrator
 """
     BIAS BASECLASS
 """
@@ -109,7 +110,7 @@ class addedPotentials(_potential1DCls):
     name: str = "Added Potential Enhanced Sampling System"
     position = sp.symbols("r")
 
-    def __init__(self, origPotential, addPotential):
+    def __init__(self, origPotential=harmonicOscillatorPotential(), addPotential=gaussPotential()):
         '''
         __init__
               This is the Constructor of the addedPotential class.
@@ -152,7 +153,7 @@ class metadynamicsPotential(_potential1DCls):
     name: str = "Metadynamics Enhanced Sampling System using grid bias"
     position = sp.symbols("r")
 
-    def __init__(self, origPotential, amplitude=0.1, sigma=1, n_trigger=100, bias_grid_min=0, bias_grid_max=10,
+    def __init__(self, origPotential=harmonicOscillatorPotential(), amplitude=0.1, sigma=1, n_trigger=100, bias_grid_min=0, bias_grid_max=10,
                  numbins=100):
 
         '''
@@ -307,7 +308,7 @@ def force(self, positions):
         -------
         '''
 
-        current_bin = self._find_nearest(self.bin_centers, positions)
+        current_bin = np.apply_over_axes(self._find_nearest, a= np.array(positions), axes=0) #self._find_nearest(self.bin_centers, positions)
         force= np.squeeze(self._calculate_dVdpos(np.squeeze(positions)) + self.bias_grid_force[current_bin])
         return force
 

ensembler/potentials/biased_potentials/biasTwoD.py

@@ -7,7 +7,7 @@
 import numpy as np
 import sympy as sp
 
-from ensembler.potentials.TwoD import gaussPotential
+from ensembler.potentials.TwoD import gaussPotential, harmonicOscillatorPotential
 from ensembler.potentials._basicPotentials import _potential2DCls
 from ensembler.util.ensemblerTypes import system
 
@@ -26,7 +26,7 @@ class addedPotentials(_potential2DCls):
     nDim: int = sp.symbols("nDim")
     position: sp.Matrix = sp.Matrix([sp.symbols("r")])
 
-    def __init__(self, origPotential, addPotential):
+    def __init__(self, origPotential=harmonicOscillatorPotential(), addPotential=gaussPotential()):
         '''
         __init__
               This is the Constructor of the addedPotential class.
@@ -44,10 +44,7 @@ def __init__(self, origPotential, addPotential):
 
         self.constants = {**origPotential.constants, **addPotential.constants}
 
-        self.V_orig = origPotential.V + self.addPotential.V
-
-        self.V = self.V_orig.subs(self.constants)
-        self.dVdpos = sp.diff(self.V, self.position)
+        self.V_functional = origPotential.V_functional + self.addPotential.V_functional
 
         super().__init__()
 
@@ -61,7 +58,7 @@ def _initialize_functions(self):
     TIME DEPENDENT BIASES 
 """
 
-
+#TODO: I don't think this does, what it should!
 class metadynamicsPotential(_potential2DCls):
     '''
     The metadynamics bias potential adds 2D Gaussian potentials on top of
@@ -76,7 +73,7 @@ class metadynamicsPotential(_potential2DCls):
     position = sp.symbols("r")
     system: system  # metadyn-coupled to system
 
-    def __init__(self, origPotential, amplitude=1., sigma=(1., 1.), n_trigger=100, bias_grid_min=(0, 0),
+    def __init__(self, origPotential=harmonicOscillatorPotential(), amplitude=1., sigma=(1., 1.), n_trigger=100, bias_grid_min=(0, 0),
                  bias_grid_max=(10, 10), numbins=(100, 100)):
         '''
 
@@ -121,10 +118,8 @@ def __init__(self, origPotential, amplitude=1., sigma=(1., 1.), n_trigger=100, b
 
         self.constants = {**origPotential.constants}
 
-        self.V_orig = origPotential.V
-        self.V_orig_part = self.V_orig.subs(self.constants)
-        self.dVdpos = sp.diff(self.V_orig_part, self.position)
-        self.V = self.V_orig_part
+        self.V_functional = origPotential.V
+        self.V_orig_part = self.V_functional.subs(self.constants)
 
         super().__init__()
 
@@ -133,11 +128,11 @@ def _initialize_functions(self):
         nDim = self.constants[self.nDim]
         self.position = sp.Matrix([sp.symbols("r_" + str(i)) for i in range(nDim)])
 
-    """
+    '''
     BIAS
-    """
+    '''
 
-    # Beautiful integration to system as Condition.
+    #Beautiful integration to system as Condition.
     def apply(self):
         self.check_for_metastep(self.system._currentPosition)
 
@@ -163,14 +158,6 @@ def check_for_metastep(self, curr_position):
         '''
         if (self.system.step % self.n_trigger == 0):
             self._update_potential(curr_position)
-        """
-        TODO: Remove
-        if self.current_n%self.n_trigger == 0:
-            self._update_potential(curr_position)
-            self.current_n += 1
-        else:
-            self.current_n += 1
-        """
 
     def _update_potential(self, curr_position):
         '''
@@ -213,8 +200,9 @@ def ene(self, positions):
         -------
         current energy
         '''
-        current_bin_x = self._find_nearest(self.x_centers, positions[0])
-        current_bin_y = self._find_nearest(self.y_centers, positions[1])
+        current_bin_x = np.apply_over_axes(self._find_nearest, a= np.array(positions).T[0], axes=0) #self._find_nearest(self.bin_centers, positions)
+        current_bin_y = np.apply_over_axes(self._find_nearest, a= np.array(positions).T[1], axes=0) #self._find_nearest(self.bin_centers, positions)
+
         # due to transposed position matrix, x and y are changed here
         return np.squeeze(
             self._calculate_energies(*np.hsplit(positions, self.constants[self.nDim])) + self.bias_grid_energy[
@@ -233,10 +221,13 @@ def force(self, positions):
         current derivative dh/dpos
         -------
         '''
+        current_bin_x = np.apply_over_axes(lambda x: self._find_nearest(self.bin_centers_x, x), a= np.array(positions).T[0], axes=0) #self._find_nearest(self.bin_centers, positions)
+        current_bin_y = np.apply_over_axes(lambda x: self._find_nearest(self.bin_centers_y, x), a= np.array(positions).T[1], axes=0) #self._find_nearest(self.bin_centers, positions)
 
-        current_bin_x = self._find_nearest(self.x_centers, positions[0])
-        current_bin_y = self._find_nearest(self.y_centers, positions[1])
+        print(current_bin_x)
         # due to transposed position matrix, x and y are changed here
+        print( self.bias_grid_force[:,current_bin_y,
+                                      current_bin_x].reshape(2, 1, 1))
         return np.squeeze(
             self._calculate_dVdpos(*np.hsplit(positions, self.constants[self.nDim])) + self.bias_grid_force[:,
                                                                                        current_bin_y,

ensembler/system/basic_system.py

@@ -106,8 +106,8 @@ def __init__(self, potential: _potentialCls, sampler: _samplerCls, conditions: I
         self.nparticles = 1  # Todo: adapt it to be multiple particles
 
         # Output
-        self.currentState: data.basicState = data.basicState(np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan)
-        self.trajectory: pd.DataFrame = pd.DataFrame(columns=list(self.state.__dict__["_fields"]))
+        self.currentState = self.state(**{key: np.nan for key in self.state.__dict__["_fields"]})
+        self.trajectory= pd.DataFrame(columns=list(self.state.__dict__["_fields"]))
 
         # tmpvars - private:
         self._currentTotE: (Number) = np.nan
@@ -212,8 +212,8 @@ def _init_position(self, initial_position=None):
             self.initial_position = initial_position
         else:
             raise Exception("did not understand the initial position!")
-
         self._currentPosition = self.initial_position
+
         self.updateCurrentState()
         return self.initial_position
 

ensembler/system/eds_system.py

@@ -42,35 +42,15 @@ def __init__(self, potential: pot.envelopedPotential = pot.envelopedPotential(
         # Declare Attributes
         #################################
 
-        self.state = data.envelopedPStstate
         self._currentEdsS = eds_s
         self._currentEdsEoffs = eds_Eoff
+        self.state = data.envelopedPStstate
 
-        ##Physical parameters
-        self.temperature: float = 298.0
-        self.mass: float = 1  # for one particle systems!!!!
-        self.nparticles: int = 1  # Todo: adapt it to be multiple particles
+        super().__init__(potential=potential, sampler=sampler, conditions=conditions, temperature=temperature,
+                         start_position=start_position)
 
-        self.nDim: int = -1
-        self.nStates: int = 1
 
         # Output
-        self.initial_position: Iterable[float] or float
-
-        self.currentState: data.basicState = data.basicState(np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan)
-        self.trajectory: pd.DataFrame = pd.DataFrame(columns=list(self.state.__dict__["_fields"]))
-
-        # tmpvars - private:
-        self._currentTotE: (Number) = np.nan
-        self._currentTotPot: (Number) = np.nan
-        self._currentTotKin: (Number) = np.nan
-        self._currentPosition: (Number or Iterable[Number]) = np.nan
-        self._currentVelocities: (Number or Iterable[Number]) = np.nan
-        self._currentForce: (Number or Iterable[Number]) = np.nan
-        self._currentTemperature: (Number or Iterable[Number]) = np.nan
-
-        super().__init__(potential=potential, sampler=sampler, conditions=conditions, temperature=temperature,
-                         start_position=start_position)
         self.set_s(self._currentEdsS)
         self.set_Eoff(self._currentEdsEoffs)
 

ensembler/system/perturbed_system.py

@@ -34,7 +34,9 @@ class perturbedSystem(system):
     def __init__(self, potential: _perturbedPotentialCls, sampler: _integratorCls,
                  conditions: Iterable[_conditionCls] = [],
                  temperature: float = 298.0, start_position: (Iterable[Number] or float) = None, lam: float = 0.0):
+
         self._currentLam = lam
+
         super().__init__(potential=potential, sampler=sampler, conditions=conditions, temperature=temperature,
                          start_position=start_position)
         self.set_lam(lam)

ensembler/tests/test_analysis.py

@@ -6,7 +6,7 @@
 
 from ensembler.analysis.freeEnergyCalculation import  zwanzigEquation, threeStateZwanzigReweighting, bennetAcceptanceRatio
 
-#tmp_potentials = tempfile.mkdtemp(dir=os.getcwd(), prefix="test_conditions")
+#tmp_potentials = tempfile.mkdtemp(dir=os.getcwd(), prefix="tmp_test_conditions")
 
 
 class test_ZwanzigEquation(unittest.TestCase):

ensembler/tests/test_conditions.py

@@ -6,7 +6,7 @@
 from ensembler.conditions.box_conditions import periodicBoundaryCondition, boxBoundaryCondition
 from ensembler.conditions.restrain_conditions import positionRestraintCondition
 
-tmp_potentials = tempfile.mkdtemp(dir=os.getcwd(), prefix="test_conditions")
+tmp_potentials = tempfile.mkdtemp(dir=os.getcwd(), prefix="tmp_test_conditions")
 
 
 class boxBoundaryCondition(unittest.TestCase):

ensembler/tests/test_integrator.py

@@ -9,7 +9,7 @@
 """
 STOCHASTIC INTEGRATORS
 """
-tmp_dir = tempfile.mkdtemp(dir=os.getcwd(), prefix="test_integrators")
+tmp_dir = tempfile.mkdtemp(dir=os.getcwd(), prefix="tmp_test_integrators")
 
 
 class standard_IntegratorTests(unittest.TestCase):