def energy_derivatives(mvals,h,FF,xyz,tky,AGrad=True):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This basically calls the finite difference subroutine on the
energy_driver subroutine also in this script.
@todo This is a sufficiently general function to be merged into openmmio.py?
@param[in] mvals Mathematical parameter values
@param[in] pdb OpenMM PDB object
@param[in] FF ForceBalance force field object
@param[in] xyzs List of OpenMM positions
@param[in] settings OpenMM settings for creating the System
@param[in] boxes Periodic box vectors
@return G First derivative of the energies in a N_param x N_coord array
"""
E0 = energy_driver(mvals, FF, xyz, tky)
ns = len(E0)
G = np.zeros((FF.np,ns))
if not AGrad:
return G
CheckFDPts = False
for i in range(FF.np):
G[i,:], _ = f12d3p(fdwrap(energy_driver,mvals,i,FF=FF,xyz=xyz,tky=tky),h,f0=E0)
if CheckFDPts:
# Check whether the number of finite difference points is sufficient. Forward difference still gives residual error of a few percent.
G1 = f1d7p(fdwrap(energy_driver,mvals,i,FF=FF,xyz=xyz,tky=tky),h)
dG = G1 - G[i,:]
dGfrac = (G1 - G[i,:]) / G[i,:]
print "Parameter %3i 7-pt vs. central derivative : RMS, Max error (fractional) = % .4e % .4e (% .4e % .4e)" % (i, np.sqrt(np.mean(dG**2)), max(np.abs(dG)), np.sqrt(np.mean(dGfrac**2)), max(np.abs(dGfrac)))
return G
def property_derivatives(mvals,h,FF,xyz,tky,kT,property_driver,property_kwargs,AGrad=True):
G = np.zeros(FF.np)
if not AGrad:
return G
ED0 = energy_driver(mvals, FF, xyz=xyz, tky=tky, dipole=True)
E0 = ED0[:,0]
D0 = ED0[:,1:]
P0 = property_driver(b=None, **property_kwargs)
if 'h_' in property_kwargs:
H0 = property_kwargs['h_'].copy()
for i in range(FF.np):
ED1 = fdwrap(energy_driver,mvals,i,FF=FF,xyz=xyz,tky=tky,dipole=True)(h)
E1 = ED1[:,0]
D1 = ED1[:,1:]
b = np.exp(-(E1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (E1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = D1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
print "Warning: Effective number of snapshots: % .1f (out of %i)" % (InfoContent, len(E0))
P1 = property_driver(b, **property_kwargs)
EDM1 = fdwrap(energy_driver,mvals,i,FF=FF,xyz=xyz,tky=tky,dipole=True)(-h)
EM1 = EDM1[:,0]
DM1 = EDM1[:,1:]
b = np.exp(-(EM1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (EM1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = DM1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
print "Warning: Effective number of snapshots: % .1f (out of %i)" % (InfoContent, len(E0))
PM1 = property_driver(b, **property_kwargs)
G[i] = (P1-PM1)/(2*h)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy()
if 'd_' in property_kwargs:
property_kwargs['d_'] = D0.copy()
return G
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
if not hasattr(self, 'ref_eigvecs_nrm'):
self.ref_eigvecs_nrm, self.ref_eigvecs_nrm_mw = self.process_vectors(self.ref_eigvecs)
def get_eigvals(mvals_):
self.FF.make(mvals_)
eigvals, eigvecs = self.vibration_driver()
eigvecs_nrm, eigvecs_nrm_mw = self.process_vectors(eigvecs)
# The overlap metric may take into account some frequency differences
dev = np.array([[(np.abs(i-j)/1000)/(1.0+np.abs(i-j)/1000) for j in self.ref_eigvals] for i in eigvals])
for i in range(dev.shape[0]):
dev[i, :] /= max(dev[i, :])
if self.reassign in ['permute', 'overlap']:
# In the matrix that we constructed, these are the column numbers (reference mode numbers)
# that are mapped to the row numbers (calculated mode numbers)
if self.reassign == 'permute':
a = np.array([[int(1e6*(1.0-np.dot(v1.flatten(),v2.flatten())**2)) for v2 in self.ref_eigvecs_nrm] for v1 in eigvecs_nrm_mw])
row, c2r = optimize.linear_sum_assignment(a)
# Commented out dependency on assignment code
# c2r = Assign(a)
eigvals = eigvals[c2r]
elif self.reassign == 'overlap':
a = np.array([[(1.0-np.dot(v1.flatten(),v2.flatten())**2) for v2 in self.ref_eigvecs_nrm] for v1 in eigvecs_nrm_mw])
a += dev
c2r = np.argmin(a, axis=0)
eigvals_p = []
for j in c2r:
eigvals_p.append(eigvals[j])
eigvals = np.array(eigvals_p)
if not in_fd():
if self.reassign == 'permute':
eigvecs_nrm_mw = eigvecs_nrm_mw[c2r]
elif self.reassign == 'overlap':
self.c2r = c2r
eigvecs_nrm_mw_p = []
for j in c2r:
eigvecs_nrm_mw_p.append(eigvecs_nrm_mw[j])
eigvecs_nrm_mw = np.array(eigvecs_nrm_mw_p)
self.overlaps = np.array([np.abs(np.dot(v1.flatten(),v2.flatten())) for v1, v2 in zip(self.ref_eigvecs_nrm, eigvecs_nrm_mw)])
return eigvals
calc_eigvals = get_eigvals(mvals)
D = calc_eigvals - self.ref_eigvals
dV = np.zeros((self.FF.np,len(calc_eigvals)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(get_eigvals, mvals, p), h = self.h, f0 = calc_eigvals)
Answer['X'] = np.dot(D,D) / self.denom**2 / (len(D) if self.normalize else 1)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(D, dV[p,:]) / self.denom**2 / (len(D) if self.normalize else 1)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:]) / self.denom**2 / (len(D) if self.normalize else 1)
if not in_fd():
self.calc_eigvals = calc_eigvals
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
def get_momvals(mvals_):
self.FF.make(mvals_)
moments = self.engine.multipole_moments(polarizability='polarizability' in self.ref_moments, optimize=self.optimize_geometry)
# Unpack from dictionary.
return self.unpack_moments(moments)
self.FF.make(mvals)
ref_momvals = self.unpack_moments(self.ref_moments)
calc_moments = self.engine.multipole_moments(polarizability='polarizability' in self.ref_moments, optimize=self.optimize_geometry)
calc_momvals = self.unpack_moments(calc_moments)
D = calc_momvals - ref_momvals
dV = np.zeros((self.FF.np,len(calc_momvals)))
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(get_momvals, mvals, p), h = self.h, f0 = calc_momvals)
Answer['X'] = np.dot(D,D)
for p in range(self.FF.np):
Answer['G'][p] = 2*np.dot(D, dV[p,:])
for q in range(self.FF.np):
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:])
if not in_fd():
self.calc_moments = calc_moments
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':zeros(self.FF.np, dtype=float), 'H':zeros((self.FF.np, self.FF.np), dtype=float)}
def get_momvals(mvals_):
self.FF.make(mvals_)
moments = self.moments_driver()
# Unpack from dictionary.
return self.unpack_moments(moments)
self.FF.make(mvals)
ref_momvals = self.unpack_moments(self.ref_moments)
calc_moments = self.moments_driver()
calc_momvals = self.unpack_moments(calc_moments)
D = calc_momvals - ref_momvals
dV = zeros((self.FF.np,len(calc_momvals)),dtype=float)
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(get_momvals, mvals, p), h = self.h, f0 = calc_momvals)
Answer['X'] = dot(D,D)
for p in range(self.FF.np):
Answer['G'][p] = 2*dot(D, dV[p,:])
for q in range(self.FF.np):
Answer['H'][p,q] = 2*dot(dV[p,:], dV[q,:])
if not in_fd():
self.FF.make(mvals)
self.calc_moments = calc_moments
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':zeros(self.FF.np, dtype=float), 'H':zeros((self.FF.np, self.FF.np), dtype=float)}
def get_eigvals(mvals_):
self.FF.make(mvals_)
eigvals, eigvecs = self.vibration_driver()
# Put reference eigenvectors in the rows and calculated eigenvectors in the columns.
# Square the dot product (pointing in opposite direction is still the same eigenvector)
# Convert to integer for the "Assign" subroutine, subtract from a million.
a = array([[int(1e6*(1.0-min(1.0,dot(v1.flatten(),v2.flatten())**2))) for v2 in self.ref_eigvecs] for v1 in eigvecs])
# In the matrix that we constructed, these are the column numbers (reference mode numbers)
# that are mapped to the row numbers (calculated mode numbers)
c2r = Assign(a)
return eigvals[c2r]
calc_eigvals = get_eigvals(mvals)
D = calc_eigvals - self.ref_eigvals
dV = zeros((self.FF.np,len(calc_eigvals)),dtype=float)
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(get_eigvals, mvals, p), h = self.h, f0 = calc_eigvals)
Answer['X'] = dot(D,D) / self.denom**2
for p in range(self.FF.np):
Answer['G'][p] = 2*dot(D, dV[p,:]) / self.denom**2
for q in range(self.FF.np):
Answer['H'][p,q] = 2*dot(dV[p,:], dV[q,:]) / self.denom**2
if not in_fd():
self.calc_eigvals = calc_eigvals
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
def get_momvals(mvals_):
self.FF.make(mvals_)
moments = self.engine.multipole_moments(polarizability='polarizability' in self.ref_moments, optimize=self.optimize_geometry)
# Unpack from dictionary.
return self.unpack_moments(moments)
self.FF.make(mvals)
ref_momvals = self.unpack_moments(self.ref_moments)
calc_moments = self.engine.multipole_moments(polarizability='polarizability' in self.ref_moments, optimize=self.optimize_geometry)
calc_momvals = self.unpack_moments(calc_moments)
D = calc_momvals - ref_momvals
dV = np.zeros((self.FF.np,len(calc_momvals)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(get_momvals, mvals, p), h = self.h, f0 = calc_momvals)
Answer['X'] = np.dot(D,D)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(D, dV[p,:])
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:])
if not in_fd():
self.calc_moments = calc_moments
self.objective = Answer['X']
return Answer
def energy_dipole_derivatives(mvals,h,FF,xyz,tky,AGrad=True):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This basically calls the finite difference subroutine on the
energy_driver subroutine also in this script.
@todo This is a sufficiently general function to be merged into openmmio.py?
@param[in] mvals Mathematical parameter values
@param[in] pdb OpenMM PDB object
@param[in] FF ForceBalance force field object
@param[in] xyzs List of OpenMM positions
@param[in] settings OpenMM settings for creating the System
@param[in] boxes Periodic box vectors
@return G First derivative of the energies in a N_param x N_coord array
"""
ED0 = energy_driver(mvals, FF, xyz=xyz, tky=tky, dipole=True)
ns = ED0.shape[0]
G = np.zeros((FF.np,ns))
GDx = np.zeros((FF.np,ns))
GDy = np.zeros((FF.np,ns))
GDz = np.zeros((FF.np,ns))
if not AGrad:
return G, GDx, GDy, GDz
CheckFDPts = False
for i in range(FF.np):
EDG, _ = f12d3p(fdwrap(energy_driver,mvals,i,FF=FF,xyz=xyz,tky=tky,dipole=True),h,f0=ED0)
G[i,:] = EDG[:,0]
GDx[i,:] = EDG[:,1]
GDy[i,:] = EDG[:,2]
GDz[i,:] = EDG[:,3]
return G, GDx, GDy, GDz
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
if not hasattr(self, 'ref_eigvecs_nrm'):
self.ref_eigvecs_nrm, self.ref_eigvecs_nrm_mw = self.process_vectors(self.ref_eigvecs)
def get_eigvals(mvals_):
self.FF.make(mvals_)
eigvals, eigvecs = self.vibration_driver()
eigvecs_nrm, eigvecs_nrm_mw = self.process_vectors(eigvecs)
# The overlap metric may take into account some frequency differences
dev = np.array([[(np.abs(i-j)/1000)/(1.0+np.abs(i-j)/1000) for j in self.ref_eigvals] for i in eigvals])
for i in range(dev.shape[0]):
dev[i, :] /= max(dev[i, :])
if self.reassign in ['permute', 'overlap']:
# In the matrix that we constructed, these are the column numbers (reference mode numbers)
# that are mapped to the row numbers (calculated mode numbers)
if self.reassign == 'permute':
a = np.array([[int(1e6*(1.0-np.dot(v1.flatten(),v2.flatten())**2)) for v2 in self.ref_eigvecs_nrm] for v1 in eigvecs_nrm_mw])
c2r = Assign(a)
eigvals = eigvals[c2r]
elif self.reassign == 'overlap':
a = np.array([[(1.0-np.dot(v1.flatten(),v2.flatten())**2) for v2 in self.ref_eigvecs_nrm] for v1 in eigvecs_nrm_mw])
a += dev
c2r = np.argmin(a, axis=0)
eigvals_p = []
for j in c2r:
eigvals_p.append(eigvals[j])
eigvals = np.array(eigvals_p)
if not in_fd():
if self.reassign == 'permute':
eigvecs_nrm_mw = eigvecs_nrm_mw[c2r]
elif self.reassign == 'overlap':
self.c2r = c2r
eigvecs_nrm_mw_p = []
for j in c2r:
eigvecs_nrm_mw_p.append(eigvecs_nrm_mw[j])
eigvecs_nrm_mw = np.array(eigvecs_nrm_mw_p)
self.overlaps = np.array([np.abs(np.dot(v1.flatten(),v2.flatten())) for v1, v2 in zip(self.ref_eigvecs_nrm, eigvecs_nrm_mw)])
return eigvals
calc_eigvals = get_eigvals(mvals)
D = calc_eigvals - self.ref_eigvals
dV = np.zeros((self.FF.np,len(calc_eigvals)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(get_eigvals, mvals, p), h = self.h, f0 = calc_eigvals)
Answer['X'] = np.dot(D,D) / self.denom**2 / (len(D) if self.normalize else 1)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(D, dV[p,:]) / self.denom**2 / (len(D) if self.normalize else 1)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:]) / self.denom**2 / (len(D) if self.normalize else 1)
if not in_fd():
self.calc_eigvals = calc_eigvals
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
def get_eigvals(mvals_):
self.FF.make(mvals_)
eigvals, eigvecs = self.vibration_driver()
# The overlap metric may take into account some frequency differences.
# Here, an element of dev is equal to 2/3 if (for example) the frequencies differ by 1000.
dev = np.array([[(np.abs(i-j)/1000)/(1.0+np.abs(i-j)/1000) for j in eigvals] for i in self.ref_eigvals])
for i in range(dev.shape[0]):
dev[i, :] /= max(dev[i, :])
if self.reassign in ['permute', 'overlap']:
# The elements of "a" matrix are the column numbers (reference mode numbers)
# that are mapped to the row numbers (calculated mode numbers).
# Highly similar eigenvectors are assigned small values because
# the assignment problem is a cost minimization problem.
a = np.array([[(1.0-vib_overlap(self.engine, v1, v2)) for v2 in eigvecs] for v1 in self.ref_eigvecs])
a += dev
if self.reassign == 'permute':
row, c2r = optimize.linear_sum_assignment(a)
eigvals = eigvals[c2r]
elif self.reassign == 'overlap':
c2r = np.argmin(a, axis=0)
eigvals_p = []
for j in c2r:
eigvals_p.append(eigvals[j])
eigvals = np.array(eigvals_p)
if not in_fd():
if self.reassign == 'permute':
eigvecs = eigvecs[c2r]
elif self.reassign == 'overlap':
self.c2r = c2r
eigvecs_p = []
for j in c2r:
eigvecs_p.append(eigvecs[j])
eigvecs = np.array(eigvecs_p)
self.overlaps = np.array([vib_overlap(self.engine, v1, v2) for v1, v2 in zip(self.ref_eigvecs, eigvecs)])
return eigvals
calc_eigvals = get_eigvals(mvals)
D = calc_eigvals - self.ref_eigvals
dV = np.zeros((self.FF.np,len(calc_eigvals)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(get_eigvals, mvals, p), h = self.h, f0 = calc_eigvals)
Answer['X'] = np.dot(D,D) / self.denom**2 / (len(D) if self.normalize else 1)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(D, dV[p,:]) / self.denom**2 / (len(D) if self.normalize else 1)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:]) / self.denom**2 / (len(D) if self.normalize else 1)
if not in_fd():
self.calc_eigvals = calc_eigvals
self.objective = Answer['X']
return Answer
def energy_derivatives(engine,
FF,
mvals,
h,
pgrad,
length,
AGrad=True,
dipole=False):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This basically calls the finite difference subroutine on the
energy_driver subroutine also in this script.
@param[in] mvals Mathematical parameter values
@param[in] h Finite difference step size
@param[in] phase The phase (liquid, gas) to perform the calculation on
@param[in] AGrad Switch to turn derivatives on or off; if off, return all zeros
@param[in] dipole Switch for dipole derivatives.
@return G First derivative of the energies in a N_param x N_coord array
@return GDx First derivative of the box dipole moment x-component in a N_param x N_coord array
@return GDy First derivative of the box dipole moment y-component in a N_param x N_coord array
@return GDz First derivative of the box dipole moment z-component in a N_param x N_coord array
"""
G = np.zeros((FF.np, length))
GDx = np.zeros((FF.np, length))
GDy = np.zeros((FF.np, length))
GDz = np.zeros((FF.np, length))
if not AGrad:
return G, GDx, GDy, GDz
def energy_driver(mvals_):
FF.make(mvals_)
if dipole:
return engine.energy_dipole()
else:
return engine.energy()
ED0 = energy_driver(mvals)
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " " * 30)))
EDG, _ = f12d3p(fdwrap(energy_driver, mvals, i), h, f0=ED0)
if dipole:
G[i, :] = EDG[:, 0]
GDx[i, :] = EDG[:, 1]
GDy[i, :] = EDG[:, 2]
GDz[i, :] = EDG[:, 3]
else:
G[i, :] = EDG[:]
#reset FF parameters
FF.make(mvals)
return G, GDx, GDy, GDz
def get_sp(self, mvals, AGrad=False, AHess=False):
""" Get the hydration free energy and first parameteric derivatives using single point energy evaluations. """
def get_hfe(mvals_):
self.FF.make(mvals_)
self.hfe_dict = self.hydration_driver_sp()
return np.array(list(self.hfe_dict.values()))
calc_hfe = get_hfe(mvals)
D = calc_hfe - np.array(list(self.expval.values()))
dD = np.zeros((self.FF.np,len(self.IDs)))
if AGrad or AHess:
for p in self.pgrad:
dD[p,:], _ = f12d3p(fdwrap(get_hfe, mvals, p), h = self.h, f0 = calc_hfe)
return D, dD
def get_sp(self, mvals, AGrad=False, AHess=False):
""" Get the hydration free energy and first parameteric derivatives using single point energy evaluations. """
def get_hfe(mvals_):
self.FF.make(mvals_)
self.hfe_dict = self.hydration_driver_sp()
return np.array(self.hfe_dict.values())
calc_hfe = get_hfe(mvals)
D = calc_hfe - np.array(self.expval.values())
dD = np.zeros((self.FF.np,len(self.IDs)))
if AGrad or AHess:
for p in self.pgrad:
dD[p,:], _ = f12d3p(fdwrap(get_hfe, mvals, p), h = self.h, f0 = calc_hfe)
return D, dD
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
if not hasattr(self, 'ref_eigvecs_nrm'):
self.ref_eigvecs_nrm, self.ref_eigvecs_nrm_mw = self.process_vectors(self.ref_eigvecs)
def get_eigvals(mvals_):
self.FF.make(mvals_)
eigvals, eigvecs = self.vibration_driver()
eigvecs_nrm, eigvecs_nrm_mw = self.process_vectors(eigvecs)
if self.reassign in ['permute', 'overlap']:
a = np.array([[int(1e6*(1.0-np.dot(v1.flatten(),v2.flatten())**2)) for v2 in self.ref_eigvecs_nrm] for v1 in eigvecs_nrm_mw])
# In the matrix that we constructed, these are the column numbers (reference mode numbers)
# that are mapped to the row numbers (calculated mode numbers)
if self.reassign == 'permute':
c2r = Assign(a)
eigvals = eigvals[c2r]
elif self.reassign == 'overlap':
c2r = np.argmin(a, axis=0)
eigvals_p = []
for j in c2r:
eigvals_p.append(eigvals[j])
eigvals = np.array(eigvals_p)
if not in_fd():
if self.reassign == 'permute':
eigvecs_nrm_mw = eigvecs_nrm_mw[c2r]
elif self.reassign == 'overlap':
self.c2r = c2r
eigvecs_nrm_mw_p = []
for j in c2r:
eigvecs_nrm_mw_p.append(eigvecs_nrm_mw[j])
eigvecs_nrm_mw = np.array(eigvecs_nrm_mw_p)
self.overlaps = np.array([np.abs(np.dot(v1.flatten(),v2.flatten())) for v1, v2 in zip(self.ref_eigvecs_nrm, eigvecs_nrm_mw)])
return eigvals
calc_eigvals = get_eigvals(mvals)
D = calc_eigvals - self.ref_eigvals
dV = np.zeros((self.FF.np,len(calc_eigvals)))
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(get_eigvals, mvals, p), h = self.h, f0 = calc_eigvals)
Answer['X'] = np.dot(D,D) / self.denom**2
for p in range(self.FF.np):
Answer['G'][p] = 2*np.dot(D, dV[p,:]) / self.denom**2
for q in range(self.FF.np):
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:]) / self.denom**2
if not in_fd():
self.calc_eigvals = calc_eigvals
self.objective = Answer['X']
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
# If the weight is zero, turn all derivatives off.
if (self.weight == 0.0):
AGrad = False
AHess = False
def callM(mvals_, dielectric=False):
logger.info("\r")
pvals = self.FF.make(mvals_)
return self.engine.interaction_energy(self.select1, self.select2)
logger.info("Executing\r")
emm = callM(mvals)
D = emm - self.eqm
dV = np.zeros((self.FF.np,len(emm)))
# Dump interaction energies to disk.
np.savetxt('M.txt',emm)
np.savetxt('Q.txt',self.eqm)
# Do the finite difference derivative.
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = emm)
# Create the force field one last time.
pvals = self.FF.make(mvals)
Answer['X'] = np.dot(self.prefactor*D/self.divisor,D/self.divisor)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(self.prefactor*D/self.divisor, dV[p,:]/self.divisor)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(self.prefactor*dV[p,:]/self.divisor, dV[q,:]/self.divisor)
if not in_fd():
self.emm = emm
self.objective = Answer['X']
## QYD: try to clean up OpenMM engine.simulation objects to free up GPU memory
try:
if self.engine.name == 'openmm':
if hasattr(self.engine, 'simulation'): del self.engine.simulation
if hasattr(self.engine, 'A'): del self.engine.A
if hasattr(self.engine, 'B'): del self.engine.B
except:
pass
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
# If the weight is zero, turn all derivatives off.
if (self.weight == 0.0):
AGrad = False
AHess = False
def callM(mvals_, dielectric=False):
logger.info("\r")
pvals = self.FF.make(mvals_)
return self.engine.interaction_energy(self.select1, self.select2)
logger.info("Executing\r")
emm = callM(mvals)
D = emm - self.eqm
dV = np.zeros((self.FF.np,len(emm)))
# Dump interaction energies to disk.
np.savetxt('M.txt',emm)
np.savetxt('Q.txt',self.eqm)
# Do the finite difference derivative.
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = emm)
# Create the force field one last time.
pvals = self.FF.make(mvals)
Answer['X'] = np.dot(self.prefactor*D/self.divisor,D/self.divisor)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(self.prefactor*D/self.divisor, dV[p,:]/self.divisor)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(self.prefactor*dV[p,:]/self.divisor, dV[q,:]/self.divisor)
if not in_fd():
self.emm = emm
self.objective = Answer['X']
## QYD: try to clean up OpenMM engine.simulation objects to free up GPU memory
try:
if self.engine.name == 'openmm':
if hasattr(self.engine, 'simulation'): del self.engine.simulation
if hasattr(self.engine, 'A'): del self.engine.A
if hasattr(self.engine, 'B'): del self.engine.B
except:
pass
return Answer
def energy_derivatives(engine, FF, mvals, h, pgrad, length, AGrad=True, dipole=False):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This basically calls the finite difference subroutine on the
energy_driver subroutine also in this script.
@param[in] mvals Mathematical parameter values
@param[in] h Finite difference step size
@param[in] phase The phase (liquid, gas) to perform the calculation on
@param[in] AGrad Switch to turn derivatives on or off; if off, return all zeros
@param[in] dipole Switch for dipole derivatives.
@return G First derivative of the energies in a N_param x N_coord array
@return GDx First derivative of the box dipole moment x-component in a N_param x N_coord array
@return GDy First derivative of the box dipole moment y-component in a N_param x N_coord array
@return GDz First derivative of the box dipole moment z-component in a N_param x N_coord array
"""
G = np.zeros((FF.np,length))
GDx = np.zeros((FF.np,length))
GDy = np.zeros((FF.np,length))
GDz = np.zeros((FF.np,length))
if not AGrad:
return G, GDx, GDy, GDz
def energy_driver(mvals_):
FF.make(mvals_)
if dipole:
return engine.energy_dipole()
else:
return engine.energy()
ED0 = energy_driver(mvals)
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " "*30)))
EDG, _ = f12d3p(fdwrap(energy_driver,mvals,i),h,f0=ED0)
if dipole:
G[i,:] = EDG[:,0]
GDx[i,:] = EDG[:,1]
GDy[i,:] = EDG[:,2]
GDz[i,:] = EDG[:,3]
else:
G[i,:] = EDG[:]
#reset FF parameters
FF.make(mvals)
return G, GDx, GDy, GDz
def energy_derivatives(engine, FF, mvals, h, pgrad, dipole=False):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This basically calls the finite difference subroutine on the
energy_driver subroutine also in this script.
In the future we may need to be more sophisticated with
controlling the quantities which are differentiated, but for
now this is okay..
@param[in] engine Engine object for calculating energies
@param[in] FF Force field object
@param[in] mvals Mathematical parameter values
@param[in] h Finite difference step size
@param[in] pgrad List of active parameters for differentiation
@param[in] dipole Switch for dipole derivatives.
@return G First derivative of the energies in a N_param x N_coord array
@return GDx First derivative of the box dipole moment x-component in a N_param x N_coord array
@return GDy First derivative of the box dipole moment y-component in a N_param x N_coord array
@return GDz First derivative of the box dipole moment z-component in a N_param x N_coord array
"""
def single_point(mvals_):
FF.make(mvals_)
if dipole:
return engine.energy_dipole()
else:
return engine.energy()
ED0 = single_point(mvals)
G = OrderedDict()
G['potential'] = np.zeros((FF.np, ED0.shape[0]))
if dipole:
G['dipole'] = np.zeros((FF.np, ED0.shape[0], 3))
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " "*30)))
edg, _ = f12d3p(fdwrap(single_point,mvals,i),h,f0=ED0)
if dipole:
G['potential'][i] = edg[:,0]
G['dipole'][i] = edg[:,1:]
else:
G['potential'][i] = edg[:]
return G
def energy_derivatives(engine, FF, mvals, h, pgrad, length, AGrad=True):
"""Compute the first derivatives of a set of snapshot energies with respect
to the force field parameters. The function calls the finite
difference subroutine on the energy_driver subroutine also in this
script.
Parameters
----------
engine : Engine
Use this Engine (`GMX`,`TINKER`,`OPENMM` etc.) object to get the energy
snapshots.
FF : FF
Force field object.
mvals : list
Mathematical parameter values.
h : float
Finite difference step size.
length : int
Number of snapshots (length of energy trajectory).
AGrad : Boolean
Switch that turns derivatives on or off; if off, return all zeros.
Returns
-------
G : np.array
Derivative of the energy in a FF.np x length array.
"""
G = np.zeros((FF.np, length))
if not AGrad:
return G
def energy_driver(mvals_):
FF.make(mvals_)
return engine.energy()
ED0 = energy_driver(mvals)
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " " * 30)))
EDG, _ = f12d3p(fdwrap(energy_driver, mvals, i), h, f0=ED0)
G[i, :] = EDG[:]
return G
def energy_derivatives(engine, FF, mvals, h, pgrad, length, AGrad=True):
"""Compute the first derivatives of a set of snapshot energies with respect
to the force field parameters. The function calls the finite
difference subroutine on the energy_driver subroutine also in this
script.
Parameters
----------
engine : Engine
Use this Engine (`GMX`,`TINKER`,`OPENMM` etc.) object to get the energy
snapshots.
FF : FF
Force field object.
mvals : list
Mathematical parameter values.
h : float
Finite difference step size.
length : int
Number of snapshots (length of energy trajectory).
AGrad : Boolean
Switch that turns derivatives on or off; if off, return all zeros.
Returns
-------
G : np.array
Derivative of the energy in a FF.np x length array.
"""
G = np.zeros((FF.np, length))
if not AGrad:
return G
def energy_driver(mvals_):
FF.make(mvals_)
return engine.energy()
ED0 = energy_driver(mvals)
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " "*30)))
EDG, _ = f12d3p(fdwrap(energy_driver, mvals, i), h, f0=ED0)
G[i,:] = EDG[:]
return G
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':zeros(self.FF.np, dtype=float), 'H':zeros((self.FF.np, self.FF.np), dtype=float)}
# If the weight is zero, turn all derivatives off.
if (self.weight == 0.0):
AGrad = False
AHess = False
def callM(mvals_, dielectric=False):
logger.info("\r")
pvals = self.FF.make(mvals_)
return self.interaction_driver_all(dielectric)
logger.info("Executing\r")
emm = callM(mvals)
D = emm - self.eqm
dV = zeros((self.FF.np,len(emm)),dtype=float)
# Dump interaction energies to disk.
savetxt('M.txt',emm)
savetxt('Q.txt',self.eqm)
# Do the finite difference derivative.
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = emm)
# Create the force field one last time.
pvals = self.FF.make(mvals)
Answer['X'] = dot(self.prefactor*D/self.divisor,D/self.divisor)
for p in range(self.FF.np):
Answer['G'][p] = 2*dot(self.prefactor*D/self.divisor, dV[p,:]/self.divisor)
for q in range(self.FF.np):
Answer['H'][p,q] = 2*dot(self.prefactor*dV[p,:]/self.divisor, dV[q,:]/self.divisor)
if not in_fd():
self.emm = emm
self.objective = Answer['X']
return Answer
def rpmd_energy_derivatives(engine, FF, mvals, h, pgrad, length, AGrad=True, dipole=False):
"""
Compute the first and second derivatives of a set of snapshot
energies with respect to the force field parameters.
This is analagous to the energy_derivatives function above, but is
specific for calculating derivatives for rpmd, which has
an additional term due to the force term in the centroid virial
estimator.
"""
G = np.zeros((FF.np,length))
GDx = np.zeros((FF.np,length))
GDy = np.zeros((FF.np,length))
GDz = np.zeros((FF.np,length))
RPMDG = np.zeros((FF.np,length))
RPMDG_frc_term = np.zeros((FF.np,length))
if not AGrad:
return G, GDx, GDy, GDz, RPMDG, RPMDG_frc_term
def rpmd_energy_driver(mvals_):
FF.make(mvals_)
if dipole:
return engine.energy_dipole_rpmd()
else:
return engine.energy_rpmd()
ED0 = rpmd_energy_driver(mvals)
for i in pgrad:
logger.info("%i %s\r" % (i, (FF.plist[i] + " "*30)))
ERPMDG, _ = f12d3p(fdwrap(rpmd_energy_driver,mvals,i),h,f0=ED0)
if dipole:
G[i,:] = ERPMDG[:,0]
GDx[i,:] = ERPMDG[:,1]
GDy[i,:] = ERPMDG[:,2]
GDz[i,:] = ERPMDG[:,3]
RPMDG[i,:] = ERPMDG[:,4]
RPMDG_frc_term[i,:] = ERPMDG[:,5]
else:
G[i,:] = ERPMDG[:,0]
RPMDG[i,:] = ERPMDG[:,1]
RPMDG_frc_term[i,:] = ERPMDG[:,2]
return G, GDx, GDy, GDz, RPMDG, RPMDG_frc_term
def FDCheckG(self):
""" Finite-difference checker for the objective function gradient.
For each element in the gradient, use a five-point finite difference
stencil to compute a finite-difference derivative, and compare it to
the analytic result.
"""
Adata = self.Objective.Full(self.mvals0,Order=1)['G']
Fdata = np.zeros(self.FF.np,dtype=float)
printcool("Checking first derivatives by finite difference!\n%-8s%-20s%13s%13s%13s%13s" \
% ("Index", "Parameter ID","Analytic","Numerical","Difference","Fractional"),bold=1,color=5)
for i in range(self.FF.np):
Fdata[i] = f1d7p(fdwrap(self.Objective.Full,self.mvals0,i,'X',Order=0),self.h)
Denom = max(abs(Adata[i]),abs(Fdata[i]))
Denom = Denom > 1e-8 and Denom or 1e-8
D = Adata[i] - Fdata[i]
Q = (Adata[i] - Fdata[i])/Denom
cD = abs(D) > 0.5 and "\x1b[1;91m" or (abs(D) > 1e-2 and "\x1b[91m" or (abs(D) > 1e-5 and "\x1b[93m" or "\x1b[92m"))
cQ = abs(Q) > 0.5 and "\x1b[1;91m" or (abs(Q) > 1e-2 and "\x1b[91m" or (abs(Q) > 1e-5 and "\x1b[93m" or "\x1b[92m"))
logger.info("\r %-8i%-20s% 13.4e% 13.4e%s% 13.4e%s% 13.4e\x1b[0m\n" \
% (i, self.FF.plist[i][:20], Adata[i], Fdata[i], cD, D, cQ, Q))
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 04-17-2013
This subroutine builds the objective function from Psi4.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
Answer = {}
Fac = 1000000
n = len(mvals)
X = 0.0
G = np.zeros(n,dtype=float)
H = np.zeros((n,n),dtype=float)
pvals = self.FF.make(mvals)
self.tdir = os.getcwd()
self.objd = OrderedDict()
self.gradd = OrderedDict()
self.hdiagd = OrderedDict()
bidirect = False
def fdwrap2(func,mvals0,pidx,qidx,key=None,**kwargs):
def func2(arg1,arg2):
mvals = list(mvals0)
mvals[pidx] += arg1
mvals[qidx] += arg2
print "\rfdwrap2:", func.__name__, "[%i] = % .1e , [%i] = % .1e" % (pidx, arg1, qidx, arg2), ' '*50,
if key != None:
return func(mvals,**kwargs)[key]
else:
return func(mvals,**kwargs)
return func2
def f2d5p(f, h):
fpp, fpm, fmp, fmm = [f(i*h,j*h) for i,j in [(1,1),(1,-1),(-1,1),(-1,-1)]]
fpp = (fpp-fpm-fmp+fmm)/(4*h*h)
return fpp
def f2d4p(f, h, f0 = None):
if f0 == None:
fpp, fp0, f0p, f0 = [f(i*h,j*h) for i,j in [(1,1),(1,0),(0,1),(0,0)]]
else:
fpp, fp0, f0p = [f(i*h,j*h) for i,j in [(1,1),(1,0),(0,1)]]
fpp = (fpp-fp0-f0p+f0)/(h*h)
return fpp
for d in self.objfiles:
print "\rNow working on", d, 50*' ','\r',
x = self.driver(mvals, d)
grad = np.zeros(n,dtype=float)
hdiag = np.zeros(n,dtype=float)
hess = np.zeros((n,n),dtype=float)
for p in range(self.FF.np):
if self.callderivs[d][p]:
if AHess:
grad[p], hdiag[p] = f12d3p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
hess[p,p] = hdiag[p]
# for q in range(p):
# if self.callderivs[d][q]:
# if bidirect:
# hessentry = f2d5p(fdwrap2(self.driver, mvals, p, q, d=d), h = self.h)
# else:
# hessentry = f2d4p(fdwrap2(self.driver, mvals, p, q, d=d), h = self.h, f0 = x)
# hess[p,q] = hessentry
# hess[q,p] = hessentry
elif AGrad:
if bidirect:
grad[p], _ = f12d3p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
else:
grad[p] = f1d2p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
self.objd[d] = x
self.gradd[d] = grad
self.hdiagd[d] = hdiag
X += x
G += grad
#H += np.diag(hdiag)
H += hess
if not in_fd():
self.objective = X
self.objvals = self.objd
# print self.objd
# print self.gradd
# print self.hdiagd
if float('Inf') in pvals:
return {'X' : 1e10, 'G' : G, 'H' : H}
return {'X' : X, 'G' : G, 'H' : H}
def submit_jobs(self, mvals, AGrad=True, AHess=True):
# This routine is called by Objective.stage() will run before "get".
# It submits the jobs to the Work Queue and the stage() function will wait for jobs to complete.
#
self.tdir = os.getcwd()
wq = getWorkQueue()
if wq is None:
return
def submit_psi(this_apath, dname, these_mvals):
""" Create a grid file and a psi4 input file in the absolute path and submit it to the work queue. """
cwd = os.getcwd()
if not os.path.exists(this_apath): os.makedirs(this_apath)
os.chdir(this_apath)
self.FF.make(these_mvals)
o = wopen('objective.dat')
for line in self.objfiles[d]:
s = line.split()
if len(s) > 2 and s[0] == 'path' and s[1] == '=':
print("path = '%s'" % os.getcwd(), file=o)
elif len(s) > 2 and s[0] == 'set' and s[1] == 'objective_path':
print("opath = '%s'" % os.getcwd(), file=o)
print("set objective_path $opath", file=o)
else:
print(line, end=' ', file=o)
o.close()
os.system("rm -f objective.out")
if wq is None:
logger.info("There is no Work Queue!!!\n")
sys.exit()
else:
input_files = [(os.path.join(this_apath, i), i)
for i in glob.glob("*")]
input_files += [(os.path.join(self.root, self.tgtdir, dname,
"build.dat"), "build.dat")]
input_files += [(os.path.join(
os.path.split(__file__)[0], "data",
"run_psi_rdvr3_objective.sh"),
"run_psi_rdvr3_objective.sh")]
logger.info("\r")
queue_up_src_dest(
wq,
"sh run_psi_rdvr3_objective.sh -c %s &> run_psi_rdvr3_objective.log"
% os.path.join(self.root, self.tgtdir, dname),
input_files=input_files,
output_files=[
(os.path.join(this_apath, i), i)
for i in ["run_psi_rdvr3_objective.log", "output.dat"]
],
verbose=False)
os.chdir(cwd)
for d in self.objfiles:
logger.info("\rNow working on" + str(d) + 50 * ' ' + '\r')
odir = os.path.join(os.getcwd(), d)
#if os.path.exists(odir):
# shutil.rmtree(odir)
if not os.path.exists(odir): os.makedirs(odir)
apath = os.path.join(odir, "current")
submit_psi(apath, d, mvals)
for p in range(self.FF.np):
def subjob(mvals_, h):
apath = os.path.join(odir, str(p), str(h))
submit_psi(apath, d, mvals_)
#logger.info("Will set up a job for %s, parameter %i\n" % (d, p))
return 0.0
if self.callderivs[d][p]:
if AHess:
f12d3p(fdwrap(subjob, mvals, p, h=self.h),
h=self.h,
f0=0.0)
elif AGrad:
if self.bidirect:
f12d3p(fdwrap(subjob, mvals, p, h=self.h),
h=self.h,
f0=0.0)
else:
f1d2p(fdwrap(subjob, mvals, p, h=self.h),
h=self.h,
f0=0.0)
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 04-17-2013
This subroutine builds the objective function from Psi4.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
Answer = {}
Fac = 1000000
n = len(mvals)
X = 0.0
G = np.zeros(n)
H = np.zeros((n, n))
pvals = self.FF.make(mvals)
self.tdir = os.getcwd()
self.objd = OrderedDict()
self.gradd = OrderedDict()
self.hdiagd = OrderedDict()
wq = getWorkQueue()
def fdwrap2(func, mvals0, pidx, qidx, key=None, **kwargs):
def func2(arg1, arg2):
mvals = list(mvals0)
mvals[pidx] += arg1
mvals[qidx] += arg2
logger.info("\rfdwrap2:" + func.__name__ +
"[%i] = % .1e , [%i] = % .1e" %
(pidx, arg1, qidx, arg2) + ' ' * 50)
if key is not None:
return func(mvals, **kwargs)[key]
else:
return func(mvals, **kwargs)
return func2
def f2d5p(f, h):
fpp, fpm, fmp, fmm = [
f(i * h, j * h)
for i, j in [(1, 1), (1, -1), (-1, 1), (-1, -1)]
]
fpp = (fpp - fpm - fmp + fmm) / (4 * h * h)
return fpp
def f2d4p(f, h, f0=None):
if f0 is None:
fpp, fp0, f0p, f0 = [
f(i * h, j * h)
for i, j in [(1, 1), (1, 0), (0, 1), (0, 0)]
]
else:
fpp, fp0, f0p = [
f(i * h, j * h) for i, j in [(1, 1), (1, 0), (0, 1)]
]
fpp = (fpp - fp0 - f0p + f0) / (h * h)
return fpp
for d in self.objfiles:
logger.info("\rNow working on" + str(d) + 50 * ' ' + '\r')
if wq is None:
x = self.driver(mvals, d)
grad = np.zeros(n)
hdiag = np.zeros(n)
hess = np.zeros((n, n))
apath = os.path.join(self.tdir, d, "current")
x = float(
open(os.path.join(
apath,
'objective.out')).readlines()[0].split()[1]) * self.factor
for p in range(self.FF.np):
if self.callderivs[d][p]:
def reader(mvals_, h):
apath = os.path.join(self.tdir, d, str(p), str(h))
answer = float(
open(os.path.join(apath, 'objective.out')).
readlines()[0].split()[1]) * self.factor
return answer
if AHess:
if wq is not None:
apath = os.path.join(self.tdir, d, "current")
x = float(
open(os.path.join(apath, 'objective.out')).
readlines()[0].split()[1]) * self.factor
grad[p], hdiag[p] = f12d3p(fdwrap(reader,
mvals,
p,
h=self.h),
h=self.h,
f0=x)
else:
grad[p], hdiag[p] = f12d3p(fdwrap(self.driver,
mvals,
p,
d=d),
h=self.h,
f0=x)
hess[p, p] = hdiag[p]
elif AGrad:
if self.bidirect:
if wq is not None:
apath = os.path.join(self.tdir, d, "current")
x = float(
open(os.path.join(apath, 'objective.out')).
readlines()[0].split()[1]) * self.factor
grad[p], _ = f12d3p(fdwrap(reader,
mvals,
p,
h=self.h),
h=self.h,
f0=x)
else:
grad[p], _ = f12d3p(fdwrap(self.driver,
mvals,
p,
d=d),
h=self.h,
f0=x)
else:
if wq is not None:
# Since the calculations are submitted as 3-point finite difference, this part of the code
# actually only reads from half of the completed calculations.
grad[p] = f1d2p(fdwrap(reader,
mvals,
p,
h=self.h),
h=self.h,
f0=x)
else:
grad[p] = f1d2p(fdwrap(self.driver,
mvals,
p,
d=d),
h=self.h,
f0=x)
self.objd[d] = x
self.gradd[d] = grad
self.hdiagd[d] = hdiag
X += x
G += grad
#H += np.diag(hdiag)
H += hess
if not in_fd():
self.objective = X
self.objvals = self.objd
# print self.objd
# print self.gradd
# print self.hdiagd
if float('Inf') in pvals:
return {'X': 1e10, 'G': G, 'H': H}
return {'X': X, 'G': G, 'H': H}
def get(self, mvals, AGrad=False, AHess=False):
Answer = {
'X': 0.0,
'G': np.zeros(self.FF.np),
'H': np.zeros((self.FF.np, self.FF.np))
}
self.PrintDict = OrderedDict()
def compute(mvals_, indicate=False):
self.FF.make(mvals_)
M_opts = None
compute.emm = []
compute.rmsd = []
for i in range(self.ns):
energy, rmsd, M_opt = self.engine.optimize(shot=i, align=False)
# Create a molecule object to hold the MM-optimized structures
compute.emm.append(energy)
compute.rmsd.append(rmsd)
if M_opts is None:
M_opts = deepcopy(M_opt)
else:
M_opts += M_opt
compute.emm = np.array(compute.emm)
compute.emm -= compute.emm[self.smin]
compute.rmsd = np.array(compute.rmsd)
if indicate:
if self.writelevel > 0:
M_opts.write('mm_minimized.xyz')
if self.ndim == 1:
import matplotlib.pyplot as plt
plt.switch_backend('agg')
fig, ax = plt.subplots()
dihedrals = np.array(
[i[0] for i in self.metadata['torsion_grid_ids']])
dsort = np.argsort(dihedrals)
ax.plot(dihedrals[dsort], self.eqm[dsort], label='QM')
if hasattr(self, 'emm_orig'):
ax.plot(dihedrals[dsort],
compute.emm[dsort],
label='MM Current')
ax.plot(dihedrals[dsort],
self.emm_orig[dsort],
label='MM Initial')
else:
ax.plot(dihedrals[dsort],
compute.emm[dsort],
label='MM Initial')
self.emm_orig = compute.emm.copy()
ax.legend()
ax.set_xlabel('Dihedral (degree)')
ax.set_ylabel('Energy (kcal/mol)')
fig.suptitle(
'Torsion profile: iteration %i\nSystem: %s' %
(Counter(), self.name))
fig.savefig('plot_torsion.pdf')
return (np.sqrt(self.wts) / self.energy_denom) * (compute.emm -
self.eqm)
compute.emm = None
compute.rmsd = None
V = compute(mvals, indicate=True)
Answer['X'] = np.dot(V, V)
# Energy RMSE
e_rmse = np.sqrt(np.dot(self.wts, (compute.emm - self.eqm)**2))
self.PrintDict[
self.
name] = '%10s %10s %6.3f - %-6.3f % 6.3f - %-6.3f %6.3f %7.4f % 7.4f' % (
','.join([
'%i' % i
for i in self.metadata['torsion_grid_ids'][self.smin]
]), ','.join([
'%i' % i for i in self.metadata['torsion_grid_ids'][
np.argmin(compute.emm)]
]), min(self.eqm), max(self.eqm), min(compute.emm),
max(compute.emm), max(compute.rmsd), e_rmse, Answer['X'])
# compute gradients and hessian
dV = np.zeros((self.FF.np, len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p, :], _ = f12d3p(fdwrap(compute, mvals, p), h=self.h, f0=V)
for p in self.pgrad:
Answer['G'][p] = 2 * np.dot(V, dV[p, :])
for q in self.pgrad:
Answer['H'][p, q] = 2 * np.dot(dV[p, :], dV[q, :])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 05-30-2012
This subroutine builds the objective function (and optionally
its derivatives) from a general software.
This subroutine interfaces with simulation software 'drivers'.
The driver is expected to give exact values, fitting values, and weights.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
global LAST_MVALS, CHECK_BASIS
# print mvals
# print LAST_MVALS
# print mvals == LAST_MVALS
if LAST_MVALS == None or not (mvals == LAST_MVALS).all():
CHECK_BASIS = False
else:
CHECK_BASIS = False
Answer = {}
Fac = 1000000
## Dictionary for derivative terms
dM = {}
# Create the new force field!!
np = len(mvals)
G = zeros(np, dtype=float)
H = zeros((np, np), dtype=float)
pvals = self.FF.make(mvals)
if float("Inf") in pvals:
return {"X": 1e10, "G": G, "H": H}
Ans = self.driver()
W = Ans[:, 2]
M = Ans[:, 1]
Q = Ans[:, 0]
D = M - Q
self.MAQ = mean(abs(Q))
ns = len(M)
# Wrapper to the driver, which returns just the part that changes.
def callM(mvals_):
self.FF.make(mvals_)
Ans2 = self.driver()
M_ = Ans2[:, 1]
D_ = M_ - Q
return Ans2[:, 1]
if AGrad:
# Leaving comment here if we want to reintroduce second deriv someday.
# dM[p,:], ddM[p,:] = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = M)
for p in range(np):
if self.call_derivatives[p] == False:
continue
dM_arr = f1d2p(fdwrap(callM, mvals, p), h=self.h, f0=M)
if max(abs(dM_arr)) == 0.0 and Counter() == 0:
print "\r Simulation %s will skip over parameter %i in subsequent steps" % (self.name, p)
self.call_derivatives[p] = False
else:
dM[p] = dM_arr.copy()
Objective = dot(W, D ** 2) * Fac
if AGrad:
for p in range(np):
if self.call_derivatives[p] == False:
continue
G[p] = 2 * dot(W, D * dM[p])
if not AHess:
continue
H[p, p] = 2 * dot(W, dM[p] ** 2)
for q in range(p):
if self.call_derivatives[q] == False:
continue
GNP = 2 * dot(W, dM[p] * dM[q])
H[q, p] = GNP
H[p, q] = GNP
G *= Fac
H *= Fac
Answer = {"X": Objective, "G": G, "H": H}
if not in_fd():
self.D = D
self.objective = Answer["X"]
LAST_MVALS = mvals.copy()
return Answer
def get(self, mvals, AGrad=False, AHess=False):
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
self.PrintDict = OrderedDict()
self.RMSDDict = OrderedDict()
#pool = Pool(processes=4)
def compute(mvals_):
# This function has automatically assigned variable names from the interaction master file
# Thus, all variable names in here are protected using an underscore.
self.FF.make(mvals_)
VectorD_ = []
for sys_ in self.sys_opts:
Energy_, RMSD_ = self.system_driver(sys_)
#print "Setting %s to" % sys_, Energy_
exec("%s = Energy_" % sys_) in locals()
RMSDNrm_ = RMSD_ / self.rmsd_denom
w_ = self.sys_opts[sys_]['rmsd_weight'] if 'rmsd_weight' in self.sys_opts[sys_] else 1.0
VectorD_.append(np.sqrt(w_)*RMSDNrm_)
if not in_fd() and RMSD_ != 0.0:
self.RMSDDict[sys_] = "% 9.3f % 12.5f" % (RMSD_, w_*RMSDNrm_**2)
VectorE_ = []
for inter_ in self.inter_opts:
Calculated_ = eval(self.inter_opts[inter_]['equation'])
Reference_ = self.inter_opts[inter_]['reference_physical']
Delta_ = Calculated_ - Reference_
Denom_ = self.energy_denom
if self.cauchy:
Divisor_ = np.sqrt(Denom_**2 + Reference_**2)
elif self.attenuate:
if Reference_ < Denom_:
Divisor_ = Denom_
else:
Divisor_ = np.sqrt(Denom_**2 + (Reference_-Denom_)**2)
else:
Divisor_ = Denom_
DeltaNrm_ = Delta_ / Divisor_
w_ = self.inter_opts[inter_]['weight'] if 'weight' in self.inter_opts[inter_] else 1.0
VectorE_.append(np.sqrt(w_)*DeltaNrm_)
if not in_fd():
self.PrintDict[inter_] = "% 9.3f % 9.3f % 9.3f % 12.5f" % (Calculated_, Reference_, Delta_, w_*DeltaNrm_**2)
# print "%-20s" % inter_, "Calculated:", Calculated_, "Reference:", Reference_, "Delta:", Delta_, "DeltaNrm:", DeltaNrm_
# The return value is an array of normalized interaction energy differences.
if not in_fd():
self.rmsd_part = np.dot(np.array(VectorD_),np.array(VectorD_))
if len(VectorE_) > 0:
self.energy_part = np.dot(np.array(VectorE_),np.array(VectorE_))
else:
self.energy_part = 0.0
if len(VectorE_) > 0 and len(VectorD_) > 0:
return np.array(VectorD_ + VectorE_)
elif len(VectorD_) > 0:
return np.array(VectorD_)
elif len(VectorE_) > 0:
return np.array(VectorE_)
V = compute(mvals)
dV = np.zeros((self.FF.np,len(V)))
if AGrad or AHess:
for p in range(self.FF.np):
dV[p,:], _ = f12d3p(fdwrap(compute, mvals, p), h = self.h, f0 = V)
Answer['X'] = np.dot(V,V)
for p in range(self.FF.np):
Answer['G'][p] = 2*np.dot(V, dV[p,:])
for q in range(self.FF.np):
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer
def get(self, mvals, AGrad=False, AHess=False):
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
self.PrintDict = OrderedDict()
self.RMSDDict = OrderedDict()
#pool = Pool(processes=4)
def compute(mvals_):
# This function has automatically assigned variable names from the interaction master file
# Thus, all variable names in here are protected using an underscore.
self.FF.make(mvals_)
VectorD_ = []
# The following code was odified by Chengwen Liu to accelarate the tinker analyze and optimize jobs
def Energy_RMSD(systems):
tinkerhome = os.environ["TINKERPATH"]
f1 = open("runAna.sh", "w")
f2 = open("runMin.sh", "w")
i = 0
for sys_ in systems:
opts = systems[sys_]
optimize = (opts['optimize'] if 'optimize' in opts else False)
if not optimize:
if (i+1)%24 == 0:
cmd = "rm -f %s.out\n%s/analyze %s.xyz -k %s.key E > %s.out \n"%(sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
else:
cmd = "rm -f %s.out\n%s/analyze %s.xyz -k %s.key E > %s.out & \n"%(sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
f1.write(cmd)
else:
if (i+1)%24 == 0:
cmd = "rm -f %s.xyz_2 %s.out \n%s/optimize %s.xyz -k %s.key 0.0001 > %s.out \n"%(sys_, sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
else:
cmd = "rm -f %s.xyz_2 %s.out \n%s/optimize %s.xyz -k %s.key 0.0001 > %s.out & \n"%(sys_, sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
f2.write(cmd)
f1.write("wait\n")
f2.write("wait\n")
f1.close()
f2.close()
os.system("sh runAna.sh")
os.system("sh runMin.sh")
for sys_ in systems:
while not os.path.isfile(os.path.join(os.getcwd(), sys_ + ".out")):
time.sleep(1.0)
Es = {}
RMSDs = {}
for sys_ in systems:
energ = 0.0
rmsd = 0.0
for line in open("%s.out"%sys_).readlines():
if "Total Potential Energy" in line:
energ = float(line.split()[-2].replace('D','e'))
Es[sys_] = energ
RMSDs[sys_] = 0.0
if "Final Function Value :" in line:
energ = float(line.split()[-1].replace('D','e'))
Es[sys_] = energ
M1 = Molecule("%s.xyz" % sys_, ftype="tinker")
M2 = Molecule("%s.xyz_2" % sys_, ftype="tinker")
M1 += M2
RMSDs[sys_] = M1.ref_rmsd(0)[1]
return Es,RMSDs
Es, RMSDs = Energy_RMSD(self.sys_opts)
for sys_ in self.sys_opts:
Energy_ = Es[sys_]
RMSD_ = RMSDs[sys_]
exec("%s = Energy_" % sys_) in locals()
RMSDNrm_ = RMSD_ / self.rmsd_denom
w_ = self.sys_opts[sys_]['rmsd_weight'] if 'rmsd_weight' in self.sys_opts[sys_] else 1.0
VectorD_.append(np.sqrt(w_)*RMSDNrm_)
if not in_fd() and RMSD_ != 0.0:
self.RMSDDict[sys_] = "% 9.3f % 12.5f" % (RMSD_, w_*RMSDNrm_**2)
VectorE_ = []
for inter_ in self.inter_opts:
Calculated_ = eval(self.inter_opts[inter_]['equation'])
Reference_ = self.inter_opts[inter_]['reference_physical']
Delta_ = Calculated_ - Reference_
Denom_ = self.energy_denom
if self.cauchy:
Divisor_ = np.sqrt(Denom_**2 + Reference_**2)
elif self.attenuate:
if Reference_ < Denom_:
Divisor_ = Denom_
else:
Divisor_ = np.sqrt(Denom_**2 + (Reference_-Denom_)**2)
else:
Divisor_ = Denom_
DeltaNrm_ = Delta_ / Divisor_
w_ = self.inter_opts[inter_]['weight'] if 'weight' in self.inter_opts[inter_] else 1.0
VectorE_.append(np.sqrt(w_)*DeltaNrm_)
if not in_fd():
self.PrintDict[inter_] = "% 9.3f % 9.3f % 9.3f % 12.5f" % (Calculated_, Reference_, Delta_, w_*DeltaNrm_**2)
# print "%-20s" % inter_, "Calculated:", Calculated_, "Reference:", Reference_, "Delta:", Delta_, "DeltaNrm:", DeltaNrm_
# The return value is an array of normalized interaction energy differences.
if not in_fd():
self.rmsd_part = np.dot(np.array(VectorD_),np.array(VectorD_))
if len(VectorE_) > 0:
self.energy_part = np.dot(np.array(VectorE_),np.array(VectorE_))
else:
self.energy_part = 0.0
if len(VectorE_) > 0 and len(VectorD_) > 0:
return np.array(VectorD_ + VectorE_)
elif len(VectorD_) > 0:
return np.array(VectorD_)
elif len(VectorE_) > 0:
return np.array(VectorE_)
V = compute(mvals)
dV = np.zeros((self.FF.np,len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(compute, mvals, p), h = self.h, f0 = V)
Answer['X'] = np.dot(V,V)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(V, dV[p,:])
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer
def submit_jobs(self, mvals, AGrad=True, AHess=True):
# This routine is called by Objective.stage() will run before "get".
# It submits the jobs to the Work Queue and the stage() function will wait for jobs to complete.
#
self.tdir = os.getcwd()
wq = getWorkQueue()
if wq == None:
return
def submit_psi(this_apath, mname, these_mvals):
""" Create a grid file and a psi4 input file in the absolute path and submit it to the work queue. """
cwd = os.getcwd()
if not os.path.exists(this_apath) : os.makedirs(this_apath)
os.chdir(this_apath)
self.FF.make(these_mvals)
o = wopen('objective.dat')
for line in self.objfiles[d]:
s = line.split()
if len(s) > 2 and s[0] == 'path' and s[1] == '=':
print >> o, "path = '%s'" % os.getcwd()
elif len(s) > 2 and s[0] == 'set' and s[1] == 'objective_path':
print >> o, "opath = '%s'" % os.getcwd()
print >> o, "set objective_path $opath"
else:
print >> o, line,
o.close()
os.system("rm -f objective.out")
if wq == None:
logger.info("There is no Work Queue!!!\n")
sys.exit()
else:
input_files = [(os.path.join(this_apath, i), i) for i in glob.glob("*")]
# input_files += [(os.path.join(self.tgtdir,d,"build.dat"), "build.dat")]
input_files += [(os.path.join(os.path.split(__file__)[0],"data","run_psi_rdvr3_objective.sh"), "run_psi_rdvr3_objective.sh")]
logger.info("\r")
queue_up_src_dest(wq,"sh run_psi_rdvr3_objective.sh %s &> run_psi_rdvr3_objective.log" % mname,
input_files=input_files,
output_files=[(os.path.join(this_apath, i),i) for i in ["run_psi_rdvr3_objective.log", "output.dat"]], verbose=False)
os.chdir(cwd)
for d in self.objfiles:
logger.info("\rNow working on" + str(d) + 50*' ' + '\r')
odir = os.path.join(os.getcwd(),d)
#if os.path.exists(odir):
# shutil.rmtree(odir)
if not os.path.exists(odir): os.makedirs(odir)
apath = os.path.join(odir, "current")
submit_psi(apath, d, mvals)
for p in range(self.FF.np):
def subjob(mvals_,h):
apath = os.path.join(odir, str(p), str(h))
submit_psi(apath, d, mvals_)
#logger.info("Will set up a job for %s, parameter %i\n" % (d, p))
return 0.0
if self.callderivs[d][p]:
if AHess:
f12d3p(fdwrap(subjob, mvals, p, h=self.h), h = self.h, f0 = 0.0)
elif AGrad:
if self.bidirect:
f12d3p(fdwrap(subjob, mvals, p, h=self.h), h = self.h, f0 = 0.0)
else:
f1d2p(fdwrap(subjob, mvals, p, h=self.h), h = self.h, f0 = 0.0)
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 04-17-2013
This subroutine builds the objective function from Psi4.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
Answer = {}
Fac = 1000000
n = len(mvals)
X = 0.0
G = np.zeros(n)
H = np.zeros((n,n))
pvals = self.FF.make(mvals)
self.tdir = os.getcwd()
self.objd = OrderedDict()
self.gradd = OrderedDict()
self.hdiagd = OrderedDict()
wq = getWorkQueue()
def fdwrap2(func,mvals0,pidx,qidx,key=None,**kwargs):
def func2(arg1,arg2):
mvals = list(mvals0)
mvals[pidx] += arg1
mvals[qidx] += arg2
logger.info("\rfdwrap2:" + func.__name__ + "[%i] = % .1e , [%i] = % .1e" % (pidx, arg1, qidx, arg2) + ' '*50)
if key != None:
return func(mvals,**kwargs)[key]
else:
return func(mvals,**kwargs)
return func2
def f2d5p(f, h):
fpp, fpm, fmp, fmm = [f(i*h,j*h) for i,j in [(1,1),(1,-1),(-1,1),(-1,-1)]]
fpp = (fpp-fpm-fmp+fmm)/(4*h*h)
return fpp
def f2d4p(f, h, f0 = None):
if f0 == None:
fpp, fp0, f0p, f0 = [f(i*h,j*h) for i,j in [(1,1),(1,0),(0,1),(0,0)]]
else:
fpp, fp0, f0p = [f(i*h,j*h) for i,j in [(1,1),(1,0),(0,1)]]
fpp = (fpp-fp0-f0p+f0)/(h*h)
return fpp
for d in self.objfiles:
logger.info("\rNow working on" + str(d) + 50*' ' + '\r')
if wq == None:
x = self.driver(mvals, d)
grad = np.zeros(n)
hdiag = np.zeros(n)
hess = np.zeros((n,n))
apath = os.path.join(self.tdir, d, "current")
x = float(open(os.path.join(apath,'objective.out')).readlines()[0].split()[1])*self.factor
for p in range(self.FF.np):
if self.callderivs[d][p]:
def reader(mvals_,h):
apath = os.path.join(self.tdir, d, str(p), str(h))
answer = float(open(os.path.join(apath,'objective.out')).readlines()[0].split()[1])*self.factor
return answer
if AHess:
if wq != None:
apath = os.path.join(self.tdir, d, "current")
x = float(open(os.path.join(apath,'objective.out')).readlines()[0].split()[1])*self.factor
grad[p], hdiag[p] = f12d3p(fdwrap(reader, mvals, p, h=self.h), h = self.h, f0 = x)
else:
grad[p], hdiag[p] = f12d3p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
hess[p,p] = hdiag[p]
elif AGrad:
if self.bidirect:
if wq != None:
apath = os.path.join(self.tdir, d, "current")
x = float(open(os.path.join(apath,'objective.out')).readlines()[0].split()[1])*self.factor
grad[p], _ = f12d3p(fdwrap(reader, mvals, p, h=self.h), h = self.h, f0 = x)
else:
grad[p], _ = f12d3p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
else:
if wq != None:
# Since the calculations are submitted as 3-point finite difference, this part of the code
# actually only reads from half of the completed calculations.
grad[p] = f1d2p(fdwrap(reader, mvals, p, h=self.h), h = self.h, f0 = x)
else:
grad[p] = f1d2p(fdwrap(self.driver, mvals, p, d=d), h = self.h, f0 = x)
self.objd[d] = x
self.gradd[d] = grad
self.hdiagd[d] = hdiag
X += x
G += grad
#H += np.diag(hdiag)
H += hess
if not in_fd():
self.objective = X
self.objvals = self.objd
# print self.objd
# print self.gradd
# print self.hdiagd
if float('Inf') in pvals:
return {'X' : 1e10, 'G' : G, 'H' : H}
return {'X' : X, 'G' : G, 'H' : H}
def func1(arg):
mvals = list(mvals0)
mvals[pidxj] += arg
return f1d5p(fdwrap(self.Objective.Full,mvals,pidxi,'X',Order=0),self.h)
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {
'X': 0.0,
'G': np.zeros(self.FF.np),
'H': np.zeros((self.FF.np, self.FF.np))
}
# If the weight is zero, turn all derivatives off.
if (self.weight == 0.0):
AGrad = False
AHess = False
def callM(mvals_, dielectric=False):
logger.info("\r")
pvals = self.FF.make(mvals_)
return self.engine.interaction_energy(self.select1, self.select2)
logger.info("Executing\r")
emm = callM(mvals)
D = emm - self.eqm
dV = np.zeros((self.FF.np, len(emm)))
if self.writelevel > 0:
# Dump interaction energies to disk.
np.savetxt('M.txt', emm)
np.savetxt('Q.txt', self.eqm)
import pickle
pickle.dump((self.name, self.label, self.prefactor, self.eqm, emm),
open("qm_vs_mm.p", 'w'))
# select the qm and mm data that has >0 weight to plot
qm_data, mm_data = [], []
for i in range(len(self.eqm)):
if self.prefactor[i] != 0:
qm_data.append(self.eqm[i])
mm_data.append(emm[i])
plot_interaction_qm_vs_mm(qm_data,
mm_data,
title="Interaction Energy " + self.name)
# Do the finite difference derivative.
if AGrad or AHess:
for p in self.pgrad:
dV[p, :], _ = f12d3p(fdwrap(callM, mvals, p), h=self.h, f0=emm)
# Create the force field one last time.
pvals = self.FF.make(mvals)
Answer['X'] = np.dot(self.prefactor * D / self.divisor,
D / self.divisor)
for p in self.pgrad:
Answer['G'][p] = 2 * np.dot(self.prefactor * D / self.divisor,
dV[p, :] / self.divisor)
for q in self.pgrad:
Answer['H'][p, q] = 2 * np.dot(
self.prefactor * dV[p, :] / self.divisor,
dV[q, :] / self.divisor)
if not in_fd():
self.emm = emm
self.objective = Answer['X']
## QYD: try to clean up OpenMM engine.simulation objects to free up GPU memory
try:
if self.engine.name == 'openmm':
if hasattr(self.engine, 'simulation'):
del self.engine.simulation
if hasattr(self.engine, 'A'): del self.engine.A
if hasattr(self.engine, 'B'): del self.engine.B
except:
pass
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
# If the weight is zero, turn all derivatives off.
if (self.weight == 0.0):
AGrad = False
AHess = False
def callM(mvals_, dielectric=False):
logger.info("\r")
pvals = self.FF.make(mvals_)
return self.engine.interaction_energy(self.select1, self.select2)
logger.info("Executing\r")
emm = callM(mvals)
D = emm - self.eqm
dV = np.zeros((self.FF.np,len(emm)))
if self.writelevel > 0:
# Dump interaction energies to disk.
np.savetxt('M.txt',emm)
np.savetxt('Q.txt',self.eqm)
import pickle
pickle.dump((self.name, self.label, self.prefactor, self.eqm, emm), open("qm_vs_mm.p",'w'))
# select the qm and mm data that has >0 weight to plot
qm_data, mm_data = [], []
for i in xrange(len(self.eqm)):
if self.prefactor[i] != 0:
qm_data.append(self.eqm[i])
mm_data.append(emm[i])
plot_interaction_qm_vs_mm(qm_data, mm_data, title="Interaction Energy "+self.name)
# Do the finite difference derivative.
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = emm)
# Create the force field one last time.
pvals = self.FF.make(mvals)
Answer['X'] = np.dot(self.prefactor*D/self.divisor,D/self.divisor)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(self.prefactor*D/self.divisor, dV[p,:]/self.divisor)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(self.prefactor*dV[p,:]/self.divisor, dV[q,:]/self.divisor)
if not in_fd():
self.emm = emm
self.objective = Answer['X']
## QYD: try to clean up OpenMM engine.simulation objects to free up GPU memory
try:
if self.engine.name == 'openmm':
if hasattr(self.engine, 'simulation'): del self.engine.simulation
if hasattr(self.engine, 'A'): del self.engine.A
if hasattr(self.engine, 'B'): del self.engine.B
except:
pass
return Answer
def get(self, mvals, AGrad=False, AHess=False):
""" Evaluate objective function. """
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
def compute(mvals_):
self.FF.make(mvals_)
Xx, Gx, Hx, freqs, normal_modes, M_opt = self.hessian_driver()
# convert into internal hessian
Xx *= 1/ Bohr2nm
Gx *= Bohr2nm/ Hartree2kJmol
Hx *= Bohr2nm**2/ Hartree2kJmol
Hq = self.IC.calcHess(Xx, Gx, Hx)
compute.Hq_flat = Hq.flatten()
compute.freqs = freqs
compute.normal_modes = normal_modes
compute.M_opt = M_opt
diff = Hq - self.ref_Hq
return (np.sqrt(self.wts)/self.denom) * (compute.Hq_flat - self.ref_Hq_flat)
V = compute(mvals)
Answer['X'] = np.dot(V,V) * len(compute.freqs) # HJ: len(compute.freqs) is multiplied to match the scale of X2 with vib freq target X2
# compute gradients and hessian
dV = np.zeros((self.FF.np,len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(compute, mvals, p), h = self.h, f0 = V)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(V, dV[p,:]) * len(compute.freqs)
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:]) * len(compute.freqs)
if not in_fd():
self.Hq_flat = compute.Hq_flat
self.Hq = self.Hq_flat.reshape(self.ref_Hq.shape)
self.objective = Answer['X']
self.FF.make(mvals)
if self.writelevel > 0:
# 1. write HessianCompare.txt
hessian_comparison = np.array([
self.ref_Hq_flat,
compute.Hq_flat,
compute.Hq_flat - self.ref_Hq_flat,
np.sqrt(self.wts)/self.denom
]).T
np.savetxt("HessianCompare.txt", hessian_comparison, header="%11s %12s %12s %12s" % ("QMHessian", "MMHessian", "Delta(MM-QM)", "Weight"), fmt="% 12.6e")
# 2. rearrange MM vibrational frequencies using overlap between normal modes in redundant internal coordinates
ref_int_normal_modes = self.calc_int_normal_mode(self.ref_xyz, self.ref_eigvecs)
int_normal_modes = self.calc_int_normal_mode(np.array(compute.M_opt.xyzs[0]), compute.normal_modes)
a = np.array([[(1.0-np.abs(np.dot(v1/np.linalg.norm(v1),v2/np.linalg.norm(v2)))) for v2 in int_normal_modes] for v1 in ref_int_normal_modes])
row, c2r = optimize.linear_sum_assignment(a)
# old arrangement method, which uses overlap between mass weighted vibrational modes in cartesian coordinates
# a = np.array([[(1.0-self.vib_overlap(v1, v2)) for v2 in compute.normal_modes] for v1 in self.ref_eigvecs])
# row, c2r = optimize.linear_sum_assignment(a)
freqs_rearr = compute.freqs[c2r]
normal_modes_rearr = compute.normal_modes[c2r]
# 3. Save rearranged frequencies and normal modes into a file for post-analysis
with open('mm_vdata.txt', 'w') as outfile:
outfile.writelines('%s\n' % line for line in compute.M_opt.write_xyz([0]))
outfile.write('\n')
for freq, normal_mode in zip(freqs_rearr, normal_modes_rearr):
outfile.write(f'{freq}\n')
for nx, ny, nz in normal_mode:
outfile.write(f'{nx:13.4f} {ny:13.4f} {nz:13.4f}\n')
outfile.write('\n')
outfile.close()
# 4. draw a scatter plot of vibrational frequencies and an overlap matrix of normal modes in cartessian coordinates
draw_vibfreq_scatter_plot_n_overlap_matrix(self.name, self.engine, self.ref_eigvals, self.ref_eigvecs, freqs_rearr, normal_modes_rearr)
return Answer
def get(self, mvals, AGrad=False, AHess=False):
Answer = {'X':0.0, 'G':np.zeros(self.FF.np), 'H':np.zeros((self.FF.np, self.FF.np))}
self.PrintDict = OrderedDict()
self.RMSDDict = OrderedDict()
EnergyDict = OrderedDict()
#pool = Pool(processes=4)
def compute(mvals_):
# This function has automatically assigned variable names from the interaction master file
# Thus, all variable names in here are protected using an underscore.
self.FF.make(mvals_)
VectorD_ = []
for sys_ in self.sys_opts:
Energy_, RMSD_ = self.system_driver(sys_)
# Energies are stored in a dictionary.
EnergyDict[sys_] = Energy_
RMSDNrm_ = RMSD_ / self.rmsd_denom
w_ = self.sys_opts[sys_]['rmsd_weight'] if 'rmsd_weight' in self.sys_opts[sys_] else 1.0
VectorD_.append(np.sqrt(w_)*RMSDNrm_)
if not in_fd() and RMSD_ != 0.0:
self.RMSDDict[sys_] = "% 9.3f % 12.5f" % (RMSD_, w_*RMSDNrm_**2)
VectorE_ = []
for inter_ in self.inter_opts:
def encloseInDictionary(matchobj):
return 'EnergyDict["' + matchobj.group(0)+'"]'
# Here we need to evaluate a mathematical expression of the stored variables in EnergyDict.
# We start by enclosing every variable in EnergyDict[""] and then calling eval on it.
evalExpr = re.sub('[A-Za-z_][A-Za-z0-9_]*', encloseInDictionary, self.inter_opts[inter_]['equation'])
Calculated_ = eval(evalExpr)
Reference_ = self.inter_opts[inter_]['reference_physical']
Delta_ = Calculated_ - Reference_
Denom_ = self.energy_denom
if self.cauchy:
Divisor_ = np.sqrt(Denom_**2 + Reference_**2)
elif self.attenuate:
if Reference_ < Denom_:
Divisor_ = Denom_
else:
Divisor_ = np.sqrt(Denom_**2 + (Reference_-Denom_)**2)
else:
Divisor_ = Denom_
DeltaNrm_ = Delta_ / Divisor_
w_ = self.inter_opts[inter_]['weight'] if 'weight' in self.inter_opts[inter_] else 1.0
VectorE_.append(np.sqrt(w_)*DeltaNrm_)
if not in_fd():
self.PrintDict[inter_] = "% 9.3f % 9.3f % 9.3f % 12.5f" % (Calculated_, Reference_, Delta_, w_*DeltaNrm_**2)
# print "%-20s" % inter_, "Calculated:", Calculated_, "Reference:", Reference_, "Delta:", Delta_, "DeltaNrm:", DeltaNrm_
# The return value is an array of normalized interaction energy differences.
if not in_fd():
self.rmsd_part = np.dot(np.array(VectorD_),np.array(VectorD_))
if len(VectorE_) > 0:
self.energy_part = np.dot(np.array(VectorE_),np.array(VectorE_))
else:
self.energy_part = 0.0
if len(VectorE_) > 0 and len(VectorD_) > 0:
return np.array(VectorD_ + VectorE_)
elif len(VectorD_) > 0:
return np.array(VectorD_)
elif len(VectorE_) > 0:
return np.array(VectorE_)
V = compute(mvals)
dV = np.zeros((self.FF.np,len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p,:], _ = f12d3p(fdwrap(compute, mvals, p), h = self.h, f0 = V)
Answer['X'] = np.dot(V,V)
for p in self.pgrad:
Answer['G'][p] = 2*np.dot(V, dV[p,:])
for q in self.pgrad:
Answer['H'][p,q] = 2*np.dot(dV[p,:], dV[q,:])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer
def property_derivatives(engine, FF, mvals, h, pgrad, kT, property_driver, property_kwargs, AGrad=True):
"""
Function for double-checking property derivatives. This function is called to perform
a more explicit numerical derivative of the property, rather than going through the
fluctuation formula. It takes longer and is potentially less precise, which means
it's here mainly as a sanity check.
@param[in] mvals Mathematical parameter values
@param[in] h Finite difference step size
@param[in] phase The phase (liquid, gas) to perform the calculation on
@param[in] property_driver The function that calculates the property
@param[in] property_driver A dictionary of arguments that goes into calculating the property
@param[in] AGrad Switch to turn derivatives on or off; if off, return all zeros
@return G First derivative of the property
"""
G = np.zeros(FF.np)
if not AGrad:
return G
def energy_driver(mvals_):
FF.make(mvals_)
return engine.energy_dipole()
ED0 = energy_driver(mvals)
E0 = ED0[:,0]
D0 = ED0[:,1:]
P0 = property_driver(None, **property_kwargs)
if 'h_' in property_kwargs:
H0 = property_kwargs['h_'].copy()
for i in pgrad:
logger.info("%s\n" % (FF.plist[i] + " "*30))
ED1 = fdwrap(energy_driver,mvals,i)(h)
E1 = ED1[:,0]
D1 = ED1[:,1:]
b = np.exp(-(E1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (E1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = D1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
logger.warn("Warning: Effective number of snapshots: % .1f (out of %i)\n" % (InfoContent, len(E0)))
P1 = property_driver(b=b,**property_kwargs)
EDM1 = fdwrap(energy_driver,mvals,i)(-h)
EM1 = EDM1[:,0]
DM1 = EDM1[:,1:]
b = np.exp(-(EM1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (EM1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = DM1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
logger.warn("Warning: Effective number of snapshots: % .1f (out of %i)\n" % (InfoContent, len(E0)))
PM1 = property_driver(b=b,**property_kwargs)
G[i] = (P1-PM1)/(2*h)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy()
if 'd_' in property_kwargs:
property_kwargs['d_'] = D0.copy()
return G
def get(self, mvals, AGrad=False, AHess=False):
Answer = {
'X': 0.0,
'G': np.zeros(self.FF.np),
'H': np.zeros((self.FF.np, self.FF.np))
}
self.PrintDict = OrderedDict()
self.RMSDDict = OrderedDict()
EnergyDict = OrderedDict()
#pool = Pool(processes=4)
def compute(mvals_):
# This function has automatically assigned variable names from the interaction master file
# Thus, all variable names in here are protected using an underscore.
self.FF.make(mvals_)
VectorD_ = []
for sys_ in self.sys_opts:
Energy_, RMSD_ = self.system_driver(sys_)
# Energies are stored in a dictionary.
EnergyDict[sys_] = Energy_
RMSDNrm_ = RMSD_ / self.rmsd_denom
w_ = self.sys_opts[sys_][
'rmsd_weight'] if 'rmsd_weight' in self.sys_opts[
sys_] else 1.0
VectorD_.append(np.sqrt(w_) * RMSDNrm_)
if not in_fd() and RMSD_ != 0.0:
self.RMSDDict[sys_] = "% 9.3f % 12.5f" % (RMSD_,
w_ * RMSDNrm_**2)
VectorE_ = []
for inter_ in self.inter_opts:
def encloseInDictionary(matchobj):
return 'EnergyDict["' + matchobj.group(0) + '"]'
# Here we need to evaluate a mathematical expression of the stored variables in EnergyDict.
# We start by enclosing every variable in EnergyDict[""] and then calling eval on it.
evalExpr = re.sub('[A-Za-z_][A-Za-z0-9_]*',
encloseInDictionary,
self.inter_opts[inter_]['equation'])
Calculated_ = eval(evalExpr)
Reference_ = self.inter_opts[inter_]['reference_physical']
Delta_ = Calculated_ - Reference_
Denom_ = self.energy_denom
if self.cauchy:
Divisor_ = np.sqrt(Denom_**2 + Reference_**2)
elif self.attenuate:
if Reference_ < Denom_:
Divisor_ = Denom_
else:
Divisor_ = np.sqrt(Denom_**2 +
(Reference_ - Denom_)**2)
else:
Divisor_ = Denom_
DeltaNrm_ = Delta_ / Divisor_
w_ = self.inter_opts[inter_][
'weight'] if 'weight' in self.inter_opts[inter_] else 1.0
VectorE_.append(np.sqrt(w_) * DeltaNrm_)
if not in_fd():
self.PrintDict[inter_] = "% 9.3f % 9.3f % 9.3f % 12.5f" % (
Calculated_, Reference_, Delta_, w_ * DeltaNrm_**2)
# print "%-20s" % inter_, "Calculated:", Calculated_, "Reference:", Reference_, "Delta:", Delta_, "DeltaNrm:", DeltaNrm_
# The return value is an array of normalized interaction energy differences.
if not in_fd():
self.rmsd_part = np.dot(np.array(VectorD_), np.array(VectorD_))
if len(VectorE_) > 0:
self.energy_part = np.dot(np.array(VectorE_),
np.array(VectorE_))
else:
self.energy_part = 0.0
if len(VectorE_) > 0 and len(VectorD_) > 0:
return np.array(VectorD_ + VectorE_)
elif len(VectorD_) > 0:
return np.array(VectorD_)
elif len(VectorE_) > 0:
return np.array(VectorE_)
V = compute(mvals)
dV = np.zeros((self.FF.np, len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p, :], _ = f12d3p(fdwrap(compute, mvals, p), h=self.h, f0=V)
Answer['X'] = np.dot(V, V)
for p in self.pgrad:
Answer['G'][p] = 2 * np.dot(V, dV[p, :])
for q in self.pgrad:
Answer['H'][p, q] = 2 * np.dot(dV[p, :], dV[q, :])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer
def property_derivatives(engine, FF, mvals, h, pgrad, kT, property_driver, property_kwargs, AGrad=True):
"""
Function for double-checking property derivatives. This function is called to perform
a more explicit numerical derivative of the property, rather than going through the
fluctuation formula. It takes longer and is potentially less precise, which means
it's here mainly as a sanity check.
@param[in] mvals Mathematical parameter values
@param[in] h Finite difference step size
@param[in] phase The phase (liquid, gas) to perform the calculation on
@param[in] property_driver The function that calculates the property
@param[in] property_driver A dictionary of arguments that goes into calculating the property
@param[in] AGrad Switch to turn derivatives on or off; if off, return all zeros
@return G First derivative of the property
"""
G = np.zeros(FF.np)
if not AGrad:
return G
def energy_driver(mvals_):
FF.make(mvals_)
return engine.energy_dipole()
ED0 = energy_driver(mvals)
E0 = ED0[:,0]
D0 = ED0[:,1:]
P0 = property_driver(None, **property_kwargs)
if 'h_' in property_kwargs:
H0 = property_kwargs['h_'].copy()
for i in pgrad:
logger.info("%s\n" % (FF.plist[i] + " "*30))
ED1 = fdwrap(energy_driver,mvals,i)(h)
E1 = ED1[:,0]
D1 = ED1[:,1:]
b = np.exp(-(E1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (E1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = D1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
logger.warn("Warning: Effective number of snapshots: % .1f (out of %i)\n" % (InfoContent, len(E0)))
P1 = property_driver(b=b,**property_kwargs)
EDM1 = fdwrap(energy_driver,mvals,i)(-h)
EM1 = EDM1[:,0]
DM1 = EDM1[:,1:]
b = np.exp(-(EM1-E0)/kT)
b /= np.sum(b)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy() + (EM1-E0)
if 'd_' in property_kwargs:
property_kwargs['d_'] = DM1.copy()
S = -1*np.dot(b,np.log(b))
InfoContent = np.exp(S)
if InfoContent / len(E0) < 0.1:
logger.warn("Warning: Effective number of snapshots: % .1f (out of %i)\n" % (InfoContent, len(E0)))
PM1 = property_driver(b=b,**property_kwargs)
G[i] = (P1-PM1)/(2*h)
if 'h_' in property_kwargs:
property_kwargs['h_'] = H0.copy()
if 'd_' in property_kwargs:
property_kwargs['d_'] = D0.copy()
return G
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 05-30-2012
This subroutine builds the objective function (and optionally
its derivatives) from a general software.
This subroutine interfaces with simulation software 'drivers'.
The driver is expected to give exact values, fitting values, and weights.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
global LAST_MVALS, CHECK_BASIS
# print mvals
# print LAST_MVALS
# print mvals == LAST_MVALS
if LAST_MVALS is None or not (mvals == LAST_MVALS).all():
CHECK_BASIS = False
else:
CHECK_BASIS = False
Answer = {}
Fac = 1000000
## Dictionary for derivative terms
dM = {}
# Create the new force field!!
NP = len(mvals)
G = np.zeros(NP)
H = np.zeros((NP,NP))
pvals = self.FF.make(mvals)
if float('Inf') in pvals:
return {'X' : 1e10, 'G' : G, 'H' : H}
Ans = self.driver()
W = Ans[:,2]
M = Ans[:,1]
Q = Ans[:,0]
D = M - Q
self.MAQ = np.mean(np.abs(Q))
ns = len(M)
# Wrapper to the driver, which returns just the part that changes.
def callM(mvals_):
self.FF.make(mvals_)
Ans2 = self.driver()
M_ = Ans2[:,1]
D_ = M_ - Q
return Ans2[:,1]
if AGrad:
# Leaving comment here if we want to reintroduce second deriv someday.
# dM[p,:], ddM[p,:] = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = M)
xgrad = []
for p in self.pgrad:
dM_arr = f1d2p(fdwrap(callM, mvals, p), h = self.h, f0 = M)
if np.max(np.abs(dM_arr)) == 0.0 and (not self.evaluated):
logger.info("\r Simulation %s will skip over parameter %i in subsequent steps\n" % (self.name, p))
xgrad.append(p)
else:
dM[p] = dM_arr.copy()
for p in xgrad:
self.pgrad.remove(p)
Objective = np.dot(W, D**2) * Fac
if AGrad:
for p in self.pgrad:
G[p] = 2 * np.dot(W, D*dM[p])
if not AHess: continue
H[p, p] = 2 * np.dot(W, dM[p]**2)
for q in range(p):
if q not in self.pgrad: continue
GNP = 2 * np.dot(W, dM[p] * dM[q])
H[q,p] = GNP
H[p,q] = GNP
G *= Fac
H *= Fac
Answer = {'X':Objective, 'G':G, 'H':H}
if not in_fd():
self.D = D
self.objective = Answer['X']
LAST_MVALS = mvals.copy()
return Answer
def get(self, mvals, AGrad=False, AHess=False):
"""
LPW 05-30-2012
This subroutine builds the objective function (and optionally
its derivatives) from a general software.
This subroutine interfaces with simulation software 'drivers'.
The driver is expected to give exact values, fitting values, and weights.
@param[in] mvals Mathematical parameter values
@param[in] AGrad Switch to turn on analytic gradient
@param[in] AHess Switch to turn on analytic Hessian
@return Answer Contribution to the objective function
"""
global LAST_MVALS, CHECK_BASIS
# print mvals
# print LAST_MVALS
# print mvals == LAST_MVALS
if LAST_MVALS is None or not (mvals == LAST_MVALS).all():
CHECK_BASIS = False
else:
CHECK_BASIS = False
Answer = {}
Fac = 1000000
## Dictionary for derivative terms
dM = {}
# Create the new force field!!
NP = len(mvals)
G = np.zeros(NP)
H = np.zeros((NP, NP))
pvals = self.FF.make(mvals)
if float('Inf') in pvals:
return {'X': 1e10, 'G': G, 'H': H}
Ans = self.driver()
W = Ans[:, 2]
M = Ans[:, 1]
Q = Ans[:, 0]
D = M - Q
self.MAQ = np.mean(np.abs(Q))
ns = len(M)
# Wrapper to the driver, which returns just the part that changes.
def callM(mvals_):
self.FF.make(mvals_)
Ans2 = self.driver()
M_ = Ans2[:, 1]
D_ = M_ - Q
return Ans2[:, 1]
if AGrad:
# Leaving comment here if we want to reintroduce second deriv someday.
# dM[p,:], ddM[p,:] = f12d3p(fdwrap(callM, mvals, p), h = self.h, f0 = M)
xgrad = []
for p in self.pgrad:
dM_arr = f1d2p(fdwrap(callM, mvals, p), h=self.h, f0=M)
if np.max(np.abs(dM_arr)) == 0.0 and (not self.evaluated):
logger.info(
"\r Simulation %s will skip over parameter %i in subsequent steps\n"
% (self.name, p))
xgrad.append(p)
else:
dM[p] = dM_arr.copy()
for p in xgrad:
self.pgrad.remove(p)
Objective = np.dot(W, D**2) * Fac
if AGrad:
for p in self.pgrad:
G[p] = 2 * np.dot(W, D * dM[p])
if not AHess: continue
H[p, p] = 2 * np.dot(W, dM[p]**2)
for q in range(p):
if q not in self.pgrad: continue
GNP = 2 * np.dot(W, dM[p] * dM[q])
H[q, p] = GNP
H[p, q] = GNP
G *= Fac
H *= Fac
Answer = {'X': Objective, 'G': G, 'H': H}
if not in_fd():
self.D = D
self.objective = Answer['X']
LAST_MVALS = mvals.copy()
return Answer
def get(self, mvals, AGrad=False, AHess=False):
Answer = {
'X': 0.0,
'G': np.zeros(self.FF.np),
'H': np.zeros((self.FF.np, self.FF.np))
}
self.PrintDict = OrderedDict()
# enable self.system_mval_masks (supported by OptGeoTarget_SMIRNOFF)
enable_system_mval_mask = hasattr(self, 'system_mval_masks')
def compute(mvals, p_idx=None):
''' Compute total objective value for each system '''
self.FF.make(mvals)
v_obj_list = []
for sysname, sysopt in self.sys_opts.items():
# ref values of each type
vref_bonds = self.internal_coordinates[sysname]['vref_bonds']
vref_angles = self.internal_coordinates[sysname]['vref_angles']
vref_dihedrals = self.internal_coordinates[sysname][
'vref_dihedrals']
vref_impropers = self.internal_coordinates[sysname][
'vref_impropers']
# counts of each type
n_bonds = len(vref_bonds)
n_angles = len(vref_angles)
n_dihedrals = len(vref_dihedrals)
n_impropers = len(vref_impropers)
# use self.system_mval_masks to skip evaluations when computing gradients
if enable_system_mval_mask and in_fd() and (
p_idx is not None) and (
self.system_mval_masks[sysname][p_idx] == False):
v_obj_list += [0] * (n_bonds + n_angles + n_dihedrals +
n_impropers)
continue
# read denominators from system options
bond_denom = sysopt['bond_denom']
angle_denom = sysopt['angle_denom']
dihedral_denom = sysopt['dihedral_denom']
improper_denom = sysopt['improper_denom']
# inverse demon to be scaling factors, 0 for denom 0
scale_bond = 1.0 / bond_denom if bond_denom != 0 else 0.0
scale_angle = 1.0 / angle_denom if angle_denom != 0 else 0.0
scale_dihedral = 1.0 / dihedral_denom if dihedral_denom != 0 else 0.0
scale_improper = 1.0 / improper_denom if improper_denom != 0 else 0.0
# calculate new internal coordinates
v_ic = self.system_driver(sysname)
# objective contribution from bonds
vtar_bonds = v_ic['bonds']
diff_bond = ((vref_bonds - vtar_bonds) *
scale_bond).tolist() if n_bonds > 0 else []
# objective contribution from angles
vtar_angles = v_ic['angles']
diff_angle = (periodic_diff(vref_angles, vtar_angles, 360) *
scale_angle).tolist() if n_angles > 0 else []
# objective contribution from dihedrals
vtar_dihedrals = v_ic['dihedrals']
diff_dihedral = (
periodic_diff(vref_dihedrals, vtar_dihedrals, 360) *
scale_dihedral).tolist() if n_dihedrals > 0 else []
# objective contribution from improper dihedrals
vtar_impropers = v_ic['impropers']
diff_improper = (
periodic_diff(vref_impropers, vtar_impropers, 360) *
scale_improper).tolist() if n_impropers > 0 else []
# combine objective values into a big result list
sys_obj_list = diff_bond + diff_angle + diff_dihedral + diff_improper
# extend the result v_obj_list by individual terms in this system
v_obj_list += sys_obj_list
# save print string
if not in_fd():
# For printing, we group the RMSD by type
rmsd_bond = compute_rmsd(vref_bonds, vtar_bonds)
rmsd_angle = compute_rmsd(vref_angles,
vtar_angles,
v_periodic=360)
rmsd_dihedral = compute_rmsd(vref_dihedrals,
vtar_dihedrals,
v_periodic=360)
rmsd_improper = compute_rmsd(vref_impropers,
vtar_impropers,
v_periodic=360)
obj_total = sum(v**2 for v in sys_obj_list)
self.PrintDict[sysname] = "% 9.3f % 7.2f % 9.3f % 7.2f % 9.3f % 7.2f % 9.3f % 7.2f %17.3f" % (rmsd_bond, \
bond_denom, rmsd_angle, angle_denom, rmsd_dihedral, dihedral_denom, rmsd_improper, improper_denom, obj_total)
return np.array(v_obj_list, dtype=float)
V = compute(mvals)
Answer['X'] = np.dot(V, V)
# write objective decomposition if wanted
if self.writelevel > 0:
# recover mvals
self.FF.make(mvals)
with open('rmsd_decomposition.txt', 'w') as fout:
for sysname in self.internal_coordinates:
fout.write("\n[ %s ]\n" % sysname)
fout.write('%-25s %15s %15s %15s\n' %
("Internal Coordinate", "Ref QM Value",
"Cur MM Value", "Difference"))
# reference data
sys_data = self.internal_coordinates[sysname]
sys_data['ic_bonds']
# compute all internal coordinate values again
v_ic = self.system_driver(sysname)
for p in ['bonds', 'angles', 'dihedrals', 'impropers']:
fout.write('--- ' + p + ' ---\n')
ic_list = sys_data['ic_' + p]
ref_v = sys_data['vref_' + p]
tar_v = v_ic[p]
# print each value
for ic, v1, v2 in zip(ic_list, ref_v, tar_v):
diff = periodic_diff(
v1, v2,
v_periodic=360) if p != 'bonds' else v1 - v2
fout.write('%-25s %15.5f %15.5f %+15.3e\n' %
(ic, v1, v2, diff))
# compute gradients and hessian
dV = np.zeros((self.FF.np, len(V)))
if AGrad or AHess:
for p in self.pgrad:
dV[p, :], _ = f12d3p(fdwrap(compute, mvals, p, p_idx=p),
h=self.h,
f0=V)
for p in self.pgrad:
Answer['G'][p] = 2 * np.dot(V, dV[p, :])
for q in self.pgrad:
Answer['H'][p, q] = 2 * np.dot(dV[p, :], dV[q, :])
if not in_fd():
self.objective = Answer['X']
self.FF.make(mvals)
return Answer