def __call__(self):
self.center_of_mass_info()
if self.reset_velocities:
self.set_velocities()
self.center_of_mass_info()
self.non_solvent_vxyz = self.vxyz.select(~self.er_data.solvent_sel)
self.non_solvent_weights = self.weights.select(
~self.er_data.solvent_sel)
self.solvent_vxyz = self.vxyz.select(self.er_data.solvent_sel)
self.solvent_weights = self.weights.select(self.er_data.solvent_sel)
#
self.non_solvent_kt = dynamics.kinetic_energy_and_temperature(
self.non_solvent_vxyz, self.non_solvent_weights)
self.solvent_kt = dynamics.kinetic_energy_and_temperature(
self.solvent_vxyz, self.solvent_weights)
self.kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.weights)
if self.stop_cm_motion:
self.stop_global_motion()
self.velocity_rescaling()
self.verlet_leapfrog_integration()
if self.verbose >= 1.0:
self.print_detailed_dynamics_stats()
def verlet_leapfrog_integration(self):
# start verlet_leapfrog_integration loop
for cycle in range(1, self.n_steps + 1, 1):
sites_cart = None
if ([self.stop_at_diff, self.states_collector].count(None) != 2):
sites_cart = self.xray_structure.sites_cart()
if (self.stop_at_diff is not None):
dist = flex.mean(
flex.sqrt((self.sites_cart_start - sites_cart).dot()))
if (dist >= self.stop_at_diff): return
accelerations = self.accelerations()
print_flag = 0
switch = math.modf(float(cycle) / self.n_print)[0]
if ((switch == 0 or cycle == 1 or cycle == self.n_steps)
and self.verbose >= 1):
print_flag = 1
if (self.states_collector is not None):
switch2 = math.modf(float(cycle) / self.n_collect)[0]
if (switch2 == 0 or cycle == 1 or cycle == self.n_steps):
self.states_collector.add(sites_cart=sites_cart)
if (print_flag == 1):
text = "integration step number = %5d" % cycle
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
self.print_dynamics_stat(text)
if (self.stop_cm_motion):
self.center_of_mass_info()
self.stop_global_motion()
# calculate velocities at t+dt/2
dynamics.vxyz_at_t_plus_dt_over_2(self.vxyz, self.atomic_weights,
accelerations, self.tstep)
# calculate the temperature and kinetic energy from new velocities
kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
self.velocity_rescaling()
if (print_flag == 1 and 0):
self.center_of_mass_info()
self.print_dynamics_stat(text)
# do the verlet_leapfrog_integration to get coordinates at t+dt
self.xray_structure.set_sites_cart(
sites_cart=self.xray_structure.sites_cart() +
self.vxyz * self.tstep)
self.xray_structure.apply_symmetry_sites()
# prevent explosions by doing very quick model geometry regularization
if (self.interleaved_minimization and cycle == self.n_steps):
self.run_interleaved_minimization()
kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if (print_flag == 1 and 0):
self.center_of_mass_info()
self.print_dynamics_stat(text)
self.accelerations()
def verlet_leapfrog_integration(self):
# start verlet_leapfrog_integration loop
for cycle in range(1,self.n_steps+1,1):
sites_cart = None
if([self.stop_at_diff,self.states_collector].count(None) != 2):
sites_cart = self.xray_structure.sites_cart()
if(self.stop_at_diff is not None):
dist = flex.mean(flex.sqrt((self.sites_cart_start - sites_cart).dot()))
if(dist >= self.stop_at_diff): return
accelerations = self.accelerations()
print_flag = 0
switch = math.modf(float(cycle)/self.n_print)[0]
if((switch==0 or cycle==1 or cycle==self.n_steps) and self.verbose >= 1):
print_flag = 1
if(self.states_collector is not None):
switch2 = math.modf(float(cycle)/self.n_collect)[0]
if(switch2==0 or cycle==1 or cycle==self.n_steps):
self.states_collector.add(sites_cart = sites_cart)
if(print_flag == 1):
text = "integration step number = %5d"%cycle
self.center_of_mass_info()
kt=dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
self.print_dynamics_stat(text)
if(self.stop_cm_motion):
self.center_of_mass_info()
self.stop_global_motion()
# calculate velocities at t+dt/2
dynamics.vxyz_at_t_plus_dt_over_2(
self.vxyz, self.atomic_weights, accelerations, self.tstep)
# calculate the temperature and kinetic energy from new velocities
kt=dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
self.velocity_rescaling()
if(print_flag == 1 and 0):
self.center_of_mass_info()
self.print_dynamics_stat(text)
# do the verlet_leapfrog_integration to get coordinates at t+dt
self.xray_structure.set_sites_cart(
sites_cart=self.xray_structure.sites_cart() + self.vxyz * self.tstep)
self.xray_structure.apply_symmetry_sites()
# prevent explosions by doing very quick model geometry regularization
if(self.interleaved_minimization and cycle==self.n_steps):
self.run_interleaved_minimization()
kt=dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if(print_flag == 1 and 0):
self.center_of_mass_info()
self.print_dynamics_stat(text)
self.accelerations()
def verlet_leapfrog_integration(self):
# start verlet_leapfrog_integration loop
for self.cycle in range(1, self.n_steps + 1, 1):
if (self.stop_at_diff is not None):
diff = flex.mean(
self.structure_start.distances(other=self.structure))
if (diff >= self.stop_at_diff): return
accelerations = self.accelerations()
if (self.stop_cm_motion):
self.center_of_mass_info()
self.stop_global_motion()
# calculate velocities at t+dt/2
dynamics.vxyz_at_t_plus_dt_over_2(self.vxyz, self.weights,
accelerations, self.tstep)
# calculate the temperature and kinetic energy from new velocities
self.non_solvent_vxyz = self.vxyz.select(~self.er_data.solvent_sel)
self.non_solvent_weights = self.weights.select(
~self.er_data.solvent_sel)
self.solvent_vxyz = self.vxyz.select(self.er_data.solvent_sel)
self.solvent_weights = self.weights.select(
self.er_data.solvent_sel)
#
self.kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.weights)
self.non_solvent_kt = dynamics.kinetic_energy_and_temperature(
self.non_solvent_vxyz, self.non_solvent_weights)
self.solvent_kt = dynamics.kinetic_energy_and_temperature(
self.solvent_vxyz, self.solvent_weights)
#Store sys, solvent, nonsolvet temperatures
if self.er_data is not None:
self.store_temperatures()
self.velocity_rescaling()
if self.verbose >= 1.0:
print('Scale factor : ', self.v_factor, file=self.log)
self.vxyz_length_sq = flex.sqrt(self.vxyz.dot())
print('vxyz_length_sq pst scale', file=self.log)
self.vxyz_length_sq.min_max_mean().show(out=self.log)
# do the verlet_leapfrog_integration to get coordinates at t+dt
self.structure.set_sites_cart(
sites_cart=self.structure.sites_cart() +
self.vxyz * self.tstep)
self.structure.apply_symmetry_sites()
if (self.interleaved_minimization_flag):
self.interleaved_minimization()
self.kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.weights)
if (self.er_data is None):
self.accelerations()
else:
self.er_data.velocities = self.vxyz
def __call__(self):
self.center_of_mass_info()
#print "0:",self.temperature, self.current_temperature
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,
self.atomic_weights)
self.current_temperature = kt.temperature
#print "1:",self.temperature, self.current_temperature
self.ekin = kt.kinetic_energy
if (self.verbose >= 1):
self.print_dynamics_stat(text="restrained dynamics start")
if (self.reset_velocities):
self.set_velocities()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(
self.vxyz, self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if (self.verbose >= 1):
self.print_dynamics_stat(text="set velocities")
if (self.stop_cm_motion):
self.stop_global_motion()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,
self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if (self.verbose >= 1):
self.print_dynamics_stat(text="center of mass motion removed")
self.velocity_rescaling()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,
self.atomic_weights)
self.current_temperature = kt.temperature
#print "2:",self.temperature, self.current_temperature
self.ekin = kt.kinetic_energy
if (self.verbose >= 1):
self.print_dynamics_stat(text="velocities rescaled")
if (self.verbose >= 1):
print("integration starts", file=self.log)
self.verlet_leapfrog_integration()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,
self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if (self.verbose >= 1):
self.print_dynamics_stat(text="after final integration step")
def verlet_leapfrog_integration(self):
# start verlet_leapfrog_integration loop
for self.cycle in range(1, self.n_steps + 1, 1):
if self.stop_at_diff is not None:
diff = flex.mean(self.structure_start.distances(other=self.structure))
if diff >= self.stop_at_diff:
return
accelerations = self.accelerations()
if self.stop_cm_motion:
self.center_of_mass_info()
self.stop_global_motion()
# calculate velocities at t+dt/2
dynamics.vxyz_at_t_plus_dt_over_2(self.vxyz, self.weights, accelerations, self.tstep)
# calculate the temperature and kinetic energy from new velocities
self.non_solvent_vxyz = self.vxyz.select(~self.er_data.solvent_sel)
self.non_solvent_weights = self.weights.select(~self.er_data.solvent_sel)
self.solvent_vxyz = self.vxyz.select(self.er_data.solvent_sel)
self.solvent_weights = self.weights.select(self.er_data.solvent_sel)
#
self.kt = dynamics.kinetic_energy_and_temperature(self.vxyz, self.weights)
self.non_solvent_kt = dynamics.kinetic_energy_and_temperature(
self.non_solvent_vxyz, self.non_solvent_weights
)
self.solvent_kt = dynamics.kinetic_energy_and_temperature(self.solvent_vxyz, self.solvent_weights)
# Store sys, solvent, nonsolvet temperatures
if self.er_data is not None:
self.store_temperatures()
self.velocity_rescaling()
if self.verbose >= 1.0:
print >>self.log, "Scale factor : ", self.v_factor
self.vxyz_length_sq = flex.sqrt(self.vxyz.dot())
print >>self.log, "vxyz_length_sq pst scale"
self.vxyz_length_sq.min_max_mean().show(out=self.log)
# do the verlet_leapfrog_integration to get coordinates at t+dt
self.structure.set_sites_cart(sites_cart=self.structure.sites_cart() + self.vxyz * self.tstep)
self.structure.apply_symmetry_sites()
if self.interleaved_minimization_flag:
self.interleaved_minimization()
self.kt = dynamics.kinetic_energy_and_temperature(self.vxyz, self.weights)
if self.er_data is None:
self.accelerations()
else:
self.er_data.velocities = self.vxyz
def __call__(self):
self.center_of_mass_info()
#print "0:",self.temperature, self.current_temperature
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
#print "1:",self.temperature, self.current_temperature
self.ekin = kt.kinetic_energy
if(self.verbose >= 1):
self.print_dynamics_stat(text="restrained dynamics start")
if(self.reset_velocities):
self.set_velocities()
self.center_of_mass_info()
kt=dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if(self.verbose >= 1):
self.print_dynamics_stat(text="set velocities")
if(self.stop_cm_motion):
self.stop_global_motion()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if(self.verbose >= 1):
self.print_dynamics_stat(text="center of mass motion removed")
self.velocity_rescaling()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
#print "2:",self.temperature, self.current_temperature
self.ekin = kt.kinetic_energy
if(self.verbose >= 1):
self.print_dynamics_stat(text="velocities rescaled")
if(self.verbose >= 1):
print >> self.log, "integration starts"
self.verlet_leapfrog_integration()
self.center_of_mass_info()
kt = dynamics.kinetic_energy_and_temperature(self.vxyz,self.atomic_weights)
self.current_temperature = kt.temperature
self.ekin = kt.kinetic_energy
if(self.verbose >= 1):
self.print_dynamics_stat(text="after final integration step")
def __call__(self):
self.center_of_mass_info()
if self.reset_velocities:
self.set_velocities()
self.center_of_mass_info()
self.non_solvent_vxyz = self.vxyz.select(~self.er_data.solvent_sel)
self.non_solvent_weights = self.weights.select(~self.er_data.solvent_sel)
self.solvent_vxyz = self.vxyz.select(self.er_data.solvent_sel)
self.solvent_weights = self.weights.select(self.er_data.solvent_sel)
#
self.non_solvent_kt = dynamics.kinetic_energy_and_temperature(self.non_solvent_vxyz, self.non_solvent_weights)
self.solvent_kt = dynamics.kinetic_energy_and_temperature(self.solvent_vxyz, self.solvent_weights)
self.kt = dynamics.kinetic_energy_and_temperature(self.vxyz, self.weights)
if self.stop_cm_motion:
self.stop_global_motion()
self.velocity_rescaling()
self.verlet_leapfrog_integration()
if self.verbose >= 1.0:
self.print_detailed_dynamics_stats()
def velocity_rescaling(self):
if self.protein_thermostat and self.er_data is not None:
if self.kt.temperature <= 1.0e-10:
self.v_factor = 1.0
else:
self.v_factor = math.sqrt(self.temperature / self.non_solvent_kt.temperature)
else:
if self.kt.temperature <= 1.0e-10:
self.v_factor = 1.0
else:
self.v_factor = math.sqrt(self.temperature / self.kt.temperature)
self.vyz_vscale_remove = self.vxyz * (1.0 - self.v_factor)
self.kt_vscale_remove = dynamics.kinetic_energy_and_temperature(self.vyz_vscale_remove, self.weights)
self.vxyz = self.vxyz * self.v_factor
def velocity_rescaling(self):
if self.protein_thermostat and self.er_data is not None:
if (self.kt.temperature <= 1.e-10):
self.v_factor = 1.0
else:
self.v_factor = math.sqrt(self.temperature /
self.non_solvent_kt.temperature)
else:
if (self.kt.temperature <= 1.e-10):
self.v_factor = 1.0
else:
self.v_factor = math.sqrt(self.temperature /
self.kt.temperature)
self.vyz_vscale_remove = self.vxyz * (1.0 - self.v_factor)
self.kt_vscale_remove = dynamics.kinetic_energy_and_temperature(
self.vyz_vscale_remove, self.weights)
self.vxyz = self.vxyz * self.v_factor
