# long as the indicator charge is on a heavy atom. TODO
result = resp.eval_ratios('regular',
ratio_limits,
start_charges,
num,
indicator_label,
regular_args,
first_verbose=True)[0]
# RATIO MINIMIZATION
print("\nMinimizing HEAVY ratio. This shouldn't take long.")
# Most arguments here are the same as in the loop with minor changes specific
# to an optimization run (output directory, verbosity)
heavy_args = (start_charges, g.field, path, min_resp_output_path, esp_fn, True)
heavy_min_ratio, heavy_min_ratio_rrms, heavy_charges = resp.minimize_ratio(
'heavy', ratio_values, heavy_result, heavy_args)
if zero_net_charge:
print("Minimizing REGULAR ratio. This shouldn't take long.")
regular_args = (start_charges, g.molecule, g.field)
reg_min_ratio, reg_min_ratio_rrms, reg_charges = resp.minimize_ratio(
'regular', ratio_values, result, regular_args)
shutil.rmtree(min_resp_output_path)
def plot(result_list, heavy, min_ratio, min_ratio_rrms):
fig, ax1 = plt.subplots()
ax1.plot(ratio_values, result_list)
ax2 = ax1.twiny()
ax2.plot(indicator_charge, result_list)
print("\nEvaluating REGULAR ratios. This may take a while.")
regular_args = (g.molecule, g.field)
# Note that indicator charge and ratio values are re-used from the heavy
# version. This is fine for ratio_values. For indicator_charge it's fine as
# long as the indicator charge is on a heavy atom. TODO
result = resp.eval_ratios('regular', ratio_limits, start_charges, num,
indicator_label, regular_args,
first_verbose=True)[0]
# RATIO MINIMIZATION
print("\nMinimizing HEAVY ratio. This shouldn't take long.")
# Most arguments here are the same as in the loop with minor changes specific
# to an optimization run (output directory, verbosity)
heavy_args = (start_charges, g.field, path, min_resp_output_path, esp_fn, True)
heavy_min_ratio, heavy_min_ratio_rrms, heavy_charges = resp.minimize_ratio(
'heavy', ratio_values, heavy_result, heavy_args)
if zero_net_charge:
print("Minimizing REGULAR ratio. This shouldn't take long.")
regular_args = (start_charges, g.molecule, g.field)
reg_min_ratio, reg_min_ratio_rrms, reg_charges = resp.minimize_ratio(
'regular', ratio_values, result, regular_args)
shutil.rmtree(min_resp_output_path)
def plot(result_list, heavy, min_ratio, min_ratio_rrms):
fig, ax1 = plt.subplots()
ax1.plot(ratio_values, result_list)
ax2 = ax1.twiny()
ax2.plot(indicator_charge, result_list)
result, indicator_charge, ratio_values = eval_ratios(
'heavy',
args.limits,
start_charges,
args.sampling,
args.indicator,
func_args,
first_verbose=True)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
print("\nOptimizing fit quality...")
if args.scale_all:
regular_args = (start_charges, molecule, esp_file.field)
reg_min_ratio, reg_min_ratio_rrms, compr_charges = minimize_ratio(
'regular', ratio_values, result, regular_args)
else:
func_args = (start_charges, esp_file.field, args.respin_location,
min_resp_calc_dir, args.esp_filename, True)
try:
min_ratio, min_ratio_rrms, compr_charges = minimize_ratio(
'heavy', ratio_values, result, func_args)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
shutil.rmtree(min_resp_calc_dir)
if not args.scale_all and args.save_resp_to is None:
shutil.rmtree(save_resp_to)
# TODO: plotting requires information about other charges. This would make this
os.mkdir(opt_output_path)
# Scan roughly various ratios to find bracket for minimization
print("\nScanning roughly various ratios. This shouldn't take long.")
heavy_args = (g.field, path, opt_output_path, esp_fn, False)
heavy_result, indicator_charge, ratio_values = resp.eval_ratios(
'heavy', (0, 2),
equiv_start_charges,
10,
vary_label1,
heavy_args,
first_verbose=True)
# Minimization
print("\nStarting minimization of charge ratio.")
heavy_args = (equiv_start_charges, g.field, path, opt_output_path, esp_fn,
True) # True for optimization
heavy_min_ratio, heavy_min_ratio_rrms, compr_charges = resp.minimize_ratio(
'heavy', ratio_values, heavy_result, heavy_args)
shutil.rmtree(opt_output_path)
# Presentation: 3D
if False:
fig = plt.figure()
ax = fig.gca(projection='3d')
surf = ax.plot_surface(read_result.inp1,
read_result.inp2,
read_result.rrms,
cmap=cm.plasma,
rstride=1,
cstride=1)
fig.colorbar(surf, label="RRMS at fitting points")
title = molecule_name + " " + esp_charge_type.upper()
plot_common(vary_label1, vary_label2, molecule, title)
regular_args, first_verbose=True)
else:
func_args = (esp_file.field, args.respin_location, save_resp_to,
args.esp_filename, False)
try:
result, indicator_charge, ratio_values = eval_ratios(
'heavy', args.limits, start_charges, args.sampling, args.indicator,
func_args, first_verbose=True)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
print("\nOptimizing fit quality...")
if args.scale_all:
regular_args = (start_charges, molecule, esp_file.field)
reg_min_ratio, reg_min_ratio_rrms, compr_charges = minimize_ratio(
'regular', ratio_values, result, regular_args)
else:
func_args = (start_charges, esp_file.field, args.respin_location,
min_resp_calc_dir, args.esp_filename, True)
try:
min_ratio, min_ratio_rrms, compr_charges = minimize_ratio(
'heavy', ratio_values, result, func_args)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
shutil.rmtree(min_resp_calc_dir)
if not args.scale_all and args.save_resp_to is None:
shutil.rmtree(save_resp_to)
# TODO: plotting requires information about other charges. This would make this
