https://gitlab.com/januseriksen/pymbe
Tip revision: f4011b28333a893a78045c02bb6e9a05e2f10cf3 authored by Janus Juul Eriksen on 15 February 2017, 08:43:23 UTC
bugfix for piping of stdout to stdout.out
bugfix for piping of stdout to stdout.out
Tip revision: f4011b2
bg_plotting.py
#!/usr/bin/env python
# -*- coding: utf-8 -*
""" bg_plotting.py: plotting utilities for Bethe-Goldstone correlation calculations."""
from copy import deepcopy
from numpy import asarray, amax
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
import seaborn as sns
__author__ = 'Dr. Janus Juul Eriksen, JGU Mainz'
__copyright__ = 'Copyright 2017'
__credits__ = ['Prof. Juergen Gauss', 'Dr. Filippo Lipparini']
__license__ = '???'
__version__ = '0.3'
__maintainer__ = 'Dr. Janus Juul Eriksen'
__email__ = 'jeriksen@uni-mainz.de'
__status__ = 'Development'
def abs_energy_plot(molecule):
#
sns.set(style='darkgrid',palette='Set2')
#
fig, ax = plt.subplots()
#
ax.set_title('Total '+molecule['model'].upper()+' energy')
#
u_limit = molecule['u_limit']
#
if (((molecule['exp'] == 'occ') or (molecule['exp'] == 'comb-ov')) and molecule['frozen']):
#
u_limit -= molecule['ncore']
#
if (molecule['corr']):
#
styles = ['--','-.','-','--','-.','-','--','-.','-','--','-.']
#
e_corr = []
#
for i in range(0,molecule['corr_order']):
#
e_corr.append([])
#
if (i == 0):
#
e_corr[i] = deepcopy(molecule['e_tot'])
#
else:
#
e_corr[i] = deepcopy(e_corr[i-1])
#
for j in range((molecule['min_corr_order']+i)-1,len(e_corr[i])):
#
e_corr[i][j] += (molecule['e_corr'][(molecule['min_corr_order']+i)-1]-molecule['e_corr'][(molecule['min_corr_order']+i)-2])
#
ax.plot(list(range(1,len(molecule['e_tot'])+1)),molecule['e_tot'],marker='x',linewidth=2,linestyle='-',\
label='BG('+molecule['model'].upper()+')')
#
if (molecule['corr']):
#
for i in range(0,molecule['corr_order']):
#
ax.plot(list(range(1,len(molecule['e_tot'])+1)),e_corr[i],\
marker='x',linestyle=styles[i],linewidth=2,label='BG('+molecule['model'].upper()+')-'+str(i+1))
#
ax.set_xlim([0.5,u_limit+0.5])
#
ax.xaxis.grid(False)
#
ax.set_xlabel('Expansion order')
ax.set_ylabel('Energy (in Hartree)')
#
ax.xaxis.set_major_locator(MaxNLocator(integer=True))
#
sns.despine()
#
with sns.axes_style("whitegrid"):
#
insert = plt.axes([.35, .50, .50, .30],frameon=True)
#
insert.plot(list(range(2,len(molecule['e_tot'])+1)),molecule['e_tot'][1:],marker='x',linewidth=2,linestyle='-')
#
if (molecule['corr']):
#
for i in range(0,molecule['corr_order']):
#
insert.plot(list(range(2,len(molecule['e_tot'])+1)),e_corr[i][1:],\
marker='x',linewidth=2,linestyle=styles[i])
#
plt.setp(insert,xticks=list(range(3,len(molecule['e_tot'])+1)))
#
insert.set_xlim([2.5,len(molecule['e_tot'])+0.5])
#
insert.locator_params(axis='y',nbins=6)
#
insert.set_ylim([molecule['e_tot'][-1]-0.01,\
molecule['e_tot'][-1]+0.01])
#
insert.xaxis.grid(False)
#
if (molecule['corr']):
#
ax.legend(loc=1,ncol=molecule['corr_order']+1)
#
else:
#
ax.legend(loc=1)
#
plt.savefig(molecule['wrk']+'/output/abs_energy_plot.pdf', bbox_inches = 'tight', dpi=1000)
#
return molecule
def n_tuples_plot(molecule):
#
sns.set(style='darkgrid',palette='Set2')
#
fig, ax = plt.subplots()
#
ax.set_title('Total number of '+molecule['model'].upper()+' tuples')
#
u_limit = molecule['u_limit']
#
if (((molecule['exp'] == 'occ') or (molecule['exp'] == 'comb-ov')) and molecule['frozen']):
#
u_limit -= molecule['ncore']
#
if (molecule['corr']):
#
corr_prim = []
theo_corr = []
#
for i in range(0,u_limit):
#
corr_prim.append(molecule['corr_n_tuples'][i])
theo_corr.append(molecule['theo_work'][i]-(molecule['prim_n_tuples'][i]+molecule['corr_n_tuples'][i]))
#
sns.barplot(list(range(1,u_limit+1)),theo_corr,bottom=[(i + j) for i,j in zip(corr_prim,molecule['prim_n_tuples'])],\
palette='BuGn_d',label='Theoretical number',log=True)
#
sns.barplot(list(range(1,u_limit+1)),corr_prim,bottom=molecule['prim_n_tuples'],palette='Reds_r',\
label='Energy corr.',log=True)
#
sns.barplot(list(range(1,u_limit+1)),molecule['prim_n_tuples'],palette='Blues_r',\
label='BG('+molecule['model'].upper()+') expansion',log=True)
#
else:
#
sns.barplot(list(range(1,u_limit+1)),[(i - j) for i,j in zip(molecule['theo_work'],molecule['prim_n_tuples'])],\
bottom=molecule['prim_n_tuples'],palette='BuGn_d',label='Theoretical number',log=True)
#
sns.barplot(list(range(1,u_limit+1)),molecule['prim_n_tuples'],palette='Blues_r',\
label='BG('+molecule['model'].upper()+') expansion',log=True)
#
ax.xaxis.grid(False)
#
ax.set_ylim(bottom=0.7)
#
ax.set_xlabel('Expansion order')
ax.set_ylabel('Number of correlated tuples')
#
plt.legend(loc=1)
#
sns.despine()
#
fig.tight_layout()
#
plt.savefig(molecule['wrk']+'/output/n_tuples_plot.pdf', bbox_inches = 'tight', dpi=1000)
#
return molecule
def orb_con_plot(molecule):
#
sns.set(style='whitegrid')
#
cmap = sns.cubehelix_palette(as_cmap=True)
#
if ((molecule['exp'] == 'occ') or (molecule['exp'] == 'comb-ov')):
#
orbital_type = 'occupied'
#
elif ((molecule['exp'] == 'virt') or (molecule['exp'] == 'comb-vo')):
#
orbital_type = 'virtual'
#
if (molecule['corr']):
#
fig, (ax1, ax2) = plt.subplots(2, 1, sharex='col', sharey='row')
#
else:
#
fig, ax1 = plt.subplots()
#
if (molecule['corr']):
#
# primary expansion
#
orb_arr = 100.0 * asarray(molecule['prim_orb_con_rel'])
#
sns.heatmap(orb_arr,ax=ax1,cmap=cmap,cbar_kws={'format':'%.0f'},\
xticklabels=False,\
yticklabels=range(1,len(molecule['prim_orb_con_rel'])+1),cbar=True,\
annot=False,fmt='.1f',vmin=0.0,vmax=amax(orb_arr))
#
ax1.set_yticklabels(ax1.get_yticklabels(),rotation=0)
#
ax1.set_title('Primary BG expansion')
#
# energy correction
#
orb_arr_corr = 100.0 * asarray(molecule['corr_orb_con_rel'])
#
diff_arr = orb_arr_corr - orb_arr
#
mask_arr = (diff_arr == 0.0)
#
sns.heatmap(diff_arr,ax=ax2,mask=mask_arr,cmap='coolwarm',cbar_kws={'format':'%.1f'},\
xticklabels=False,\
yticklabels=range(1,len(molecule['corr_orb_con_rel'])+1),cbar=True,\
annot=False,fmt='.1f',vmax=amax(diff_arr))
#
ax2.set_yticklabels(ax2.get_yticklabels(),rotation=0)
#
ax2.set_title('Energy correction')
#
fig.text(0.42,0.0,'Relative contribution (in %) from individual {0:} orbitals'.format(orbital_type),ha='center',va='center')
fig.text(0.0,0.5,'Bethe-Goldstone order',ha='center',va='center',rotation='vertical')
#
else:
#
# primary expansion
#
orb_arr = 100.0 * asarray(molecule['prim_orb_con_rel'])
#
sns.heatmap(orb_arr,ax=ax1,cmap=cmap,cbar_kws={'format':'%.0f'},\
xticklabels=False,\
yticklabels=range(1,len(molecule['prim_orb_con_rel'])+1),cbar=True,\
annot=False,fmt='.1f',vmin=0.0,vmax=amax(orb_arr))
#
ax1.set_yticklabels(ax1.get_yticklabels(),rotation=0)
#
ax1.set_title('Primary BG expansion')
#
ax1.set_xlabel('Relative contribution (in %) from individual {0:} orbitals'.format(orbital_type))
ax1.set_ylabel('Bethe-Goldstone order')
#
sns.despine(left=True,bottom=True)
#
fig.tight_layout()
#
plt.savefig(molecule['wrk']+'/output/orb_con_plot.pdf', bbox_inches = 'tight', dpi=1000)
#
return molecule
def dev_ref_plot(molecule):
#
sns.set(style='darkgrid',palette='Set2')
sns.despine()
#
fig, ( ax1, ax2 ) = plt.subplots(2, 1, sharex='col', sharey='row')
#
kcal_mol = 0.001594
#
if (molecule['corr']):
#
styles = ['--','-.','-','--','-.','-','--','-.','-','--','-.']
#
e_corr = []
#
for i in range(0,molecule['corr_order']):
#
e_corr.append([])
#
if (i == 0):
#
e_corr[i] = deepcopy(molecule['e_tot'])
#
else:
#
e_corr[i] = deepcopy(e_corr[i-1])
#
for j in range((molecule['min_corr_order']+i)-1,len(e_corr[i])):
#
e_corr[i][j] += (molecule['e_corr'][(molecule['min_corr_order']+i)-1]-molecule['e_corr'][(molecule['min_corr_order']+i)-2])
#
e_diff_tot_abs = []
e_diff_corr_abs = []
e_diff_tot_rel = []
e_diff_corr_rel = []
#
for j in range(0,len(molecule['e_tot'])):
#
e_diff_tot_abs.append((molecule['e_tot'][j]-molecule['e_ref'])/kcal_mol)
e_diff_tot_rel.append((molecule['e_tot'][j]/molecule['e_ref'])*100.)
#
if (molecule['corr']):
#
for i in range(0,molecule['corr_order']):
#
e_diff_corr_abs.append([])
e_diff_corr_rel.append([])
#
for j in range(0,len(molecule['e_tot'])):
#
e_diff_corr_abs[i].append((e_corr[i][j]-molecule['e_ref'])/kcal_mol)
e_diff_corr_rel[i].append((e_corr[i][j]/molecule['e_ref'])*100.)
#
ax1.set_title('Absolute difference from E('+molecule['model'].upper()+')')
#
u_limit = molecule['u_limit']
#
if (((molecule['exp'] == 'occ') or (molecule['exp'] == 'comb-ov')) and molecule['frozen']):
#
u_limit -= molecule['ncore']
#
ax1.axhline(0.0,color='black',linewidth=2)
#
ax1.plot(list(range(1,len(molecule['e_tot'])+1)),e_diff_tot_abs,marker='x',linewidth=2,linestyle='-',\
label='BG('+molecule['model'].upper()+')')
#
if (molecule['corr']):
#
for i in range(0,molecule['corr_order']):
#
ax1.plot(list(range(1,len(molecule['e_tot'])+1)),e_diff_corr_abs[i],marker='x',linewidth=2,linestyle=styles[i],\
label='BG('+molecule['model'].upper()+')-'+str(i+1))
#
ax1.set_ylim([-3.4,3.4])
#
ax1.xaxis.grid(False)
#
ax1.set_ylabel('Difference (in kcal/mol)')
#
ax1.xaxis.set_major_locator(MaxNLocator(integer=True))
#
ax1.legend(loc=1)
#
ax2.set_title('Relative recovery of E('+molecule['model'].upper()+')')
#
ax2.axhline(100.0,color='black',linewidth=2)
#
ax2.plot(list(range(1,len(molecule['e_tot'])+1)),e_diff_tot_rel,marker='x',linewidth=2,linestyle='-',\
label='BG('+molecule['model'].upper()+')')
#
if (molecule['corr']):
#
for i in range(0,molecule['corr_order']):
#
ax2.plot(list(range(1,len(molecule['e_tot'])+1)),e_diff_corr_rel[i],marker='x',linewidth=2,linestyle=styles[i],\
label='BG('+molecule['model'].upper()+')-'+str(i+1))
#
ax2.set_xlim([0.5,u_limit+0.5])
#
ax2.xaxis.grid(False)
#
ax2.set_ylim([93.,107.])
#
ax2.set_ylabel('Recovery (in %)')
ax2.set_xlabel('Expansion order')
#
ax2.xaxis.set_major_locator(MaxNLocator(integer=True))
#
ax2.legend(loc=1)
#
sns.despine()
#
fig.tight_layout()
#
plt.savefig(molecule['wrk']+'/output/dev_ref_plot.pdf', bbox_inches = 'tight', dpi=1000)
#
return molecule
def mpi_time_plot(molecule):
#
fig, ax = plt.subplots()
#
ax.set_title('MPI timings')
#
labels = 'Idle ({0:.0f} %)'.format(molecule['mpi_time_idle'][1]),'Comm ({0:.0f} %)'.format(molecule['mpi_time_comm'][1]),'Work ({0:.0f} %)'.format(molecule['mpi_time_work'][1])
#
sizes = [molecule['mpi_time_idle'][1],molecule['mpi_time_comm'][1],molecule['mpi_time_work'][1]]
#
ax.pie(sizes,colors=sns.color_palette("Set2",3),shadow=True,startangle=45)
#
plt.legend(labels,frameon=True,fancybox=True,shadow=True,loc=6,bbox_to_anchor=(0.3, 0.4))
#
ax.axis('equal')
#
fig.tight_layout()
#
plt.savefig(molecule['wrk']+'/output/mpi_time_plot.pdf', bbox_inches = 'tight', dpi=1000)
#
return molecule
def ic_plot(molecule):
#
# --- plot total energies ---
#
abs_energy_plot(molecule)
#
# --- plot number of calculations from each orbital ---
#
n_tuples_plot(molecule)
#
# --- plot total orbital contribution matrix ---
#
orb_con_plot(molecule)
#
# --- plot deviation from reference calc ---
#
if (molecule['ref']): dev_ref_plot(molecule)
#
# --- plot mpi timings ---
#
if (molecule['mpi_parallel']): mpi_time_plot(molecule)
#
return molecule