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In [1]:



    


import MagicTools



    











In [2]:



    


%pylab inline



    


















    






Populating the interactive namespace from numpy and matplotlib

















In [3]:



    


MagicTools.Deviation(['0magic0.out','0magic1.out','0magic2.out','0magic3.out'])



    


















    






0magic0.out.iter1    S:   5.52561       RDF:   3.37115
0magic0.out.iter2    S:   2.39021       RDF:   0.69364
0magic0.out.iter3    S:   1.48770       RDF:   0.43659
0magic0.out.iter4    S:   1.03896       RDF:   0.45803
0magic0.out.iter5    S:   0.85950       RDF:   0.30883
0magic0.out.iter6    S:   0.74291       RDF:   0.29362
0magic0.out.iter7    S:   0.72854       RDF:   0.27098
0magic0.out.iter8    S:   0.64791       RDF:   0.23766
0magic0.out.iter9    S:   0.61064       RDF:   0.21673
0magic0.out.iter10    S:   0.60868       RDF:   0.18731
0magic1.out.iter1    S:   0.46928       RDF:   0.15734
0magic1.out.iter2    S:   1.16588       RDF:   0.48066
0magic1.out.iter3    S:   1.41678       RDF:   0.57081
0magic1.out.iter4    S:   1.45686       RDF:   0.57529
0magic1.out.iter5    S:   1.31140       RDF:   0.51230
0magic1.out.iter6    S:   0.39708       RDF:   0.14900
0magic1.out.iter7    S:   0.36810       RDF:   0.14673
0magic1.out.iter8    S:   0.38558       RDF:   0.16176
0magic1.out.iter9    S:   0.33607       RDF:   0.15052
0magic1.out.iter10    S:   0.28330       RDF:   0.15601
0magic2.out.iter1    S:   0.28138       RDF:   0.14967
0magic2.out.iter2    S:   0.18970       RDF:   0.08410
0magic2.out.iter3    S:   0.18404       RDF:   0.03791
0magic2.out.iter4    S:   0.18306       RDF:   0.05579
0magic2.out.iter5    S:   0.11599       RDF:   0.04050
0magic2.out.iter6    S:   0.07843       RDF:   0.03290
0magic2.out.iter7    S:   0.25446       RDF:   0.12119
0magic2.out.iter8    S:   0.18376       RDF:   0.08919
0magic2.out.iter9    S:   0.14580       RDF:   0.04161
0magic2.out.iter10    S:   0.11295       RDF:   0.03040
0magic3.out.iter1    S:   0.09846       RDF:   0.04370
0magic3.out.iter2    S:   0.18243       RDF:   0.04362
0magic3.out.iter3    S:   0.17147       RDF:   0.05027
0magic3.out.iter4    S:   0.11582       RDF:   0.03514
0magic3.out.iter5    S:   0.07416       RDF:   0.02440

















In [5]:



    


MagicTools.AnalyzeIMCOuput('0magic3.out')



    


















    






Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 5
Total number of checks per iteration: 7
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 3
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 4
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 5
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 5
Total number of checks per iteration: 7
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2

















In [6]:



    


import MagicTools



    











In [199]:



    


rdf = []
rdf.append(MagicTools.GetDFsFromFile_magic('0magic0.out'));
rdf.append(MagicTools.GetDFsFromFile_magic('0magic1.out'));
rdf.append(MagicTools.GetDFsFromFile_magic('0magic2.out'));
rdf.append(MagicTools.GetDFsFromFile_magic('0magic3.out'));



    


















    






Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 10
Total number of checks per iteration: 22
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 3
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 4
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 5
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 6
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 7
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 8
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 9
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 10
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 10
Total number of checks per iteration: 7
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 3
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 4
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 5
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 6
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 7
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 8
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 9
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 10
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 10
Total number of checks per iteration: 7
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 3
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 4
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 5
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 6
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 7
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 8
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 9
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 10
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Automatically defining list of interactions from input file. If this does not work well for your input, edit subroutine GetDFsFromFile_magic in MagicTools.py and manualy add list of your beads to PairNamesList
3  intermolecular pairs detected  ['N-N', 'N-C', 'C-C']
2  pairwise bonds detected  ['N1-C1', 'C1-C2']
1  angles detected  ['N1-C2-C1']
Total number of iterations: 5
Total number of checks per iteration: 7
Iteration 1
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 2
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 3
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 4
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1
Iteration 5
Pair N-N
Pair N-C
Pair C-C
Pair N1-C1
Pair C1-C2
Pair N1-C2-C1










    
Out[199]:








35

















In [284]:



    


r2 = np.array(rdf)
rx =[]
its = [10,10,10,5]
for i in xrange(len(its)):
    for j in xrange(its[i]):
        rx.append(r2[i][j][0])
print len(r2)



    


















    






4

















In [3]:



    


p1=[]
p1.append(MagicTools.GetPotsFromFile_pot('imc5dmdds.i006.pot',mcmfile=['M3dmdds.mcm','M3br.mcm'],Ucut= 1000))
p1.append(MagicTools.GetPotsFromFile_pot('imc5dmdds.i003.pot',mcmfile=['M3dmdds.mcm','M3br.mcm'],Ucut= 1000))
p1.append(MagicTools.TotalPots(p1[0],70))



    











In [94]:



    


MagicTools.PlotAllDFs([p1[0]])



    


















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    
























In [4]:



    


import matplotlib.cm as cm
plt.figure(figsize=(15,7), dpi=300)
j=2
plt.xlabel(r'$r,\  (\AA)$',fontsize=20)
plt.ylabel(r'$\mathcal{U}(r),\ (\frac{kJ}{mol})$',fontsize=20)
plt.axis([3, 20, -3,10])
plt.plot(p1[0][0].g[:,0],p1[0][0].g[:,1],'g-',label='Ni-Ni')
plt.plot(p1[1][0].g[:,0],p1[1][0].g[:,1],'r-',label='Ni-Ni Incorporated')
plt.plot(p1[2][0].g[:,0],p1[2][0].g[:,1],'b-',label='Ni-Ni + Electrostatics')
plt.plot(p1[0][2].g[:,0],p1[0][2].g[:,1],'g-',label='Ni-Nn')
plt.plot(p1[1][2].g[:,0],p1[1][2].g[:,1],'r-',label='Ni-Nn Incorporated')
plt.plot(p1[0][7].g[:,0],p1[0][7].g[:,1],'g--',label='Nn-Nn')
plt.plot(p1[1][7].g[:,0],p1[1][7].g[:,1],'r--',label='Nn-Nn Incorporated')
plt.legend( title='Potentials',loc='upper right')
plt.grid(True)
savefig("NNCha.png",bbox_inches='tight', dpi=300)
plt.show()



    


















    
























In [6]:



    


import matplotlib.cm as cm
for j in xrange(13):
    plt.figure(figsize=(20,10), dpi=300)
    if (j == 12):
        plt.axis([60, 180, -1,50])
    plt.xlabel(r'$r,\  (\AA)$',fontsize=20)
    plt.ylabel(r'$\mathcal{U}(r),\ (\frac{kJ}{mol})$',fontsize=20)
    plt.plot(p1[0][j].g[:,0],p1[0][j].g[:,1],'g-',label=p1[0][j].Name)
    plt.plot(p1[1][j].g[:,0],p1[1][j].g[:,1],'r-',label=p1[0][j].Name + ' Incorporated')
    plt.plot(p1[2][j].g[:,0],p1[2][j].g[:,1],'b-',label=p1[0][j].Name + ' + Electrostatics')
    plt.legend( title='Potentials',loc='upper right')
    plt.grid(True)
    savefig("PtsChargedSys{0:}.png".format(j),bbox_inches='tight', dpi=300)
    plt.show()



    


















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    

















    
























In [ ]:

Content source: acnz/summer-prj

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