Most people who have used gaussian will be familiar with molecules that are rotated multiple times during optimisation. Occasionally, the molecule is rotated repeatedly without any sign of convergence, and without any changes in atom positions.
Uploading the video to blogspot has lead to some distortion (i.e. the molecule is translated -- look at the x,y,z axes in the bottom left) but the general behaviour should still be clear:
The energies aren't really changing:
Solution:
Turning off rotation using 'nosymm' might yield faster convergence:
In ECCE, just uncheck 'Use available symmetry'.
Note that NoSymm doesn't turn off symmetry completely -- it just prevent reorientation:
From http://www.gaussian.com/g_tech/g_ur/k_symmetry.htm
How the figures were made:
First I used this script to extract the .xyz coordinates of the geometry steps:
Then I turned all the .xyz files into one .xyz file:
Which I then opened in vmd with a view to make a video. Select New Molecule and load structure.xyz. Then go to Extensions, Visualization/Movie Maker. Making a movie using VMD didn't yield to anything of sufficient quality. Instead, I selected Tachyon as the renderer. Under Movie Settings I unchecked Delete Image Files.
Once I had the ppm files I did
The key to getting a decent quality video was picking a high enough bit rate, which is probably obvious to most people who know what bit rate means, but not to a happy amateur like myself (well, now it is).
I made the energy plot using gnuplot and the energies.dat file which the python script above generates.
Uploading the video to blogspot has lead to some distortion (i.e. the molecule is translated -- look at the x,y,z axes in the bottom left) but the general behaviour should still be clear:
The energies aren't really changing:
Solution:
Turning off rotation using 'nosymm' might yield faster convergence:
#P rB3LYP/GEN 5D Opt=() Freq=() SCF=(MaxCycle=128 ) NoSymm Punch=(MO)
In ECCE, just uncheck 'Use available symmetry'.
Note that NoSymm doesn't turn off symmetry completely -- it just prevent reorientation:
From http://www.gaussian.com/g_tech/g_ur/k_symmetry.htm
The NoSymmetry keyword prevents molecule reorientation and causes all computations to be performed in the input orientation (although the program still attempts to identify the appropriate point group). Symmetry use can be completely disabled by Symmetry=None; use this option if NoSymm generates an error when identifying the point group.
How the figures were made:
First I used this script to extract the .xyz coordinates of the geometry steps:
#!/usr/bin/python
import sys
def getrawdata(infile):
f=open(infile,'r')
opt=0
geo=0
struct=[]
structure=[]
energies=[]
energy=[]
for line in f:
if opt==1 and geo==1 and not ("---" in line):
structure+=[line.rstrip()]
if 'Coordinates (Angstroms)' in line:
if opt==0:
opt=1
structure=[]
if opt==1 and "--------------------------" in line:
if geo==0:
geo=1
elif geo==1:
geo=0
opt=0
if 'SCF Done' in line:
energy=filter(None,line.rstrip('\n').split(' '))
# if 'Optimization completed' in line and (opt==0 and geo==0):
energies+=[float(energy[4])]
opt=0
geo=0
struct+=[structure]
structure=[]
return struct, energies
def periodictable(elementnumber):
ptable={1:'H',2:'He',\
3:'Li', 4:'Be',5:'B',6:'C',7:'N',8:'O',9:'F',10:'Ne',\
11:'Na',12:'Mg',13:'Al',14:'Si',15:'P',16:'S',17:'Cl',18:'Ar',\
19:'K',20:'Ca',\
21:'Sc',22:'Ti',23:'V',24:'Cr',25:'Mn',26:'Fe',27:'Co',28:'Ni',29:'Cu',30:'Zn',\
31:'Ga',32:'Ge',33:'As',34:'Se',35:'Br',36:'Kr',\
37:'Rb',38:'Sr',\
39:'Y',40:'Zr',41:'Nb',42:'Mo',43:'Tc',44:'Ru',45:'Rh',46:'Pd',47:'Ag',48:'Cd',\
49:'In',50:'Sn',51:'Sb',52:'Te',53:'I',54:'Xe',\
55:'Cs',56:'Ba',\
57:'La',58:'Ce',59:'Pr',60:'Nd',61:'Pm',62:'Sm',63:'Eu',64:'Gd',65:'Tb',66:'Dy',67:'Ho',68:'Er',69:'Tm',70:'Yb',71:'Lu',\
72:'Hf', 73:'Ta', 74:'W',75:'Re', 76:'Os', 77:'Ir',78:'Pt', 79:'Au', 80:'Hg',\
81:'Tl', 82:'Pb', 83:'Bi',84:'Po',85:'At',86:'Rn',\
87:'Fr',88:'Ra',\
89:'Ac',90:'Th',91:'Pa',92:'U',93:'Np',94:'Pu',95:'Am',96:'Cm',97:'Bk',98:'Cf',99:'Es',100:'Fm',101:'Md',102:'No',\
103:'Lr',104:'Rf',105:'Db',106:'Sg',107:'Bh',108:'Hs',109:'Mt',110:'Ds',111:'Rg',112:'Cn',\
113:'Uut',114:'Fl',115:'Uup',116:'Lv',117:'Uus',118:'Uuo'}
element=ptable[elementnumber]
return element
def genxyzstring(coords,elementnumber):
x_str='%10.5f'% coords[0]
y_str='%10.5f'% coords[1]
z_str='%10.5f'% coords[2]
element=periodictable(int(elementnumber))
xyz_string=element+(3-len(element))*' '+10*' '+\
(8-len(x_str))*' '+x_str+10*' '+(8-len(y_str))*' '+y_str+10*' '+(8-len(z_str))*' '+z_str+'\n'
return xyz_string
def getstructures(rawdata):
n=0
for structure in rawdata:
n=n+1
num="%03d" % (n,)
g=open('structure_'+num+'.xyz','w')
itson=False
cartesian=[]
for item in structure:
coords=filter(None,item.split(' '))
coordinates=[float(coords[3]),float(coords[4]),float(coords[5])]
element=coords[1]
cartesian+=[genxyzstring(coordinates,element)]
g.write(str(len(cartesian))+'\n')
g.write('Structure '+str(n)+'\n')
for line in cartesian:
g.write(line)
g.close()
cartesian=[]
return 0
if __name__ == "__main__":
infile=sys.argv[1]
rawdata,energies=getrawdata(infile)
structures=getstructures(rawdata)
g=open('energies.dat','w')
for n in range(0,len(energies)):
g.write(str(n)+'\t'+str(energies[n])+'\n')
g.close()
Then I turned all the .xyz files into one .xyz file:
cat *.xyz > structures.xyz
Which I then opened in vmd with a view to make a video. Select New Molecule and load structure.xyz. Then go to Extensions, Visualization/Movie Maker. Making a movie using VMD didn't yield to anything of sufficient quality. Instead, I selected Tachyon as the renderer. Under Movie Settings I unchecked Delete Image Files.
Once I had the ppm files I did
ffmpeg -r 2 -i symm.%05d.ppm -vcodec mpeg4 -b 5000k video.avi
The key to getting a decent quality video was picking a high enough bit rate, which is probably obvious to most people who know what bit rate means, but not to a happy amateur like myself (well, now it is).
I made the energy plot using gnuplot and the energies.dat file which the python script above generates.
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
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