514. Extracting Frequency data from a gaussian 09 calculation for gnuplot

This is another python script.

Say you've done a computation along the lines of this:

#P rBP86/GEN 5D Pseudo(Read) Opt=() Freq=() SCF=(MaxCycle=999 ) Punch=(MO) Pop=()

and want the data in a neat data file, like this:

33.237 0.0023 0.0536
39.9976 0.0043 0.8305
69.7345 0.0129 0.3348
84.7005 0.0173 0.7027
[..]
3133.0068 6.2938 0.6114
3143.8021 6.3551 0.3775
3164.9242 6.4685 0.8829
3221.8787 6.6972 4.6005

Then you can use the following python (2.x) script, g09freq:

#!/usr/bin/python
# Compatible with python 2.7 
# Reads frequency output from a g09 (gaussian) calculation
# Usage ex.: g09freq g09.log ir.dat
import sys 

def ints2float(integerlist):
    for n in range(0,len(integerlist)):
        integerlist[n]=float(integerlist[n])
    return integerlist

def parse_in(infile):
    g09output=open(infile,'r')
    captured=[]
    for line in g09output:
        if ('Frequencies' in line) or ('Frc consts' in line) or ('IR Inten' in line):
            captured+=[line.strip('\n')]
    g09output.close()
    return captured
    
def format_captured(captured):
    vibmatrix=[]
    steps=len(captured)
    for n in range(0,steps,3):
        freqs=ints2float(filter(None,captured[n].split(' '))[2:5])
        forces=ints2float(filter(None,captured[n+1].split(' '))[3:6])
        intensities=ints2float(filter(None,captured[n+2].split(' '))[3:6])
        for m in range(0,3):
            vibmatrix+=[[freqs[m],forces[m],intensities[m]]]
    return vibmatrix

def write_matrix(vibmatrix,outfile):
    f=open(outfile,'w')
    for n in range(0,len(vibmatrix)):
        item=vibmatrix[n]
        f.write(str(item[0])+'\t'+str(item[1])+'\t'+str(item[2])+'\n')
    f.close()
    return 0

if __name__ == "__main__":
    infile=sys.argv[1]
    outfile=sys.argv[2]

    captured=parse_in(infile)

    if len(captured)%3==0:
        vibmatrix=format_captured(captured)
    else:
        print 'Number of elements not divisible by 3 (freq+force+intens=3)'
        exit()
    success=write_matrix(vibmatrix,outfile)
    if success==0:
        print 'Read %s, parsed it, and wrote %s'%(infile,outfile)

Run it as e.g.

g09freq g09.log test.out

The output is compatible with gnuplot:

gnuplot> set xrange [3500:0]
gnuplot> set yrange [10:-1]
gnuplot> plot './test.out' u 1:2 w impulse

It's trivial to add gaussian broadening (see e.g. this post)

439. Calculate frequencies from a hessian file from NWChem: example in Octave (matlab)

I wanted to calculate normal modes (frequencies) for specific atoms in a calculation, and so I had to write my own code.

This Octave code calculates frequencies for the first N atoms, where N is given in the input.mass file.

---

Background
The format that NWChem uses for the Hessian is that of a flat, triangular matrix i.e. a triangular matrix such as

1  
2 3 
4 5 6

is represented as

1
2
3
4
5
6

The Hessian is symmetric around the diagonal, so the full Hessian matrix is

1 2 4
2 3 5
4 5 6

The Hessian is independent of the masses of the atom pairs, while the frequencies are heavily dependent on the masses (isotope effects are quite visible for light elements).

To get the mass-weighted matrix we divide by the square root of the product of the masses (H * /(sqrt(m1*m2))). Note that the matrix reported in the nwchem output ("MASS-WEIGHTED NUCLEAR HESSIAN (Hartree/Bohr/Bohr/Kamu)") is multiplied by 1,000.

Once you have the mass-weighted hessian you need to calculate the eigenvalues, sort them and convert them to cm-1 using a scaling factor.

That's it.

---

The code:
See below for example input.mass and input.hess

%% prepare
clear;
format long

%%Calculate conversion factor from H/B/B/amu to cm-1

%% csi=299792458; %speed of light, m/s 
%% t2au=2.418884326505E-17; % seconds per a.u.
%% Better to do it by hand to avoid rounding errors:
cau=(2.99792458 * 2.418884326505)*1E-9; %c in metres per t(a.u.)

%% 1 electron (au)=9.10938291E-31 kg
%% 1 amu = 1.66053892E-27 kg
%% Better to do by hand to avoid rounding errors:
amu2au=(1.66053892/9.10938291)*1E4;% 1 amu in a.u. (via kgs)
%% For clarity
cmtom=1/100; %m per cm
%% And finally we get our scaling factor:
scaling=cmtom*(1/(2*pi*cau*sqrt(amu2au))); %( m/cm * 1/((m/au) * au) = m/cm * 1/m = 1/cm)


%%read masses
% The mass file contains the masses of the atoms
% The first line is the number of atoms in the file
% The remaining lines are the atom masses in the same order
% as the atoms are given in the nwchem input
protomasses=fopen("input.mass");
natoms=str2num(fgetl(protomasses));
for i = 1:natoms
 mass(end+1)=str2num(fgetl(protomasses));
end
fclose(protomasses);

%% Read and construct hessian from flat hessian in .hess file
%% The .hess file provided by nwchem is flat (i.e. one
%% dimensional) and is the triangular form (i.e half) of 
%% the full hessian. We use fgetl/str2num so that we can deal 
%% with instances of scientific notation in the hessian file.
%% While we"re at it we construct the mass-weighted force matrix too.
protohessian=fopen("input.hess"); 
hessian=zeros(3*natoms);
massweighted=zeros(3*natoms);

for i = 1:3*natoms
 for j=1:i
  hessian(i,j)=str2num(fgetl(protohessian));
  massweighted(i,j)=hessian(i,j)/sqrt( mass(ceil(i/3))*mass(ceil(j/3)));
 end
end

for i=1:3*natoms
 for j=1:i
  hessian(j,i)=hessian(i,j);
  massweighted(j,i)=massweighted(i,j);
 end
end

%% Diagonalize and compute frequencies in cm^{-1}
eigen=sort(eig(massweighted));
freqs=sqrt(eigen).*scaling;

%% Make imaginary frequencies negative and store them 
%% in a new array
for n=1:size(freqs,1)
 if imag(freqs(n))==0
  frequencies(end+1,1)=real(freqs(n));
 else
  frequencies(end+1,1)=-imag(freqs(n));
 end
end

%% Echo frequencies to stdout
printf("%10.4f \n",frequencies)
%% Save frequencies as well to modes.outs
outfile=fopen("normal.out","w");
fprintf(outfile,"%i \n",natoms);
fprintf(outfile,"%10.10f \n",frequencies);
fclose(outfile);
%save 'modes.out' -ascii  frequencies

---

input.mass (for water):

3
1.5994910D+01
1.0078250D+00
1.0078250D+00

---

input.hess (this one has imaginary frequencies as well):

     6.6177469151D-01
    -5.8658669668D-12
    -1.0013075598D-05
     1.0754299967D-09
     4.5060920407D-10
     3.6644723357D-01
    -3.3088202114D-01
     2.1099357839D-10
     1.6617441386D-01
     3.6163164885D-01
     2.5270659061D-12
     4.0920019206D-06
     3.2209366184D-11
     1.6382988861D-11
     8.3427731090D-07
     2.3904755566D-01
    -2.2311539742D-10
    -1.8322029567D-01
    -2.0261099118D-01
     1.1292349908D-10
     1.7796238990D-01
    -3.3088202212D-01
    -2.4469194991D-10
    -1.6617441477D-01
    -3.0749615389D-02
     1.2368245322D-10
    -3.6436594678D-02
     3.6163164980D-01
     2.5272503844D-12
     4.0920029550D-06
     3.2022391582D-11
     1.6289326095D-11
    -4.9229359909D-06
    -1.5407535297D-11
    -1.8816632580D-11
     8.3427660670D-07
    -2.3904755666D-01
    -2.2750774181D-10
    -1.8322029575D-01
     3.6436523006D-02
     1.1512005611D-10
     5.2580053385D-03
     2.0261099171D-01
     1.1238793371D-10
     1.7796238961D-01

---

Output:

 
  -11.0036 
   -1.6327 
    3.1676 
    3.9298 
    7.5811 
   12.2862 
 1619.0207 
 3616.0904 
 3781.1341

c.f.

 ----------------------------------------------------------------------------
 Normal Eigenvalue ||                 Infra Red Intensities
  Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
 ------ ---------- || -------------- ----------------- ---------- -----------
    1      -11.004 ||    0.426523           9.840       415.796      59.477
    2       -1.633 ||    0.000029           0.001         0.028       0.004
    3        3.168 ||    0.000003           0.000         0.003       0.000
    4        3.930 ||    0.000700           0.016         0.682       0.098
    5        7.581 ||    0.134394           3.101       131.014      18.741
    6       12.286 ||    0.000000           0.000         0.000       0.000
    7     1619.021 ||    0.070174           1.619        68.409       9.786
    8     3616.091 ||    0.004517           0.104         4.404       0.630
    9     3781.135 ||    0.009065           0.209         8.837       1.264
 ----------------------------------------------------------------------------