508. Very, very briefly: why apt-get purge exists (anecdote)

Sometimes my brain and I fall out, and we refuse to communicate. Yesterday was a day like that.

Having put my TV computer back together again (see post), I realised that I hadn't installed conky or guake on it. So I did. Having edited my default conky.conf (a bit like the one in this post) to change eth0 to eth1, I was wondering why my wireless card wasn't showing up in the ifconfig -a output. lspci showed that I had a broadcom chip, so I installed broadcom-sta-dkms. Nothing much happened, so I rebooted. And...no network card whatsoever recognised (including the ethernet one).

Face palm. I don't have a wireless pci/pci-e card on that computer. I should know -- I had just rebuilt it...

Oh well. apt-get autoremove broadcom-sta-dkms. Nothing. Reboot. Still no eth card -- also, the eth card was obviously the broadcom one (broadcom 4401). But why wasn't it working? I had uninstalled the broadcom package after all.

A bit of googling suggested loading b44 so modprobe b44 it was. Still nothing. Then a thought hit me -- ls /etc/modprobe.d/*blacklist*

And yes -- the broadcom package had installed a broadcom-wl-blacklist.conf file in /etc/modprobe.d -- and b44 was blacklisted. At this point I could either edited the file and comment out b44, delete the file entirely or purge the package and everything would be back to normal. So I did.

So remember: just because you uninstall a package (apt-get autoremove) doesn't mean that you've restore your system to the state it was before you installed the package. To at least have a chance of restoring it you need to purge your package so that settings files are removed too (apt-get purge).

507. (re)assembling a Dell C521 -- pictures

I finally got around to getting a new (well, refurbished) power supply for my old Dell C521. While the PSU worked fine, on trying to shut down the computer before it booted linux I managed to get the power button stuck. As it turns out, it's not that easy to access things on the front panel on this particular model...

So I took everything apart. EVERYTHING. Except for removing the front panel, ironically. If this post has a lesson for anyone else it's that you shouldn't be afraid to attack (gently) your desktop with a screwdriver. Computers ain't magic.

Anyway, here are some pictures from me reassembling it. For most people it will probably be more useful to look at these pictures in reverse.

Empty case. The arrow indicates where the screws for the panel go. I forget to attach them the first time I reassembled the case...

The plastic bits go to the lights on the front panel

The arrow indicates the front button thingy which I had to attack (gently) with a screw driver to get the power button to release.

The power button. Not sure why I took a picture of it, but there you go.

Front panel screws.

The (very dusty) fan swings out in the direction shown by the arrow. Because of this, you must remove the mobo before removing the fan, which you need to remove in order to remove the front panel. Not a very good design.

The mobo gets stuck in the fabric, so you might need to poke it with a narrow plastic pen or something like that in order to get it to release when removing it. Lift up this side and then slide out the mobo when dismantling.

Another odd design feature -- the heatsink must (more or less) be removed in order to reach the front panel. Also, the CPU is in dire need of a clean and some thermal paste.

The heatsink is now attached -- the plastic bit funnels the airflow from the fan at the front across the heat sink.

The PSU is now in place, but not connected

The P1 main power connector

ATX12V (labelled p2 here) in place

The HDD in place

The CD/DVD ROM in place

PCI and PCI-E in place (and nvidia graphics card and a DTV 1000S tv card)

And it's back in one piece.

506. Extracting optimized structures from a potential energy scan in nwchem

Another update:
It now dumps the energies in a file, energies.dat, as well.

Update:
some programmes, like ecce, are more picky about the xyz format than others (e.g. jmol, vmd). I've updated the code to output xyz files that ecce too can read.

Original post:
When you use scan_input() in nwchem to do a PES scan (see e.g. here: http://verahill.blogspot.com.au/2013/08/503-relaxed-pes-scanning-in-nwchem.html) you get the energies and the gradients for the optimized structures returned as the results. However, for a casual user the atomic actual coordinates is more informative.

Here's a very simple parser written in python (2.7) which extracts the optimized structures from the output file:

#!/usr/bin/python
import sys

def getrawdata(infile):
        f=open(infile,'r')
        opt=0
        geo=0
        energy=[]
        energies=[]
        struct=[]
        structure=[]
        for line in f:
                if "Total DFT" in line:
                        line=filter(None,line.rstrip('\n').split(' '))
                        energy=float(line[4])
                if 'Optimization converged' in line:
                        opt=1
                if opt==1 and 'Geometry' in line:
                        geo=1
                if      'Atomic Mass' in line and (opt==1 and geo==1):
                        opt=0
                        geo=0
                        struct+=[structure]
                        energies+=[energy]
                        structure=[]
                if opt==1 and geo==1:
                        structure+=[line.rstrip()]
        return struct,energies

def genxyzstring(coords,element):
        x_str='%10.5f'% coords[0]
        y_str='%10.5f'% coords[1]
        z_str='%10.5f'% coords[2]
 
        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:
                        
                        if itson and not(item==""):
                                coords=filter(None,item.split(' '))
                                coordinates=[float(coords[3]),float(coords[4]),float(coords[5])]
                                element=coords[1]
                                cartesian+=[genxyzstring(coordinates,element)]
                                #cartesian+=[coords[1]+'\t'+coords[3]+'\t'+coords[4]+'\t'+coords[5]+'\n']
                
                        if "---" in item:
                                itson=True
                        if item=="" and itson==True:
                                itson=False
                                if not(len(cartesian)==0):
                                        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()

Presuming that you've saved it as pes_parse.py you can then generate a series of xyz files with the structures, catenate them into a trajectory file, and open it in e.g. jmol. I'm using the output from example 1 in http://verahill.blogspot.com.au/2013/08/503-relaxed-pes-scanning-in-nwchem.html as the example:

chmod +x pes_parse.py
./pes_parse.py nwch.nwout
ls

nwch.nwout    structure_001.xyz  structure_003.xyz  structure_005.xyz  structure_007.xyz  structure_009.xyz  structure_011.xyz  structure_013.xyz  structure_015.xyz  structure_017.xyz  structure_019.xyz
pes_parse.py  structure_002.xyz  structure_004.xyz  structure_006.xyz  structure_008.xyz  structure_010.xyz  structure_012.xyz  structure_014.xyz  structure_016.xyz  structure_018.xyz

cat structure_*.xyz >> trajectory.xyz 
jmol trajectory.xyz

You can go through the structures by clicking on the arrows indicated by the white arrow:

Finally, using VMD it's easy to make videos -- note that they for some reason look awful here (seems like a lot of frames are removed, in particular from the beginning of the run):

And here's the SN2 reaction from post 503: