To find min of column 2 awk ‘NR == 1 || $2 > min {line = $0; min = $2}END{print line}’ To find max of column 3 awk ‘NR == 1 || $3 > max {line = $0; max = $3}END{print line}’ Continue reading Find min/max in one line with awk
After a long wait, the GPU VM has become generally available on MS Azure service. I will use it to test the capability of VASP-GPU version before deciding to invest in the pricey GPU servers at our center. As a beginning, I reference by setting on the previous work, which setup a previewed NC6 unit for deep learning application [Cortana Intelligence and ML Blog Team]. For our test, I used the cheapest model of NC6 VM at South Central US equipped with 6 CPU cores + 1 K80 GPU pricing at $1.08/hr. To minimize the cost, I put it on a HDD storage. At … Continue reading Compiling VASP-GPU on MS Azure GPU VM
Create ‘oplsaa_subset.prm’ from ‘oplsaa.prm’ by delete all lines starting with keyword ‘atom’ that does not use in our system. Generate ‘oplsaa.lt’ file using the following moltemplate command: oplsaa_omltemplate.py oplsaa_subset.prm As a result, ‘oplsaa.lt’ file will be created. For each type of molecule used in the system, create ‘[MOLNAME].lt’ file containing atomic data of that molecule (i.e. atom coordinate, atom species corresponding to the oplsaa.lt and covalent bonding). For example, file for ethylene molecule is formatted as the following: import “oplsaa.lt“ Ethylene inherits OPLSAA { # atom–id mol–id atom–type charge X Y Z write(‘Data Atoms’) … Continue reading Create and run mixed liquid system with OPLS-AA force fields using moltemplate + LAMMPS
Today, I struggled trying to access amember variable of ASE‘s Atoms instance but I don’t know exactly the variable name. Printing out instance show some data but not what I need: >>>print(centerImage) Atoms(symbols=’OH2′, positions=…, cell=[15.0, 15.0, 15.0], pbc=[True, True, True], calculator=SinglePointCalculator(…)) This can be easily found using the following statement: [instance].__dict__.keys() __dict__.keys() is a python built-in feature to list instance/object’s member variable. Here is the result: >>>print(centerImage.__dict__.keys()) [‘info’, ‘adsorbate_info’, ‘_celldisp’, ‘_calc’, ‘arrays’, ‘_pbc’, ‘_cell’, ‘_constraints’] And thus, all the member variables of an object is shown! Continue reading Listing object’s member variables in python
I found that my MBP is out of space almost all the time. Using GrandPerspective (Free), I found that most of my space were taken by uncompressed movie files (simulation movies). Thus, I want to reduce the file size without compromising much of the quality. Here is the solution. Using ffmpeg to reduce movie file size: ffmpeg -i GrapheneAlNP-3kms-full.mov -c:v libx264 -r 30 -pix_fmt yuv420p out.mp4 The original movie file was created using old QTime (v.6 or 7?) using image sequence thus uncompressed. Seems that solution 1 fix the file size pretty well (3-7x reduction factor) with almost the same video … Continue reading Reduce movie file size & creating movie from images
This is the excerpt for your very first post. Continue reading First blog post
mattkunaseth 