Sysadmin at 17:48, 21 October 2022

2022-10-21T17:48:48Z

← Older revision		Revision as of 17:48, 21 October 2022
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	\| Sends all files from source directory to destination directory. Must be in source directory when typing this line		\| Sends all files from source directory to destination directory. Must be in source directory when typing this line
	\|-		\|-
	\| scp * ~~kilin~~@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/~~Meade~~/DIMER/DIMabsorptionspec		\| scp * username@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/username/DIMER/DIMabsorptionspec
	\| Example of scp		\| Example of scp
	\|-		\|-
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	~~kilin~~@cori07:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/TDESMD_112_116/COOL_INTERMED_Mead/absorptionSpec/TEST
			username@cori07:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/TDESMD_112_116/COOL_INTERMED_Mead/absorptionSpec/TEST

	<br />		<br />
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	\|		\|
	\|-		\|-
	\| scp * ~~kilin~~@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/Meade/DIMER/TDESMD_112_116/COOL_INTERMED_Mead/absorptionSpec		\| scp * username@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/Meade/DIMER/TDESMD_112_116/COOL_INTERMED_Mead/absorptionSpec
	\| example make sure you are in the directory of the files you want to send. Send it to a premade directory in photon		\| example make sure you are in the directory of the files you want to send. Send it to a premade directory in photon
	\|-		\|-
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	\| '''Generating CANDIDATES file for Photofragmentation'''		\| '''Generating CANDIDATES file for Photofragmentation'''
	\| <br />		\| <br />
	\|-
	~~\| This is after calculations have been ran for MD???~~
	\|
	~~Watch this first‼ Part 2 of Dr.Kilins video for how to generate the CANDIDATES file.~~

	~~[https://www.youtube.com/watch?v=NIrs1yXJj1Y&feature=youtu.be <u>https://www.youtube.com/watch?v=NIrs1yXJj1Y&feature=youtu.be</u>]~~
	\|-
	\| We want to get information from the WAVECAR that can help us determine the “electron hopping” so we have to find the OS_STRENGTH (oscillator strength) that is high. Since higher OS_Strength the higher the probability that given pair of orbitals is excited. STATES file should have been generated before I think.
	\|
	~~Watch this second‼ Part 1 of Dr. Kilins video for what to do after CANDIDATES file was generated and explains what is in it.~~

	~~[https://www.youtube.com/watch?v=A8BXT-FnuxM&t=212s <u>https://www.youtube.com/watch?v=A8BXT-FnuxM&t=212s</u>]~~
	\|-		\|-
	\| grep –A 700 fermi OUTCAR \| tail –n 700 > STATES1		\| grep –A 700 fermi OUTCAR \| tail –n 700 > STATES1
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	\|-		\|-
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	~~Kilins~~ Guidance to make PARCHG ~~files… I think~~		Guidance to make PARCHG files:

	~~Dear Meade,~~

	~~below are steps I did for creating orbitals~~ files ~~on nersc.~~

	~~I will let you know when they are ready and instruct on how to visualize.~~

	~~slides are good, under given limits.~~

	~~In the given time, you may add conclusions as you see them..~~

	~~Best wishes,~~

	~~Dmitri~~

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> mkdir ORBITALS		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> mkdir ORBITALS

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp WAVECAR ORBITALS/		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp WAVECAR ORBITALS/

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp CONTCAR ORBITALS/POSCAR		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp CONTCAR ORBITALS/POSCAR

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp POTCAR ORBITALS/		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp POTCAR ORBITALS/

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp *.sh ORBITALS/		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp *.sh ORBITALS/

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp KPOINTS ORBITALS/		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER> cp KPOINTS ORBITALS/

	> cd ORBITALS/		> cd ORBITALS/

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> grep NBA ../OUTCAR		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> grep NBA ../OUTCAR

	k-points NKPTS = 1 k-points in BZ NKDIM = 1 number of bands NBANDS= 160		k-points NKPTS = 1 k-points in BZ NKDIM = 1 number of bands NBANDS= 160

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> cp ~/bin/INCAR/INCAR-pc ./INCAR		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> cp ~/bin/INCAR/INCAR-pc ./INCAR

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> tail INCAR		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> tail INCAR

	IBRION=2 #conjugate-gradient algorithm used to relax ions (bad		IBRION=2 #conjugate-gradient algorithm used to relax ions (bad
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	LVTOT = .TRUE.		LVTOT = .TRUE.

	~~kilin~~@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> sbatch cori_debug.sh		username@cori11:/global/cfs/cdirs/m1251/vasp/CHEM676/meade/DIMER/ORBITALS> sbatch cori_debug.sh

	Submitted batch job 32413471		Submitted batch job 32413471
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	d. download these files and open then in the VMD - the same software you have used for the trajectories.		d. download these files and open then in the VMD - the same software you have used for the trajectories.

	~~I will have a look on the slides and let you nko if any quicl changes are needed or we can go ahead with this version~~

	~~Best wishes,~~

	~~Dmitri~~

	~~<br />~~
	\|		\|
	\|-		\|-
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	generate TDESMD_###_### directories		generate TDESMD_###_### directories
	\|-		\|-
	\| scp ~~kilin~~@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/Meade/DIMER/TDESMD_##_###/movieALL.xyz .		\| scp username@photon.chem.ndsu.nodak.edu:/scratch001/Chem_476/CHEM676_2019/Meade/DIMER/TDESMD_##_###/movieALL.xyz .
	\| WHILE IN THE TDESMD DIRECTORY THAT YOU WANT TO BE THE DESTINATION take “movieALL.xyz” from photon and put into specific directory		\| WHILE IN THE TDESMD DIRECTORY THAT YOU WANT TO BE THE DESTINATION take “movieALL.xyz” from photon and put into specific directory
	\|-		\|-
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	\| <br />		\| <br />
	\| Polymer/Monomer Photodegradation: TDESMD 91 121 Bond Data		\| Polymer/Monomer Photodegradation: TDESMD 91 121 Bond Data
	\|-
	~~\| <br />~~
	\|
	~~Bond lengths shown (white lettering) are chosen to see if this degradation simulation relates to the photo cleavage explained in this specified paper.~~

	~~Angew. Chem. Int. Ed. 2015, 54, 1159 –1163~~

	~~The transition energy for this excitation is 0.24386664.~~

	~~From conformation labeled as "DIMER"~~

	~~Acknowledgements: Dr. Dmitri Kilin~~
	\|-		\|-
	\| '''Obtaining MASSPECTRUM Data from FERWE TDESMD Calculations'''		\| '''Obtaining MASSPECTRUM Data from FERWE TDESMD Calculations'''

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2022-10-21T17:45:45Z

removed top info

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Sysadmin: Revised formatting

2022-09-26T21:32:19Z

Revised formatting

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← Older revision

Revision as of 21:16, 26 September 2022

Sysadmin: Imported from text file

2022-09-26T19:21:18Z