Re: [Pw_forum] Phonon of single layer MoS2
Dear "Shopping", Adding to Paolo's and Nicola's comments, I would rather use 'ibrav = 4' and 'a' and 'c' to define the lattice, making sure that the hexagonal symmetry group is indeed found, so that the k points are reduced into the irreducible wedge of the Brillouin zone - I am not sure whether it is a good idea of shifting the k points away from Gamma, as there is an issue with the Monkhorst-Pack (or, uniform) grid of k points (the Appendix of my PhD thesis from billions of years ago contains some examples, and a short version is, this shift was indeed introduced so that the sampling in hexagonal cell _could_ include the Gamma point). In order to make the coordinates look more symmetric, I would put the coordinate of Mo along the high-symmetry axis and the corresponding coordinates of S to +-0.04907565. Just to make the message clearer - also in the phonons there is no need to sample along the direction corresponding to the direction of the vacuum - 'nq3 = 1'. If you want accurate frequencies, I would consider reducing 'tr2_ph' for example to 10^-14, but this you can test. Greetings from Paris, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Mon, 13 Jul 2015, Shopping wrote: Dear all: I am calculating phonons of singel-layer MoS2 (SLMoS2). I have two confusions here. First is usually it takes me two days to complete the phonon calculation for just 3 atom unit cell of SLMoS2. I am wondering if any settings in my input file is too high like some threshold, but no idea why it takes so long. I have attached the scf.in and phonon.in file for scf calculation below. The second is do I have to include smearing in the scf calculation? Does it have large influence on the results? Since it takes too long to calculate I have not got the chance to try, anyone has similar experience willing to give me some advice here? I will be very appreciated, thanks. scf.in: &control calculation='scf', restart_mode='from_scratch', nstep=50 tstress = .true. tprnfor = .true. prefix='SLMoS2', pseudo_dir='/home/jpeng/Downloads/espresso-5.2.0/mypotential/' outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/', / &system ibrav= 0, A=3.192, nat= 3, ntyp= 2, / &electrons conv_thr=1e-10 mixing_beta = 0.7 / CELL_PARAMETERS 1.0 0.0 0.0 0.5 0.866 0.0 0.0 0.0 10 ATOMIC_SPECIES Mo 95.94 Mo.pbe-spn-kjpaw_psl.0.2.UPF S 32.065 S.pbe-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS (crystal) Mo 2/3 2/3 0.04907565 S 1/3 1/3 0 S 1/3 1/3 0.0981513 K_POINTS automatic 6 6 6 1 1 1 phonon.in: phonons of SLMoS2 &inputph tr2_ph=1.0d-12, prefix='SLMoS2', ldisp=.true nq1=4 nq2=4 nq3=4 amass(1)=95.94, amass(2)=32.065, fildyn='SLMoS2.dyn', outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/' / Best Jie Peng PhD student University of Maryland ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Phonon of single layer MoS2
Also no need to sample perp to layer - start with 3 3 1 1 1 1. Sent from a tiny keyboard... > On 13 Jul 2015, at 21:04, Shopping wrote: > > Dear all: > > I am calculating phonons of singel-layer MoS2 (SLMoS2). I have two confusions > here. > > First is usually it takes me two days to complete the phonon calculation for > just 3 atom unit cell of SLMoS2. I am wondering if any settings in my input > file is too high like some threshold, but no idea why it takes so long. I > have attached the scf.in and phonon.in file for scf calculation below. > > The second is do I have to include smearing in the scf calculation? Does it > have large influence on the results? Since it takes too long to calculate I > have not got the chance to try, anyone has similar experience willing to give > me some advice here? I will be very appreciated, thanks. > > scf.in: > &control >calculation='scf', >restart_mode='from_scratch', >nstep=50 >tstress = .true. >tprnfor = .true. >prefix='SLMoS2', >pseudo_dir='/home/jpeng/Downloads/espresso-5.2.0/mypotential/' >outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/', > / > &system >ibrav= 0, >A=3.192, >nat= 3, ntyp= 2, > / > &electrons >conv_thr=1e-10 >mixing_beta = 0.7 > / > CELL_PARAMETERS > 1.0 0.0 0.0 > 0.5 0.866 0.0 > 0.0 0.0 10 > ATOMIC_SPECIES > Mo 95.94 Mo.pbe-spn-kjpaw_psl.0.2.UPF > S 32.065 S.pbe-n-kjpaw_psl.0.1.UPF > ATOMIC_POSITIONS (crystal) > Mo 2/3 2/3 0.04907565 > S 1/3 1/3 0 > S 1/3 1/3 0.0981513 > K_POINTS automatic > 6 6 6 1 1 1 > > phonon.in: > phonons of SLMoS2 > &inputph > tr2_ph=1.0d-12, > prefix='SLMoS2', > ldisp=.true > nq1=4 > nq2=4 > nq3=4 > amass(1)=95.94, > amass(2)=32.065, > fildyn='SLMoS2.dyn', > outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/' > / > > Best > Jie Peng > PhD student > University of Maryland > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Phonon of single layer MoS2
On Mon, Jul 13, 2015 at 8:59 PM, Shopping wrote: choosing "Shopping" as name is a good way to end up in the spam folder. &system ibrav= 0, > A=3.192, > nat= 3, ntyp= 2, > / > cutoff? Paolo -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Phonon of single layer MoS2
Dear all: I am calculating phonons of singel-layer MoS2 (SLMoS2). I have two confusions here. First is usually it takes me two days to complete the phonon calculation for just 3 atom unit cell of SLMoS2. I am wondering if any settings in my input file is too high like some threshold, but no idea why it takes so long. I have attached the scf.in and phonon.in file for scf calculation below. The second is do I have to include smearing in the scf calculation? Does it have large influence on the results? Since it takes too long to calculate I have not got the chance to try, anyone has similar experience willing to give me some advice here? I will be very appreciated, thanks. scf.in: &control calculation='scf', restart_mode='from_scratch', nstep=50 tstress = .true. tprnfor = .true. prefix='SLMoS2', pseudo_dir='/home/jpeng/Downloads/espresso-5.2.0/mypotential/' outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/', / &system ibrav= 0, A=3.192, nat= 3, ntyp= 2, / &electrons conv_thr=1e-10 mixing_beta = 0.7 / CELL_PARAMETERS 1.0 0.0 0.0 0.5 0.866 0.0 0.0 0.0 10 ATOMIC_SPECIES Mo 95.94 Mo.pbe-spn-kjpaw_psl.0.2.UPF S 32.065 S.pbe-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS (crystal) Mo 2/3 2/3 0.04907565 S 1/3 1/3 0 S 1/3 1/3 0.0981513 K_POINTS automatic 6 6 6 1 1 1 phonon.in: phonons of SLMoS2 &inputph tr2_ph=1.0d-12, prefix='SLMoS2', ldisp=.true nq1=4 nq2=4 nq3=4 amass(1)=95.94, amass(2)=32.065, fildyn='SLMoS2.dyn', outdir='/home/jpeng/Downloads/espresso-5.2.0/tmpdir/' / Best Jie Peng PhD student University of Maryland ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Smearing Problem
Thanks so much dear PANG Rui and Arellano for sharing your experience with me I agree with you about gaussian smearing. I for determine degauss, amont of deguss is good that (-TS) is zero and tot magnetization is converged for magnetic systems. I use 0.001 Ry for pure surface relaxation is good and magnetic property is true and 0.003Ry for DOS calculation. but when I add molecule in surface use this degauss is not good for magnetic properties I run ferromagnetic state but I see the tot=0 and absolute=0.85 (anti ferromagnetic state) Is it True or not? With this graph how to detrmine best smaring (Ry)? [image: Inline image 1] and I don't totally clear for me this sentence from this link " http://theossrv1.epfl.ch/Main/ElectronicTemperature";? For large temperatures, the results will be independent of k-sampling - i.e. all k-point samplings are sufficient to get statistically accurate results. Atlower temperatures, the curves will start separating from each other - the first one to go is the one with the smaller sampling, since at smaller temperature it will have the largest integration errors. Thanks so much ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
"Segmentation violation" in example01 == bad compilation, bad libraries, or something very wrong in your machine Paolo On Mon, Jul 13, 2015 at 12:08 PM, Surykant Mishra wrote: > ok i am trying thank you > > > Thanks & regards > Suryakant Mishra > Indian Institute of Technology Indore > > On Mon, Jul 13, 2015 at 3:31 PM, Bramha Pandey > wrote: > >> Hi, Firstly you see the results folder. There will be xxx.scf.out file. >> open and see what is printed in xx.scf.out file. >> Then accordingly you have to act. >> >> >> >> -- >> Regards >> Dr. Bramha P Pandey >> Asstt. Prof. ECE Deptt. >> GLA University, Mathura (U.P) >> India-281406. >> >> On Mon, Jul 13, 2015 at 3:20 PM, Surykant Mishra < >> phd1401251...@iiti.ac.in> wrote: >> >>> Sir >>> I am runnig example01 in examples in PW folder in Espresso folder >>> >>> Thanks & regards >>> Suryakant Mishra >>> Indian Institute of Technology Indore >>> >>> On Mon, Jul 13, 2015 at 1:02 PM, Bramha Pandey >>> wrote: >>> Dear suryakant No one can help, until and unless you provide your input file and output file or example name which you are running. On 13-Jul-2015 12:19 PM, "Surykant Mishra" wrote: > Can any budy resolve my problem > > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/stm/espresso-5.2.0/bin > pseudo directory: /home/stm/espresso-5.2.0/pseudo > temporary directory: /home/stm/espresso-5.2.0/tempdir > checking that needed directories and files exist... done > > running pw.x as: /home/stm/espresso-5.2.0/bin/pw.x -nk 1 -nd 1 > -nb 1 -nt 1 > > running the scf calculation for Si...Segmentation fault (core dumped) > Error condition encountered during test: exit status = 139 > Aborting > stm@stm:~/espresso-5.2.0/PW/examples/example01$ > > Thanks in advance > > > > Thanks & regards > Suryakant Mishra > Indian Institute of Technology Indore > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
ok i am trying thank you Thanks & regards Suryakant Mishra Indian Institute of Technology Indore On Mon, Jul 13, 2015 at 3:31 PM, Bramha Pandey wrote: > Hi, Firstly you see the results folder. There will be xxx.scf.out file. > open and see what is printed in xx.scf.out file. > Then accordingly you have to act. > > > > -- > Regards > Dr. Bramha P Pandey > Asstt. Prof. ECE Deptt. > GLA University, Mathura (U.P) > India-281406. > > On Mon, Jul 13, 2015 at 3:20 PM, Surykant Mishra > wrote: > >> Sir >> I am runnig example01 in examples in PW folder in Espresso folder >> >> Thanks & regards >> Suryakant Mishra >> Indian Institute of Technology Indore >> >> On Mon, Jul 13, 2015 at 1:02 PM, Bramha Pandey >> wrote: >> >>> Dear suryakant >>> No one can help, until and unless you provide your input file and >>> output file or example name which you are running. >>> On 13-Jul-2015 12:19 PM, "Surykant Mishra" >>> wrote: >>> Can any budy resolve my problem This example shows how to use pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni. executables directory: /home/stm/espresso-5.2.0/bin pseudo directory: /home/stm/espresso-5.2.0/pseudo temporary directory: /home/stm/espresso-5.2.0/tempdir checking that needed directories and files exist... done running pw.x as: /home/stm/espresso-5.2.0/bin/pw.x -nk 1 -nd 1 -nb 1 -nt 1 running the scf calculation for Si...Segmentation fault (core dumped) Error condition encountered during test: exit status = 139 Aborting stm@stm:~/espresso-5.2.0/PW/examples/example01$ Thanks in advance Thanks & regards Suryakant Mishra Indian Institute of Technology Indore ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
Hi, Firstly you see the results folder. There will be xxx.scf.out file. open and see what is printed in xx.scf.out file. Then accordingly you have to act. -- Regards Dr. Bramha P Pandey Asstt. Prof. ECE Deptt. GLA University, Mathura (U.P) India-281406. On Mon, Jul 13, 2015 at 3:20 PM, Surykant Mishra wrote: > Sir > I am runnig example01 in examples in PW folder in Espresso folder > > Thanks & regards > Suryakant Mishra > Indian Institute of Technology Indore > > On Mon, Jul 13, 2015 at 1:02 PM, Bramha Pandey > wrote: > >> Dear suryakant >> No one can help, until and unless you provide your input file and output >> file or example name which you are running. >> On 13-Jul-2015 12:19 PM, "Surykant Mishra" >> wrote: >> >>> Can any budy resolve my problem >>> >>> >>> This example shows how to use pw.x to calculate the total energy and >>> the band structure of four simple systems: Si, Al, Cu, Ni. >>> >>> executables directory: /home/stm/espresso-5.2.0/bin >>> pseudo directory: /home/stm/espresso-5.2.0/pseudo >>> temporary directory: /home/stm/espresso-5.2.0/tempdir >>> checking that needed directories and files exist... done >>> >>> running pw.x as: /home/stm/espresso-5.2.0/bin/pw.x -nk 1 -nd 1 -nb >>> 1 -nt 1 >>> >>> running the scf calculation for Si...Segmentation fault (core dumped) >>> Error condition encountered during test: exit status = 139 >>> Aborting >>> stm@stm:~/espresso-5.2.0/PW/examples/example01$ >>> >>> Thanks in advance >>> >>> >>> >>> Thanks & regards >>> Suryakant Mishra >>> Indian Institute of Technology Indore >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
Sir I am runnig example01 in examples in PW folder in Espresso folder Thanks & regards Suryakant Mishra Indian Institute of Technology Indore On Mon, Jul 13, 2015 at 1:02 PM, Bramha Pandey wrote: > Dear suryakant > No one can help, until and unless you provide your input file and output > file or example name which you are running. > On 13-Jul-2015 12:19 PM, "Surykant Mishra" > wrote: > >> Can any budy resolve my problem >> >> >> This example shows how to use pw.x to calculate the total energy and >> the band structure of four simple systems: Si, Al, Cu, Ni. >> >> executables directory: /home/stm/espresso-5.2.0/bin >> pseudo directory: /home/stm/espresso-5.2.0/pseudo >> temporary directory: /home/stm/espresso-5.2.0/tempdir >> checking that needed directories and files exist... done >> >> running pw.x as: /home/stm/espresso-5.2.0/bin/pw.x -nk 1 -nd 1 -nb 1 >> -nt 1 >> >> running the scf calculation for Si...Segmentation fault (core dumped) >> Error condition encountered during test: exit status = 139 >> Aborting >> stm@stm:~/espresso-5.2.0/PW/examples/example01$ >> >> Thanks in advance >> >> >> >> Thanks & regards >> Suryakant Mishra >> Indian Institute of Technology Indore >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] charge analysis
Dear Rajkamal A. projwfc.x can read pw.x wavefunctions (provided it finds them somewhere...) and it gives you an output containing a) projections of all the Kohn-Sham orbitals on a Lowdin basis set, and b) Lowdin charges on all the atoms. This is a typical input: &projwfc prefix = 'same_prefix_of_pw.x_calculation' outdir = 'same_outdir_of_pw.x_calculation' filproj = 'prefix.proj' filpdos = 'prefix.pdos' ngauss = 0, degauss = 0.01, DeltaE = 0.01, / HTH Giuseppe On Saturday, July 11, 2015 04:06:08 PM Raj kamal wrote: > hi , i am new to this quantum espresso i need to calculate charge > analysis for graphene intercalated single lithium atom .can u please anyone > give me input files for that. thanks in advance. - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] About Optical Properties in Quantum Espresso
Dear unknown user Please sign all the posts to this forum with name and scientific affiliation. What optical properties? HTH Giuseppe On Friday, July 10, 2015 10:18:21 PM Vîpîñ Kúmår wrote: > Dear all, > > How can we calculate Optical properties of a system using quantum > espresso? > > If anybody have idea about this then please tell me... - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
Dear suryakant No one can help, until and unless you provide your input file and output file or example name which you are running. On 13-Jul-2015 12:19 PM, "Surykant Mishra" wrote: > Can any budy resolve my problem > > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/stm/espresso-5.2.0/bin > pseudo directory: /home/stm/espresso-5.2.0/pseudo > temporary directory: /home/stm/espresso-5.2.0/tempdir > checking that needed directories and files exist... done > > running pw.x as: /home/stm/espresso-5.2.0/bin/pw.x -nk 1 -nd 1 -nb 1 > -nt 1 > > running the scf calculation for Si...Segmentation fault (core dumped) > Error condition encountered during test: exit status = 139 > Aborting > stm@stm:~/espresso-5.2.0/PW/examples/example01$ > > Thanks in advance > > > > Thanks & regards > Suryakant Mishra > Indian Institute of Technology Indore > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
