Re: [Pw_forum] Saving charge density file
Dear HedgeI will advise that you post your nscf input file too to enable us look at both input files for possible solutionsBut still make sure both scf and nscf are in the same directory by checking the "outdir" in their input files and also make sure they have the same "prefix" then rerun both calculations I believe that will work Agbaoye Ridwan OlamideCMP_NETWORK UNAABFederal university of Agriculture Abeokuta Nigeria Sent from Yahoo Mail on Android On Tue, Jan 3, 2017 at 17:48, Manu Hegde wrote: Hello QE Users, Happy new year. I am getting this unusual error after SCF run, while I am trying to run NSCF calculations, it was able to read the charge density file. However, when I was trying to run the band structure calculations, it was shown that, "Cannot read rho : file not found" What is the reason?. I am using QE 5.4.0. I have attached my input file as well for SCF calculations. Is something missing in my input file?. I never had this problem before. Manu Hegde University of Waterloo ___ 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 about inputfile
Please check how you spell the atomic position in ATOMIC POSITION CARD that shoud help Agbaoye Ridwan OlamideCMP_Network Unaab Federal University of Agriculture, Abeokuta On Sunday, January 1, 2017 4:17 PM, Nasim Ha wrote: I want run pw.x but it stopped with this eroor : Error in routine read_cards_pw (1): atomic position info missing I insert inputfile. -- N.H.Jazi PhD student of Physics. Physics Department,Central Tehran Branch,Islamic Azad University,Tehran,88074907,Iran. ___ 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] BAND STRUCTURE CAL SHOWS ERROR
I guess you are using pw.x instead of bands.x for your calculation thats the reason for your error, your input is good enough use bin/band.x for the calculation On Thursday, May 5, 2016 1:23 PM, Manu Hegde wrote: I might be wrong but just try .dat instead of dat1. It might work. On Thu, May 5, 2016 at 1:15 PM, Raj kamal wrote: DEAR QE experts this is my error when i try to calculate bands.x calculation in quantum espresso 5.3.0 task # 0 from bands : error # 1 reading bands namelistmy input&BANDS outdir = '/home/ran/espresso-5.3.0/temp/' , prefix = 'RGOvcd3scf' ,filband= 'bands.dat1',/please suggest me ...to rectify this problem.thanks in advance. -- Best regards,Rajkamal.A.Research Scholar,(SRM UNIV). ___ 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] High symmetry Kpoint for band structure calculation for ibrav=-12
Good day all I appreciate the forum support all this while, i am grateful I have been working on a molecular crystal for a while, now i am at the stage of plotting the band structure. please i need to be guided on how to determine my high symmetry kpoint required for band structure plot for a monoclinic system with ibrav=-12 . I will appreciate if i can get literatures that can guide me on how to determine the high symmetry point Agbaoye, Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc(in view)___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Error on band structure plot: only points showing
Good day Everyone Iplotted a band structure of a compound and i realized that instead of thewavefunction showing lines connected with points i only have points on my plot.i dont know where the point disappear to.. Iperform my calculations on a cluster machine, i will appreciate if i can getideas on how to fix this challenge copiesof the band structure plot are attached to this mail AgbaoyeRidwan Olamide FederalUniversity of Agriculture, Abeokuta M.Sc(inview) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] help on how to compute celldm(4), celldm(5) and celldm(6)
Thank you very much sir, now I have gotten a cl ear picture of how to calculate celldm(4)-celldm(6) Now my question is that in the case where celldm(4)=0.00 for monoclinic structure can we say the crystal structure is similar or same as that of orthorhombic sinc On Mon, Feb 22, 2016 at 9:54, Giovanni Cantele wrote: > On 20 Feb 2016, at 20:34, Ridwan Agbaoye wrote: > > Please I need clarification on how to compute celldm(4), celldm(5) and > celldm(6) for ibrav 12, 13 and 14 > > I have conflicting opinion on how it should be calculated though it is stated > as for ibrav =12 and 13 celldm(4)=cos(ab),for ibrav 14 celldm(4)=cos(bc), > celldm(5)=cos(ac)and celldm(6)=(ab). Although cos(ab) is the cosine of angle > between lattice parameters a and b as stated in INPUT_PW.HTML of quantum > espresso > > Please I need clarifications > > Agbaoye Ridwan Olamide > Federal University of Agriculture, Abeokuta > M.Sc. (in view) > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum Example for ibrav=12 cosAB = cosine of the angle between axis a and b (gamma) So if you know the lattice vector coordinates, that is, a=(ax,ay,az) and b=(bx,by,bz), just calculate cosAB = a . b / ( |a| |b| ) where a . b = dot product of a and b = ax bx + ay by + az bz |a| = length of vector a = sqrt( ax^2 + ay^2 + az^2 ) and same for |b|. Instead, if you know, directly gamma, just compute cos( gamma ). Similar consideration apply to cos(bc) and cos(ac) for the other lattices. Giovanni -- Giovanni Cantele, PhD CNR-SPIN c/o Dipartimento di Fisica Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy e-mail: giovanni.cant...@spin.cnr.it Phone: +39 081 676910 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele ___ 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] help on how to compute celldm(4), celldm(5) and celldm(6)
Please I need clarification on how to compute celldm(4), celldm(5) and celldm(6) for ibrav 12, 13 and 14 I have conflicting opinion on how it should be calculated though it is stated as for ibrav =12 and 13 celldm(4)=cos(ab),for ibrav 14 celldm(4)=cos(bc), celldm(5)=cos(ac)and celldm(6)=(ab). Although cos(ab) is the cosine of angle between lattice parameters a and b as stated in INPUT_PW.HTML of quantum espresso Please I need clarifications Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. (in view)___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] how to espress fractional coordinates in quantum espresso input
Good day everybody I want to do some calculations on a crystal whose atomic coordinates are given in fractional coordinates How do I convert the fractional coordinates to quantum espresso unit of atomic coordinates Which flag do I need to use is it (crystal), (alat), (Bohr) or (angstrom) I appreciate everyone support towards answering questions to educate pwscf users Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. (in view)___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Atomic position for Vc-relax
I did vc-relax calculations for silicon and at the end of the calculation i got my final lattice parameter and atomic positions, but to my surprise when i viewed my new structure with my new atomic positions, it does not look like a face centered crystal structure but preparing the input file with the old atomic position its look perfecting like the face centered crystal structure with atom on all of the faces Does this mean that the new atomic positions should not be used for calculation after vc-relax because the old atomic position looks better when viewed with xcrysden Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. in view___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Elastic constant for monoclinic structure crystal lattice
Please help I am working on getting the elastic constant of a monoclinic structure using quantum espresso and i cannot get the required stress required to be applied to the system in order to get my Bulk modulus matrix, shear modulus etc to help me get my C11 to C66 i will appreciate if anybody can recommend any text or research material or anything to help Agbaoye Ridwan Olamide Federal University of Agriculture, AbeokutaM.Sc. in view___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Calculating stable lattice parameter for non-cubic structure
1.Ensure you compute your input file correctly, check your ibrav to confirm if it correlate with that of orthorombic and tetragonal, check the required celldm(1)..celldm(6) and make sure you used the correct cell dimension assigned to your lattice structure through INPUT_PW.html 2. You should have an idea of the experimental lattice or optimized lattice parameter from other research work you can find around, then set your celldm(1) to + or - the optimized lattice parameter you got while other lattice parameters become constante.g if the optimized celldm(1) from other research or experimental value is 10 bohr you can vary your celldm(1) from 8 bohr to 12 bohr with an increment of 0.02, which depends on how much computation resource or how expensive your computation is. if you get a linear graph with positive gradient you next celldm trial should be less than your minimum celldm from your graph but if your linear graph is such that its gradient is negative you next trial for celldm should be higher than your minimum celldm from your graph... Good luck. Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. in view On Thursday, January 21, 2016 12:49 AM, efi dwi indari wrote: Dear All, I am now on my way in determining stable lattice parameter of both orthorhombic and tetragonal structures. Previously everything was going well when I calculated the cubic one as I obtained the U-curve from which I got the value of stable lattice parameter which corresponds to the lowest total energy. Yet, when I move forward to the orthorhombic and tetragonal ones and when I varied one of the lattice parameters (while the other(s) remains constant), I could not obtain the U-curve. Instead, I got a linear curve, with lower total energy as I go to smaller lattice parameter. Does anyone have any idea how to deal with this issue? I have already googled but unfortunately not yet found any solution. Any help would be really appreciated. Thank you in advance. Best Regards, Efi Dwi Indari Research assistant, Bandung Institute of Technology ___ 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] Error running thermo examples
Good day EverybodyI want to calculate the elastic constant of a monoclinic compound using quantum espresso on my computer, i decide to use the thermo_pw package since i do not understand any other method.After compiling installing the thermo_pw package with make join_qe and make thermo_pw then i decide to run the examples to see how it works but i got the following errortask #from mp_start_images :error #invalid number of images, out of range and i realized thermo_pw attempt running as : mpirun -np 4 /home/agbaoyeridwanolamide/espresso-5.2.1/bin/thermo_pw.x -ni 2 -nk 1 -nd 1 -nb 1 -nt 1 How do i run on my computer as i do not have access to computer clusters Agbaoye Ridwan OlamideM.Sc. in view Federal University of Agriculture AbeokutaNigeria ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Access to High Performing Computing cluster resources
Good day EverybodyI am a research student working on a monoclinc crystal structured organic compound , whose calculation cannot be done on minicomputer(Dell laptop computer 4gig RAM and Intel core i3), because of how large the system is and its very High computation time.Hence, the need for access on High Performing Computing cluster is necessary, I have tried registering with CHPC South Africa, but access was not allocated to me because i could not get South African Collaborator.I will appreciate support from individual and organization that could help me in getting access to HPC to enable me carry out my research with accuracy and less computation time. Agbaoye Ridwan OlamideFederal University of Agricuture, AbeokutaNigeria.M.Sc. (in view) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Interpretation of vc-relax output
Does this answer work for all systems be it FCC or monoclinic or Hexagonal "final_alat = input_alat * 0.487685488 / 0.5 = 10,345371472 bohr " where does 0.5 come from If i am working on a monoclinic or Hexagonal crystal structure do i still use the 0.5 or how do i calculate the 0.5 For the atomic position i got ATOMIC POSITIONS(alat)si -0.035697193 -0.035697193 -0.035697193si 0.208182292 0.208182292 0.208182292 is there a rule to use in converting to 0 0 0 and 1/4 1/4 1/4 Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. (in view)On Monday, December 21, 2015 1:18 AM, stefano de gironcoli wrote: if nor celldm(1) [in Bohr] nor A [in \AA] are given in input and the CELL_PARAMETERS card is given then alat is defined as the length (in bohr) of the first vector in CELL_PARAMETERS in your case 7.5*sqrt(2.0)=10.60660172 bohr if celldm(1) or A are given then the CELL_PARAMETERS are interpreted as given in those units. In input atomic positions are given in the selected units, in output they are always given in unit of the alat value computed/defined in input. If you want to use AA as your input/output length unit the easiest way is to define A=1.0 or celldm(1)=1.889726878 in the &system namelist CELL_PARAMETERS ... ATOMIC_POSITIONS Angstrom [or alat since they are the same] ... in output the positions and cell information will be given in (input) alat units, that is in AA again. HTH stefano PS in your case the silicon cell contracted by 0.487685488 * alat / 7.5 = 0.487685488 * sqrt(2) the final cell corresponds to an FCC with final_alat = input_alat * 0.487685488 / 0.5 = 10,345371472 bohr In these units the atomic coordinates are just 0 0 0 and 1/4 1/4 1/4 (plus a small shift away from the origin due to the fact that the center of mass remain fixed during relaxation) On 21/12/2015 07:30, Ridwan Agbaoye wrote: Good Morning Everybody, I need some help with the interpretation of vc-relax output and conversion from alat to bohr I want to do vc-relax calculation for a monoclinic system but i decide to start with silicon a face-centered cubic system to understand the concept of vc-relax properly I tried vc-relax for silicon and i got the following output Begin Final Coordinate New Unit Cell volume = 276.90769au^3 CELL PARAMETERS(alat=10.60660172) -0.487685488 -0.0 0.487685488 0.000117363 0.487685488 0.487685488 -0.487685488 0.487685488 -0.0 ATOMIC POSITIONS(alat) si -0.035697193 -0.035697193 -0.035697193 si 0.208182292 0.208182292 0.208182292 End of Final coordinate My input file has ibrav=0 nat=2 ntyp=2 CELL PARAMETER cubic -7.5000 0. 7.5000 0. 7.5000 7.5000 -7.5000 7.5000 0. How exactly do we derive our celldm(1) and how do we convert to bohr Do we need to convert the atomic position from alat to Bohr or Angstrom must i use bohr as the unit of CELL PARAMETERS or i can use Angstrom and declare it as CELL PARAMETER(angstrom) Agbaoye Ridwan Olamide Federal University of Agriculture, Abeokuta M.Sc.(in view) agbaoyerid...@yahoo.com ___ 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] Clarification of celldm(4) in monoclinic
I am very grateful Prof. Giovanni Cantele, you have saved me a lot of stress Of course cos(ab) was defined in PW.html within A,B,C cos(ab) but not defined in among celldm(1)-celldm(6) Many Thanks to all forum members On Monday, December 21, 2015 5:27 AM, Giovanni Cantele wrote: cos(ab) means cosine of the angle between lattice AXIS a and lattice AXIS b, so xcrysden gives you the correct view see also Doc/INPUT_PW.txt at the description of the variable A, B, C, cosAB, cosAC, cosBC Giovanni On 21 Dec 2015, at 12:16, Ridwan Agbaoye wrote: Good day everyone I need some help with clarification on celldm(4)=cos(ab) Does cos(ab) mean the cosine of angle between lattice parameter a and b or it means the cosine of the product of the lattice parameter a and b that is cosine(lattice parameter a*lattice parameter b) when i view my input file using xcrysden it looks like a cubic structure when i used celldm(4)=cos(ab)=0 since angle between a and b is 90 degree but looked like a monoclinic structure when i used cosine(lattice parameter a*lattice parameter b) Am i getting the cos(ab) wrong Many Thanks to everyone on this 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] Clarification of celldm(4) in monoclinic
Good day everyone I need some help with clarification on celldm(4)=cos(ab) Does cos(ab) mean the cosine of angle between lattice parameter a and b or it means the cosine of the product of the lattice parameter a and b that is cosine(lattice parameter a*lattice parameter b) when i view my input file using xcrysden it looks like a cubic structure when i used celldm(4)=cos(ab)=0 since angle between a and b is 90 degree but looked like a monoclinic structure when i used cosine(lattice parameter a*lattice parameter b) Am i getting the cos(ab) wrong Many Thanks to everyone on this forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Interpretation of vc-relax output
Good Morning Everybody, I need some help withthe interpretation of vc-relax output and conversion from alat to bohr I want to do vc-relax calculation for a monoclinic system but i decide to start with silicon a face-centered cubic system to understand the concept of vc-relax properly I tried vc-relax forsilicon and i got the following output Begin Final Coordinate New Unit Cell volume =276.90769au^3 CELLPARAMETERS(alat=10.60660172) -0.487685488 -0.0 0.487685488 0.000117363 0.487685488 0.487685488 -0.487685488 0.487685488 -0.0 ATOMICPOSITIONS(alat) si -0.035697193 -0.035697193 -0.035697193 si 0.208182292 0.208182292 0.208182292 Endof Final coordinate Myinput file has ibrav=0 nat=2 ntyp=2 CELLPARAMETER cubic -7.5000 0. 7.5000 0. 7.5000 7.5000 -7.5000 7.5000 0. How exactly do we derive our celldm(1) and how do we convert to bohr Do we need to convert the atomic position from alat to Bohr or Angstrom must i use bohr as the unit of CELL PARAMETERS or i can use Angstrom and declare it as CELL PARAMETER(angstrom) Agbaoye Ridwan Olamide Federal University of Agriculture, Abeokuta M.Sc.(in view) agbaoyerid...@yahoo.com ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Manual Kpoint Optimization for a Monoclinic lattice structured organic compound
Good day allI am very grateful for the response to this forum and every individual for contributing to help me with my challenges so far I have corrected the errors on my atomic position, now my kpoint grid has been sorted out all thanks to profs. Kim and Brendas and Prof. Giovani Now im considering doing vc-relax calculation or structural optimization of my structure, I need help with the most appropriate pseudopotential to use considering van der well on the organic compound pedot i have attached a copy of my crystal structure visualized with xcrysden to this mail Thank you all, im very grateful Agbaoye Ridwan OlamideM.Sc. Physics(in View)Federal University of Agriculture, abeokutaagbaoyerid...@yahoo.com On Friday, December 4, 2015 9:01 AM, Giovanni Cantele wrote: 1) what kind of convergence you haven’t reached yet? a) convergence of structural optimisation (atomic positions), or b) convergence of unit cell optimisation (e.g. if you use calculation=‘vc-relax’), or c) self-consistency cycle 2) if by improving the sampling of the Brillouin zone (2x2x2, 3x3x3, ….) nothing happens, maybe it can be that the parameter that prevents you system from reaching convergence is not the k-point grid!!! Which pseudo potentials do you use, and with which cutoff? For organic crystals, van der Waals interactions might be important as well, have you already tried to switch them on? Are you sure that the input positions are right, for example by visualising your input file with XCrysden (such a practice is advisable BEFORE any, maybe computationally expensive, run is started!) 3) the “acceptable" size of the k-point grid depends on the system under investigation and on the property you are interested in (for a given grid, there are properties that might be converged, and others that might be not!). 4) concerning grids that look like n x m x l instead of n x n x n , usually if for example axes a and b are in the ratio a/b = u, than n and m have the inverse ratio (n/m ~ 1/u). For example: a = b = c, use 4 x 4 x 4 ; a = b, c = 2a, use 4 x 4 x 2 (THIS ARE JUST EXAMPLES, THAT DO NOT PROVIDE CONVERGENCE CRITERIA!). GIOVANNI > On 04 Dec 2015, at 14:23, Ridwan Agbaoye wrote: > > > > On Thursday, December 3, 2015 11:41 AM, Ridwan Agbaoye > wrote: > > > I am doing structural optimization for a monoclinic latice structured organic > compound with 13 atoms, 4 types of atom (C,H,O and S) and , i need expertise > advice on how my automatic kpoint grid required for optimization will look > like, i tried 2 2 2 1 1 1, 3 3 3 1 1 1, 4 4 4 1 1 1... 9 9 9 1 1 1 but the > result havent reached convergence yet even with the very very high > computation time it require > > Recently i learnt i am not suppose to use the uniform kpoint grid but the > ones that looked like 6 4 6 1 1 1 , 6 1 1 1 1 1, 8 4 8 1 1 1 etc > > please help me with the best automatic kpoint grid required for my system and > how to determine the kind of kpoint grid to use for subsequent system > calculation > > Thank you very much > > > Agbaoye Ridwan Olamide > M.Sc. (in view) > Federal University of Agriculture, Abeokuta > > > ___ > 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] Manual Kpoint Optimization for a Monoclinic lattice structured organic compound
On Thursday, December 3, 2015 11:41 AM, Ridwan Agbaoye wrote: I am doing structural optimization for a monoclinic latice structured organic compound with 13 atoms, 4 types of atom (C,H,O and S) and , i need expertise advice on how my automatic kpoint grid required for optimization will look like, i tried 2 2 2 1 1 1, 3 3 3 1 1 1, 4 4 4 1 1 1... 9 9 9 1 1 1 but the result havent reached convergence yet even with the very very high computation time it require Recently i learnt i am not suppose to use the uniform kpoint grid but the ones that looked like 6 4 6 1 1 1 , 6 1 1 1 1 1, 8 4 8 1 1 1 etc please help me with the best automatic kpoint grid required for my system and how to determine the kind of kpoint grid to use for subsequent system calculation Thank you very much Agbaoye Ridwan OlamideM.Sc. (in view)Federal University of Agriculture, Abeokuta ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
