Thanks for your help once again. I do not have XCrysDen and I have been having problems installing it. This is weird as with Crystal builder the atoms were well separated and different. One more thing: Where can I find the ccorect coordinates? any idea how to form the atomic positions?
Thanks ________________________________ From: [email protected] <[email protected]> on behalf of Duc-Long NGUYEN <[email protected]> Sent: Monday, January 11, 2016 9:53 PM To: PWSCF Forum Subject: Re: [Pw_forum] Atomic positions for Black Phosphorus calculations Hi, You could use xcrysden to check your input. This is the result with your input: Number of Atoms: 8 Number of Frames: 12 WARNING: Atom 1 and atom 3 overlap !!! Atom 3 deleted !!! WARNING: Atom 2 and atom 7 overlap !!! Atom 7 deleted !!! WARNING: Atom 4 and atom 8 overlap !!! Atom 8 deleted !!! WARNING: Atom 5 and atom 6 overlap !!! Atom 6 deleted !!! That was also why pwscf showed that error. Duc-Long On 1/12/2016 7:46 AM, Elio Physics wrote: Dear Duc-Long, thanks for your response. I do not think they have the same coordinate. The "y" coordinate of one is 0.10168 while that of the 2nd is 1.10168, that is a difference of 1 ang. Elio ________________________________ From: [email protected]<mailto:[email protected]> <[email protected]><mailto:[email protected]> on behalf of Duc-Long NGUYEN <[email protected]><mailto:[email protected]> Sent: Monday, January 11, 2016 9:38 PM To: PWSCF Forum Subject: Re: [Pw_forum] Atomic positions for Black Phosphorus calculations Dear Elio, ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 P -0.10168 0.10168 0.08056 P 0.10168 0.89832 0.91944 P -0.10168 1.10168 0.08056 P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 These two atom positions have the same coordinate. This could be the problem. Duc-Long On 1/12/2016 6:44 AM, Elio Physics wrote: Dear all, I am trying to perform some calculations on Black Phosphorus (BP). To get the atomic positions I used the Crystal Builder, where I have chosen the lattice type to be base centered orthorhombic. The "builder" produced a set of cartesian and fractional (in terms of the primitive cell vectors) . I have used the fractional ones and I have also used ibrav=0 with the CELL_PARAMETERS defined as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I have got the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from check_atoms : error # 1 atoms # 1 and # 4 overlap! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Doing the same calculation with ibrav=8 and using the coordinates produced by the Crystal builder for a simple orthorhombic does not produce any errors. Can anyone please tell me what is wrong with atoms (1) and (4). Is BP simple or base centered orthorhombic..Where can I find the coorect atomic position of bulk BP? The scf input is below: &CONTROL prefix='bp', calculation='scf', restart_mode='from_scratch', wf_collect=.true., forc_conv_thr=1.D-4 etot_conv_thr=1.D-5 tstress=.true., tprnfor=.true., pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo', outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT' / &SYSTEM ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, ecutrho=40, occupations='smearing', london=.true., smearing='mp', degauss=0.035,nbnd=32 / &ELECTRONS conv_thr=1.D-8, mixing_beta=0.1 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='bfgs' press=0.0 / ATOMIC_SPECIES P 30.97376 P.pbe-n-van.UPF ATOMIC_POSITIONS crystal P -0.89832 0.89832 0.91944 P -0.39832 0.39832 0.58056 P -0.10168 0.10168 0.08056 P 0.10168 0.89832 0.91944 P -0.10168 1.10168 0.08056 P -0.60168 0.60168 0.41944 P -0.39832 1.39832 0.58056 P 0.39832 0.60168 0.41944 K_POINTS automatic 2 2 2 0 0 0 CELL_PARAMETERS alat 0.5000 -1.58106 0.0000 0.500 1.58106 0.0000 0.0000 0.00000 4.3763 thanks Elio Arbid University of Nottingham UK _______________________________________________ Pw_forum mailing list [email protected]<mailto:[email protected]> http://pwscf.org/mailman/listinfo/pw_forum -- Duc-Long Nguyen Graduate Student, Molecular Science and Technology Program, TIGP Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan Phone +886 979279073 _______________________________________________ Pw_forum mailing list [email protected]<mailto:[email protected]> http://pwscf.org/mailman/listinfo/pw_forum
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