[QE-users] Large difference between lattice structure simulated by pwscf code and cp.x code
Jie Peng
jiepeng at umd.edu
Thu Apr 12 19:24:31 CEST 2018
Stefano:
Hi, here are just some follow ups on the comparison between pwscf and cp.x.
Thank you very much for the suggestions, I did vc-relax in cp.x using
different size supercells, and just from eyebow, a 2*2*2 supercell already
gives considerable agreement with pwscf results. Right now I am quantifying
the difference between the lattice structure from cp.x and pw.x by writing
a code to calculate Radial Distribution Function.
I have read your papers on Quasi-harmonic phonons and thermal properties
calculation, which also helps me understand a lot of concepts in thermal
heat transport simulations via DFT. Just want to share my appreciation
here..
Thanks for your help.
On Thu, Apr 5, 2018 at 2:02 PM, Stefano Baroni <baroni at sissa.it> wrote:
> not “unphysical” just inaccurate … SB
>
>
> On 5 Apr 2018, at 19:39, Jie Peng <jiepeng at umd.edu> wrote:
>
> Stefano:
>
> I think that is right on the spot! Let me do a calculation using Gamma
> point only in pwscf and then compare again.
>
> So for cp.x, in order to get an accurate lattice structure, one would have
> to use a n*n*n supercell instead of a unit cell since it can only process
> real wavefunctions that are located at Gamma point only. Computations done
> on a single unit cell using cp.x code, therefore usually produces results
> that are unphysical. Is this the correct way to interpretate?
>
> Thank you very much!
>
> Best
> Jie
>
> On Thu, Apr 5, 2018 at 2:22 AM, Stefano de Gironcoli <degironc at sissa.it>
> wrote:
>
>> Dear Jie Peng,
>>
>> the cp.x code assumes gamma point sampling and does not process your
>> k-point definition card, while pw.x is using, a rather dense, grid of
>> points in the BZ.
>>
>> I think this is the most relevant difference in your two inputs.
>>
>> To see if this is the case you can repeat the pw.x calculation with
>>
>> K_POINT Gamma
>>
>> Is the 10 8 8 grid really necessary ? is the system metallic ?
>>
>> if not I guess a smaller grid (like 6 4 4 or less) could be sufficient
>> and then you could use the cp.x code with a corresponding supercell if you
>> wish so.
>>
>> stefano
>>
>> On 05/04/2018 04:16, Jie Peng wrote:
>>
>> Dear all Quantum Espresso users:
>>
>> I have used pw.x and cp.x code to compute equilibrium lattice structure
>> of 1T-HfS2 (Halfnium Disulfide) respectively, and I find that they give
>> very different results.
>>
>> *For pwscf simulation, the input file are given below.*
>> *&control*
>> * calculation='vc-relax',*
>> *! restart_mode='from_scratch',*
>> * tstress = .true.*
>> * tprnfor = .true.*
>>
>> * wf_collect=.true.*
>> * etot_conv_thr=1e-6*
>> * forc_conv_thr=1e-5*
>> * prefix='Hf',*
>> * pseudo_dir='/potential'*
>> * outdir='./tmp/',*
>> * /*
>> * &system*
>> * ibrav= 4,*
>> * a=3.6529*
>> * c=5.6544*
>> * nat= 3, ntyp= 2,*
>> * ecutwfc =50*
>> * vdw_corr='DFT-D',*
>> * ! lspinorb=.true.*
>> * ! noncolin=.true.*
>> * ! ecutrho=300*
>> * ! nbnd=14*
>> *! occupations='smearing'*
>> *! smearing='gaussian'*
>> *! degauss=0.01*
>> * ! nspin=2*
>> * ! starting_magnetization(1)=0.1*
>> */*
>> * &electrons*
>> * conv_thr=1e-12*
>> * mixing_beta = 0.7*
>> */*
>> * &ions*
>> * ion_dynamics = 'bfgs'*
>> * /*
>> * &cell*
>> * cell_dynamics = 'bfgs'*
>>
>> */*
>> *ATOMIC_SPECIES*
>> * Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> * S 32.065 S.pbe-mt_fhi.UPF*
>> *ATOMIC_POSITIONS (crystal)*
>> *Hf -0.000000000 -0.000000000 -0.000000000*
>> *S 0.666666667 0.333333333 0.257234636*
>> *S 0.333333333 0.666666667 -0.257234636*
>> * K_POINTS automatic*
>> *10 8 8 0 0 0*
>>
>> The relaxed lattice structure is the one included in this input file (I
>> first did the full relaxation after which I copied the resulting relaxed
>> lattice structure into this input file, then modified this file to compute
>> electronic structure and phonons). The forces acting on atoms are small and
>> I believe this should be the equilibrium structure of 1T-HfS2.
>>
>> * Forces acting on atoms (Ry/au):*
>>
>> * atom 1 type 1 force = 0.00000000 0.00000000
>> 0.00000000*
>> * atom 2 type 2 force = 0.00000000 0.00000000
>> -0.00001404*
>> * atom 3 type 2 force = -0.00000000 0.00000000
>> 0.00001404*
>>
>> * Total force = 0.000020 Total SCF correction = 0.000001*
>>
>>
>> * entering subroutine stress ...*
>>
>> * total stress (Ry/bohr**3) (kbar) P=
>> -0.16*
>> * -0.00000129 -0.00000000 0.00000000 -0.19 -0.00
>> 0.00*
>> * -0.00000000 -0.00000129 0.00000000 -0.00 -0.19
>> 0.00*
>> * 0.00000000 0.00000000 -0.00000078 0.00 0.00
>> -0.12*
>>
>> *For cp.x, *I carefully follow the steps required to carry out a CP
>> simulations: Relax electronic structure to ground state -> Relax the ion
>> positions -> relax the cells. The input files are attached below.
>>
>> *Electronic relaxation*
>> *&control*
>> * calculation='cp',*
>> * title='Halfnium disulfide'*
>> * restart_mode='from_scratch',*
>> * ndr=50,*
>> * ndw=50,*
>> * nstep=10000,*
>> * iprint=100*
>> * isave=100,*
>> * tstress = .true.*
>> * tprnfor = .true.*
>> * dt=10,*
>> * wf_collect=.true.*
>> * etot_conv_thr=1e-6*
>> * forc_conv_thr=1e-3*
>> * ekin_conv_thr=1e-5*
>> * prefix='HfS2',*
>> * pseudo_dir='/home/jpeng/HfS2/potential'*
>> * outdir='./tmp/',*
>> * /*
>> * &system*
>> * ibrav= 4,*
>> * a=3.6529*
>> * c=5.6544*
>> * nat= 3, ntyp= 2,*
>> * ecutwfc =50*
>> * vdw_corr='DFT-D',*
>> * ! lspinorb=.true.*
>> * ! noncolin=.true.*
>> * ! ecutrho=300*
>> * ! nbnd=14*
>> *! occupations='smearing'*
>> *! smearing='gaussian'*
>> *! degauss=0.01*
>> * ! nspin=2*
>> * ! starting_magnetization(1)=0.1*
>> *! Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> *! S 32.065 S.pbe-mt_fhi.UPF*
>> */*
>> * &electrons*
>> * electron_dynamics='damp'*
>> *! electron_velocities='zero'*
>> * emass=400*
>> * emass_cutoff=1*
>> * electron_damping=0.1*
>> */*
>> * &ions*
>> * ion_dynamics = 'none'*
>> * /*
>> * &cell*
>> * cell_dynamics = 'none'*
>>
>> */*
>> *ATOMIC_SPECIES*
>> * Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> * S 32.065 S.pbe-mt_fhi.UPF*
>> *ATOMIC_POSITIONS (crystal)*
>> *Hf -0.000000000 -0.000000000 -0.000000000*
>> *S 0.666666667 0.333333333 0.257234636*
>> *S 0.333333333 0.666666667 -0.257234636*
>> * K_POINTS automatic*
>> *10 8 8 0 0 0*
>>
>> Ion relaxation
>> *&control*
>> * calculation='cp',*
>> * title='Halfnium disulfide'*
>> * restart_mode='restart',*
>> * ndr=50,*
>> * ndw=51,*
>> * nstep=50000,*
>> * iprint=100*
>> * isave=100,*
>> * tstress = .true.*
>> * tprnfor = .true.*
>> * dt=10,*
>> * wf_collect=.true.*
>> * etot_conv_thr=1e-6*
>> * forc_conv_thr=1e-3*
>> * ekin_conv_thr=1e-5*
>> * prefix='HfS2',*
>> * pseudo_dir='/home/jpeng/HfS2/potential'*
>> * outdir='./tmp/',*
>> * /*
>> * &system*
>> * ibrav= 4,*
>> * a=3.6529*
>> * c=5.6544*
>> * nat= 3, ntyp= 2,*
>> * ecutwfc =50*
>> * vdw_corr='DFT-D',*
>> * ! lspinorb=.true.*
>> * ! noncolin=.true.*
>> * ! ecutrho=300*
>> * ! nbnd=14*
>> *! occupations='smearing'*
>> *! smearing='gaussian'*
>> *! degauss=0.01*
>> * ! nspin=2*
>> * ! starting_magnetization(1)=0.1*
>> *! Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> *! S 32.065 S.pbe-mt_fhi.UPF*
>> */*
>> * &electrons*
>> * electron_dynamics='damp'*
>> *! electron_velocities='zero'*
>> * emass=400*
>> * emass_cutoff=1*
>> * electron_damping=0.1*
>> */*
>> * &ions*
>> * ion_dynamics = 'damp'*
>> * ion_damping=0.1*
>> * ion_nstepe=10*
>> * /*
>> * &cell*
>> * cell_dynamics = 'none'*
>>
>> */*
>> *ATOMIC_SPECIES*
>> * Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> * S 32.065 S.pbe-mt_fhi.UPF*
>> *ATOMIC_POSITIONS (crystal)*
>> *Hf -0.000000000 -0.000000000 -0.000000000*
>> *S 0.666666667 0.333333333 0.257234636*
>> *S 0.333333333 0.666666667 -0.257234636*
>> * K_POINTS automatic*
>> *10 8 8 0 0 0*
>>
>> Cell relaxation
>> *&control*
>> * calculation='vc-cp',*
>> * title='Halfnium disulfide'*
>> * restart_mode='reset_counters',*
>> * ndr=51,*
>> * ndw=52,*
>> * nstep=50000,*
>> * iprint=100*
>> * isave=100,*
>> * tstress = .true.*
>> * tprnfor = .true.*
>> * dt=10,*
>> * wf_collect=.true.*
>> * etot_conv_thr=1e-6*
>> * forc_conv_thr=1e-3*
>> * ekin_conv_thr=1e-5*
>> * prefix='HfS2',*
>> * pseudo_dir='/home/jpeng/HfS2/potential'*
>> * outdir='./tmp/',*
>> * /*
>> * &system*
>> * ibrav= 4,*
>> * a=3.6529*
>> * c=5.6544*
>> * nat= 3, ntyp= 2,*
>> * ecutwfc =50*
>> * vdw_corr='DFT-D',*
>> * ! lspinorb=.true.*
>> * ! noncolin=.true.*
>> * ! ecutrho=300*
>> * ! nbnd=14*
>> *! occupations='smearing'*
>> *! smearing='gaussian'*
>> *! degauss=0.01*
>> * ! nspin=2*
>> * ! starting_magnetization(1)=0.1*
>> *! Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> *! S 32.065 S.pbe-mt_fhi.UPF*
>> */*
>> * &electrons*
>> * electron_dynamics='damp'*
>> *! electron_velocities='zero'*
>> * emass=400*
>> * emass_cutoff=1*
>> * electron_damping=0.1*
>> */*
>> * &ions*
>> * ion_dynamics = 'damp'*
>> * ion_damping=0.1*
>> * ion_nstepe=10*
>> * /*
>> * &cell*
>> * cell_dynamics = 'pr'*
>> *! cell_damping=0.1*
>> *! cell_dofree=volume*
>> */*
>> *ATOMIC_SPECIES*
>> * Hf 95.94 Hf.pbe-mt_fhi.UPF*
>> * S 32.065 S.pbe-mt_fhi.UPF*
>> *ATOMIC_POSITIONS (crystal)*
>> *Hf -0.000000000 -0.000000000 -0.000000000*
>> *S 0.666666667 0.333333333 0.257234636*
>> *S 0.333333333 0.666666667 -0.257234636*
>> * K_POINTS automatic*
>> *10 8 8 0 0 0*
>>
>> The final equilibrium lattice structure obtained by cp.x is:
>> * CELL_PARAMETERS*
>> * 8.27944202 -3.49986616 -1.28541441*
>> * 0.43381045 6.25063702 -0.26433640*
>> * -1.81611680 -0.30736678 9.28229385*
>>
>> * System Density [g/cm^3] : 3.7550323993*
>>
>>
>> * System Volume [A.U.^3] : 477.6950599279*
>>
>>
>> * Center of mass square displacement (a.u.): 0.271737*
>>
>> * Total stress (GPa)*
>> * -0.00003957 0.00000336 0.00017132*
>> * 0.00000336 -0.00001393 0.00003875*
>> * 0.00017132 0.00003875 0.00048005*
>> * ATOMIC_POSITIONS*
>> * Hf -0.57392945538368E+00 -0.32523714658422E+00
>> -0.78842946683202E-01*
>> * S 0.61817237992192E+01 0.34715217744206E+01
>> 0.20852180260292E+00*
>> * S 0.31507619982481E+00 0.41860506478142E+01
>> -0.20961035507250E+01*
>>
>> * ATOMIC_VELOCITIES*
>> * Hf -0.49417894612947E-07 -0.41246570825668E-07
>> -0.28182774835127E-06*
>> * S 0.29443574450584E-06 0.17988901894696E-06
>> 0.34817154465079E-06*
>> * S -0.14657506118618E-06 -0.56477323752712E-07
>> 0.49507043808484E-06*
>>
>> * Forces acting on atoms (au):*
>> * Hf -0.18727766763523E-03 -0.15291863668542E-03
>> -0.99976280595181E-03*
>> * S 0.33856074345196E-03 0.20689440901408E-03
>> 0.40153992932368E-03*
>> * S -0.17602213243772E-03 -0.68887225779463E-04
>> 0.57298561574671E-03*
>>
>> A visualization is attached here
>> <image.png>
>>
>> while by pwscf, the equilibrium lattice structure is:
>> * CELL_PARAMETERS*
>> * 6.90298059 -3.45149030 0.00000000*
>> * 0.00000000 5.97815655 0.00000000*
>> * 0.00000000 0.00000000 10.68526745*
>>
>> * System Density [g/cm^3] : 4.0679453101*
>>
>>
>> * System Volume [A.U.^3] : 440.9499858676*
>>
>>
>> * Center of mass square displacement (a.u.): 0.000000*
>>
>> * Total stress (GPa)*
>> * 32.06481501 -0.01335027 -0.00956254*
>> * -0.01335027 32.07951164 -0.00592770*
>> * -0.00956139 -0.00592704 2.04176052*
>> * ATOMIC_POSITIONS*
>> * Hf 0.00000000000000E+00 -0.00000000000000E+00
>> -0.00000000000000E+00*
>> * S 0.34514902988605E+01 0.19927188491672E+01
>> 0.27486208819801E+01*
>> * S -0.34514902047533E-08 0.39854377043125E+01
>> -0.27486208819801E+01*
>>
>> * ATOMIC_VELOCITIES*
>> * Hf 0.00000000000000E+00 0.00000000000000E+00
>> 0.00000000000000E+00*
>> * S 0.00000000000000E+00 0.00000000000000E+00
>> 0.00000000000000E+00*
>> * S 0.00000000000000E+00 0.00000000000000E+00
>> 0.00000000000000E+00*
>>
>> * Forces acting on atoms (au):*
>> * Hf 0.70847502228925E-03 0.43071957102166E-03
>> -0.17703368862259E-04*
>> * S -0.52668423530029E-03 -0.28607208606422E-03
>> -0.81547327015321E-01*
>> * S -0.41998284595312E-03 -0.22039679837681E-03
>> 0.81837284893753E-01*
>>
>> A visulization is attached below
>> <image.png>
>>
>>
>> I am expecting some difference because pw.x uses DFT and BFGS algorithm
>> to relax the lattice structure while cp.x uses CP method, but not so large
>> a difference. Especially since the lattice structure given by pw.x agrees
>> with experiments and other published works, I am suspecting is it because I
>> have not correctly carried out variable cell CP simulations.
>>
>> Can anyone help me understand the discrepancy I see in the results
>> produced by pw.x and cp.x code? Or pointing out any mistake I have made
>> during my simulations?
>>
>> Thank you in advance for your help, sincerely!
>>
>> Best
>> Jie
>> --
>> ------------------------------------------------------------
>> ------------------------------------------------------------
>> Jie Peng
>> PhD student
>> 2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland
>> College Park, Maryland, USA
>> Phone:(+1) 240-495-9445
>> Email: jiepeng at umd.edu
>>
>>
>>
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>
>
>
> --
> ------------------------------------------------------------
> ------------------------------------------------------------
> Jie Peng
> PhD student
> 2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland
> College Park, Maryland, USA
> Phone:(+1) 240-495-9445
> Email: jiepeng at umd.edu
>
> _______________________________________________
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> https://lists.quantum-espresso.org/mailman/listinfo/users
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--
------------------------------------------------------------------------------------------------------------------------
Jie Peng
PhD student
2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland
College Park, Maryland, USA
Phone:(+1) 240-495-9445
Email: jiepeng at umd.edu
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