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QE 快速上手

2019-07-25
cndaqiang
 
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QE 快速上手记录
仅是一个快速上手了。。。。。
后续学习笔记Learn QE1 电子结构计算,Learn QE2 原子结构相关:结构优化,MD,NEB

参考

QE的那点B事儿

安装

mkdir ~/soft/intel17
cd ~/soft/intel17/
module load mpi/intelmpi/2017.4.239
wget https://github.com/QEF/q-e/releases/download/qe-6.4.1/qe-6.4.1_release_pack.tgz
tar xzvf qe-6.4.1_release_pack.tgz 
cd qe-6.4.1/
./configure -h
./configure FC=ifort CC=icc MPIF90=mpiifort
make -j20 pwall
#如果要生成赝势,需要编译
make -j20 ld1
make -j20 upf

程序说明

alpha2f.x     epa.x         fermi_velocity.x               iotk                molecularpdos.x       plotband.x  pw2bgw.x        q2qstar.x       wfck2r.x
average.x     epsilon.x     fqha.x                         iotk_print_kinds.x  neb.x                 plotproj.x  pw2critic.x     q2r.x
bands.x       ev.x          fs.x                           iotk.x              open_grid.x           plotrho.x   pw2gw.x         q2trans_fd.x
cell2ibrav.x  fd_ef.x       generate_rVV10_kernel_table.x  kpoints.x           path_interpolation.x  pmw.x       pw2wannier90.x  q2trans.x
dist.x        fd_ifc.x      generate_vdW_kernel_table.x    lambda.x            phcg.x                ppacf.x     pwcond.x        sumpdos.x
dos.x         fd.x          ibrav2cell.x                   manypw.x            ph.x                  pp.x        pwi2xsf.x       wannier_ham.x
dynmat.x      fermi_proj.x  initial_state.x                matdyn.x            plan_avg.x            projwfc.x   pw.x            wannier_plot.x

各个文件夹里面有不同程序的example
各个程序的输入文件参考INPUT DATA DESCRIPTION

计算模块

pw平面波

  • pw.x PWscf 自洽
  • ph.x 声子

后处理模块

  • pp.x
  • dos.x
  • bands.x

pw.x 输入文件

input.in

参考Input File Description

! !开头是注释
! 控制参数模块
! &开始
! /结束

&CONTROL
calculation="scf", !scf自洽计算
restart_mode="from_scratch", !从之前的计算结果中提取
prefix="Pt", !前缀
pseudo_dir=".",
outdir="./out",
!! ...更多参数
/

&SYSTEM
!计算体系
ibrav=1, !晶格的形状,参见https://www.quantum-espresso.org/Doc/INPUT_PW.html!idm199
celldm(1)=4.981, !晶格参数a,b,c,cos(ab),cos(ac),cos(bc)
           !a,b,c是原子单位制 1 Bohr = 1 a0= 0.52917720859˚A
           !1˚A=1/0.52917720859=1.8897
           !根据ibrav参数,决定要设置的celldm(i),i的取值范围
#celldm()也可以用A,B,C,(单位是Angstrom),cosAB, cosAC, cosBC代替
nat=1,  ! num of atoms
ntyp=1, ! type of species  ,同位素,赝势不同,等为不同species
ecutwfc=25, !原子单位制Ry
             !1 Ry = 1/2 Ha = 13.60569193 eV
             !与VASP相同,可以通过看赝势选择
!ecutrho=,   !与赝势,ecutwfc能有关
             !越大收敛的越平滑,震荡少
             !default 4 times ecutwfc
/

&ELECTRONS
!电子步参数
mixing_beta=0.7, !old 30% new 70%
conv_thr=1d-6,   !收敛标准
/

![ &IONS
!  ...
! / ]

![ &CELL
!  ...
! / ]

ATOMIC_SPECIES
Pt 195.084 Pt.pbe-n-kjpaw_psl.1.0.0.UPF
! X  Mass_X  PseudoPot_X
! Y  Mass_Y  PseudoPot_Y
! Z  Mass_Z  PseudoPot_Z

ATOMIC_POSITIONS alat
Pt 0.0 0.0 0.0
!{ alat 分子坐标| bohr | crystal | angstrom | crystal_sg }
!  X 0.0  0.0  0.0  {if_pos(1) if_pos(2) if_pos(3)}
!  Y 0.5  0.0  0.0
!  Z O.0  0.2  0.2
!控制行不能这样注释
!ATOMIC_POSITIONS alat !{ alat 分子坐标| bohr | crystal | angstrom | crystal_sg }


K_POINTS automatic 
10 10 10 1 1 1
!{ tpiba | automatic 自动 | crystal | gamma 只有k=0的点| tpiba_b | crystal_b | tpiba_c | crystal_c }
!if (gamma)
!   nothing to read
!if (automatic)
!   nk1, nk2, nk3, k1, k2, k3
#nk1,nk2,nk3 k点数量, k1,k2,k3平移项,只能0,1
#nk为奇数时,取样过gamma点
!if (not automatic)
!   nks
!   xk_x, xk_y, xk_z,  wk

赝势

下载pseudopotentials
里面有建议的截断能

    Suggested minimum cutoff for wavefunctions:  39. Ry
    Suggested minimum cutoff for charge density: 401. Ry

可以帮助设置

ecutwfc=40,  !要大于赝势中的Suggested minimum cutoff for wavefunctions:  39. Ry
             !原子单位制Ry
             !1 Ry = 1/2 Ha = 13.60569193 eV
             !
!ecutrho=,   !!要大于赝势中的Suggested minimum cutoff for charge density: 401. Ry
             !与赝势,ecutwfc能有关
             !越大收敛的越平滑,震荡少
             !default 4 times ecutwfc

示例

[cndaqiang@admin1 Pt-cutoff]$ vi Pt.pbe-n-kjpaw_psl.1.0.0.UPF 

<UPF version="2.0.1">
  <PP_INFO>
Generated using "atomic" code by A. Dal Corso  v.6.3
Author: ADC
Generation date:  6Sep2018
Pseudopotential type: PAW
Element: Pt
Functional:  SLA  PW   PBX  PBC
    Suggested minimum cutoff for wavefunctions:  39. Ry
    Suggested minimum cutoff for charge density: 401. Ry
    The Pseudo was generated with a Scalar-Relativistic Calculation
    Local Potential by smoothing AE potential with Bessel fncs, cutoff radius:   2.4000
    Pseudopotential contains additional information for GIPAW reconstruction.
    Valence configuration:
    nl pn  l   occ       Rcut    Rcut US       E pseu
    6S  1  0  1.00      2.000      2.200    -0.415930
    6P  2  1  0.00      2.300      2.500    -0.061766
    5D  3  2  9.00      1.000      2.200    -0.451355
    Generation configuration:
    6S  1  0  1.00      2.000      2.200    -0.415928
    6S  1  0  0.00      2.000      2.200     4.400000
    6P  2  1  0.00      2.300      2.500    -0.061766
    6P  2  1  0.00      2.300      2.500     6.400000
    5D  3  2  9.00      1.000      2.200    -0.451352
    5D  3  2  0.00      1.000      2.200     0.800000
    Pseudization used: troullier-martins

...

运行

#进行电子自洽scf计算
mpirun -np 4 pw.x < input.in | tee result

分析

energy=$(grep ! result |awk '{ print $5}')
time=$(grep  PWSCF  result  |grep CPU | awk '{print $5 }')

pp.x电荷密度分析

准备输入文件,语法INPUT_PP

pp.x < input.pp.in > result.pp

输入文件示例

&INPUTPP
outdir="./out", !同input.in
prefix="Pt",    !同input.in
plot_num=0, !功能0 电荷密度
/

&PLOT
iflag=3, !3=3D,2=2D
output_format=6, !保存数据格矢 6  = format as gaussian cube file  (3D)     (can be read by many programs)
fileout="Pt.cube",
nx=64,ny=64,nz=64,
/

用VESTA打开Pt.cube查看电荷密度,如图 @李二狗-QE的那点B事儿1

报错

参数错误


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine  read_namelists (1):
      bad line in namelist &system: "ntype=1, ! type of species  ,同位素,赝势不同,等为不同species" (error could be in the previous line)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

语法错误,ntyp而不是ntype

并行错误

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine n_plane_waves (1):
     No plane waves found: running on too many processors?
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

核太多了,减少mpirun -np后面跟的核数

赝势读取失败

     DEPRECATED: use true lattice parameter, not A to a.u. conversion factor
FoX_NODE_IS_NULL           
210 extractDataContentRealDpArr
abort: 

换赝势即可


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