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
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.xPWscf 自洽ph.x声子- …
后处理模块
pp.xdos.xbands.x- …
pw.x 输入文件
input.in
! !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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