QUANTUM ESPRESSO：vc-relax - 谢华的博客

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QUANTUM ESPRESSO：vc-relax

vc-relax:对晶体的晶格常数和原子位置进行结构优化，需要设置cell_dynamics,press_conv_thr等参数。由于后续需要进行phonon计算，最好在relax过程中将相应的计算精度设置的高一些，否则容易在phonon计算中出现虚频，包括conv_thr、etot_conv_thr、forc_conv_thr参数。对于二维材料，在计算中可以使用参数assume_isolated='2D' 对于低维材料体系（该参数的设置好像会导致在Wannier拟合中导致WFs虚部太大，可能是由于该参数的设置导致的，在Graphene的能带拟合中，注释掉该参数后，得到的WFs变成实数。），在优化时对于k点设置要设置的多一点，否则容易导致结构优化的晶格常数不准确，以及phonon计算中的声子谱不收敛。例如：对于石墨烯，需要设置到36*36*1,同时对于smearing设置成mp比较合适，参考QE_forrum中Graphene的phonon计算的相关内容。并且，ecutwfc和ecutrho也不能使用Standard solid-state pseudopotentials(SSP),使用未收敛的截断能，导致计算得到的声子谱在$\Gamma$点出现虚频。

采用ibrav=0设置结构的 vc-relax输入文件

note:采用分数坐标时，坐标给到小数点后10位比较合适，在小数点位数不够时，容易在phonon计算中，对于q点对称性的计算会有问题。最好将outdir统一设置为outdir='./',由于后续epw计算中需要使用outdir='./'

&CONTROL

calculation = "vc-relax"

restart_mode = "from_scratch"

prefix = "carbyne"

outdir = "./"

pseudo_dir = "./pseudo/"

verbosity = "high"

tprnfor = .true.

tstress = .true.

etot_conv_thr = 1.0d-8

forc_conv_thr = 1.0d-7

&SYSTEM

ibrav = 0

nat = 2

ntyp = 1

nbnd = 22

occupations = 'fixed'

ecutwfc = 50

ecutrho = 400

&ELECTRONS

conv_thr = 1.000e-12

electron_maxstep = 200

mixing_beta = 0.7

startingpot = "atomic"

startingwfc = "atomic+random"

&IONS

ion_dynamics = "bfgs"

&CELL

cell_dofree = "x"

cell_dynamics = "bfgs"

press_conv_thr = 0.01

K_POINTS {automatic}

200 1 1 0 0 0

ATOMIC_SPECIES

C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF

CELL_PARAMETERS (angstrom)

2.565600000 0.000000000 0.000000000

0.000000000 10.000000000 0.000000000

0.000000000 0.000000000 10.000000000

ATOMIC_POSITIONS (angstrom)

C 0.0000000000 5.0000000000 5.0000000000 0 0 0

C 1.2640800000 5.0000000000 5.0000000000 1 0 0

计算过程中使用下列命令可以查看优化过程中的收敛情况：

查看优化过程中各原子总的受力情况:

grep " Total force =" vc-relax.out

查看优化过程中各原子的受力情况：

grep -A 20 "Forces acting on atoms (cartesian axes, Ry/au):" vc-relax.out

查看优化过程中能量的变化过程

grep ! vc-relax.out

查看优化过程中压力张量大小

grep -A 12 " Total force =" vc-relax.out

计算结束后，运行

awk '/Begin final coordinates/,/End final coordinates/{print $0}' vc-relax.out |sed -n '5,$p'

得到以下输出（或在输出文件中可以找到）（vc-relax的结果）

Begin final coordinates

new unit-cell volume = 1731.30152 a.u.^3 ( 256.55242 Ang^3 )

density = 0.15548 g/cm^3

CELL_PARAMETERS (angstrom)

2.565524159 0.000000000 0.000000000

0.000000000 10.000000000 0.000000000

0.000000000 0.000000000 10.000000000

ATOMIC_POSITIONS (angstrom)

C 0.0000000000 5.0000000000 5.0000000000 0 0 0

C 1.2639655349 5.0000000000 5.0000000000 1 0 0

End final coordinates

采用 $ibrav \neq 0$ 以及A, B, C, cosAB, cosAC, cosBC的结构进行结构优化

&CONTROL

calculation = "vc-relax"

restart_mode = "from_scratch"

prefix = "carbyne"

outdir = "./outdir/"

pseudo_dir = "./pseudo/"

verbosity = "high"

tprnfor = .true.

tstress = .true.

etot_conv_thr = 1.0d-6

forc_conv_thr = 1.0d-5

&SYSTEM

ibrav = 6

A = 10.0

C = 2.5656

nat = 2

ntyp = 1

nbnd = 22

occupations = 'fixed'

ecutwfc = 50

ecutrho = 400

&ELECTRONS

conv_thr = 1.000e-9

electron_maxstep = 200

mixing_beta = 0.7

startingpot = "atomic"

startingwfc = "atomic+random"

&IONS

ion_dynamics = "bfgs"

&CELL

cell_dofree = "ibrav+z"

cell_dynamics = "bfgs"

press_conv_thr = 0.01

K_POINTS {automatic}

1 1 100 0 0 0

ATOMIC_SPECIES

C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS (angstrom)

C 5.0000000000 5.0000000000 0.0000000000 0 0 0

C 5.0000000000 5.0000000000 1.2640800000 0 0 1

计算结束后，运行

awk '/Begin final coordinates/,/End final coordinates/{print $0}' vc-relax.out

得到以下输出（或在输出文件中可以找到）（vc-relax的结果）

Begin final coordinates

new unit-cell volume = 1731.30161 a.u.^3 ( 256.55243 Ang^3 )

density = 0.15548 g/cm^3

CELL_PARAMETERS (alat= 18.89726125)

1.000000000 0.000000000 0.000000000

0.000000000 1.000000000 0.000000000

0.000000000 0.000000000 0.256552429

ATOMIC_POSITIONS (angstrom)

C 5.0000000000 5.0000000000 0.0000000000 0 0 0

C 5.0000000000 5.0000000000 1.2640744811 0 0 1

End final coordinates

采用A, B, C, cosAB, cosAC, cosBC或者celldm进行vc-relax后，如果优化中设置了cell_dofree = "ibrav"，会输出新的ibrav以及celldm(i)的值。采用下列命令将可以得到新的ibrav参数和celldm(i):

grep -B 40 "Begin final coordinates" vc-relax.out

Energy error = 1.3E-12 Ry

Gradient error = 3.0E-31 Ry/Bohr

Cell gradient error = 6.9E-04 kbar

ibrav = 4

celldm(1) = 4.66232677

celldm(3) = 8.10636498

Input lattice vectors:

1.00000020 0.00000000 0.00000000

-0.50000010 0.86602557 0.00000000

0.00000000 0.00000000 8.10636657

New lattice vectors in INITIAL alat:

1.00000020 0.00000000 0.00000000

-0.50000010 0.86602557 0.00000000

0.00000000 0.00000000 8.10636657

New lattice vectors in NEW alat (for information only):

1.00000000 0.00000000 0.00000000

-0.50000000 0.86602540 0.00000000

0.00000000 0.00000000 8.10636498

Discrepancy in bohr = 0.000000 0.000000 0.000000

bfgs converged in 2 scf cycles and 1 bfgs steps

(criteria: energy < 1.0E-08 Ry, force < 1.0E-07Ry/Bohr, cell < 1.0E-03kbar)

End of BFGS Geometry Optimization

Final enthalpy = -36.8880451464 Ry

File ./outdir/graphene.bfgs deleted, as requested

Begin final coordinates

采用 $ibrav \neq 0$ 以及celldm(i), i=1,6的结构进行结构优化

&CONTROL

calculation = "vc-relax"

restart_mode = "from_scratch"

prefix = "carbyne"

outdir = "./outdir/"

pseudo_dir = "./pseudo/"

verbosity = "high"

tprnfor = .true.

tstress = .true.

etot_conv_thr = 1.0d-6

forc_conv_thr = 1.0d-5

&SYSTEM

ibrav = 6

celldm(1) = 18.89726125

celldm(3) = 0.256552429

nat = 2

ntyp = 1

nbnd = 22

occupations = 'fixed'

ecutwfc = 50

ecutrho = 400

&ELECTRONS

conv_thr = 1.000e-9

electron_maxstep = 200

mixing_beta = 0.7

startingpot = "atomic"

startingwfc = "atomic+random"

&IONS

ion_dynamics = "bfgs"

&CELL

cell_dofree = "ibrav+z"

cell_dynamics = "bfgs"

press_conv_thr = 0.01

K_POINTS {automatic}

1 1 100 0 0 0

ATOMIC_SPECIES

C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS (angstrom)

C 5.0000000000 5.0000000000 0.0000000000 0 0 0

C 5.0000000000 5.0000000000 1.2640800000 0 0 1

计算结束后，运行

awk '/Begin final coordinates/,/End final coordinates/{print $0}' vc-relax.out

如果设置了`cell_dofree = "ibrav"`，则可以使用下列命令查到新的celldm(i)

grep -B 40 "Begin final coordinates" vc-relax.out

得到以下输出（或在输出文件中可以找到）（vc-relax的结果）

Begin final coordinates

new unit-cell volume = 1731.29310 a.u.^3 ( 256.55117 Ang^3 )

density = 0.15548 g/cm^3

CELL_PARAMETERS (alat= 18.89726125)

1.000000000 0.000000000 0.000000000

0.000000000 1.000000000 0.000000000

0.000000000 0.000000000 0.256551169

ATOMIC_POSITIONS (angstrom)

C 5.0000000000 5.0000000000 0.0000000000 0 0 0

C 5.0000000000 5.0000000000 1.2640744811 0 0 1

End final coordinates

Notes1

如果设置了cell_dofree = "ibrav",优化过程保持布拉维格子的种类不变，vc-relax.out中会有优化后的优化后的celldm,见：

grep -B 40 "Begin final coordinates" vc-relax.out

ibrav = 7

celldm(1) = 10.37600462

celldm(3) = 1.97244178

Input lattice vectors:

0.49999668 -0.49999668 0.98621435

0.49999668 0.49999668 0.98621435

-0.49999668 -0.49999668 0.98621435

New lattice vectors in INITIAL alat:

0.49999668 -0.49999668 0.98621435

0.49999668 0.49999668 0.98621435

-0.49999668 -0.49999668 0.98621435

New lattice vectors in NEW alat (for information only):

0.50000000 -0.50000000 0.98622089

0.50000000 0.50000000 0.98622089

-0.50000000 -0.50000000 0.98622089

QE中Fortran代码如下：

IF(enforce_ibrav) CALL remake_cell( ibrav, alat, at(1,1),at(1,2),at(1,3), new_alat )

SUBROUTINE remake_cell(ibrav, alat, a1,a2,a3, new_alat)

USE kinds, ONLY : DP

USE io_global, ONLY : stdout

IMPLICIT NONE

INTEGER,INTENT(in) :: ibrav

REAL(DP),INTENT(in) :: alat

REAL(DP),INTENT(out) :: new_alat

REAL(DP),INTENT(inout) :: a1(3),a2(3),a3(3)

REAL(DP) :: e1(3), e2(3), e3(3)

REAL(DP) :: celldm_internal(6), lat_internal, omega

! Better not to do the following, or it may cause problems with ibrav=0 from input

! ibrav = at2ibrav (a(:,1), a(:,2), a(:,3))

! Instead, let's print a warning and do nothing:

IF(ibrav==0)THEN

WRITE(stdout,'(a)') "WARNING! With ibrav=0, cell_dofree='ibrav' has no effect. "

RETURN

ENDIF

CALL at2celldm (ibrav,alat,a1, a2, a3,celldm_internal)

WRITE(stdout,'("ibrav = ",i6)') ibrav

WRITE(stdout,'(" celldm(1) = ",f15.8)') celldm_internal(1)

IF( celldm_internal(2) /= 0._dp) WRITE(stdout,'(" celldm(2) = ",f15.8)') celldm_internal(2)

IF( celldm_internal(3) /= 0._dp) WRITE(stdout,'(" celldm(3) = ",f15.8)') celldm_internal(3)

IF( celldm_internal(4) /= 0._dp) WRITE(stdout,'(" celldm(4) = ",f15.8)') celldm_internal(4)

IF( celldm_internal(5) /= 0._dp) WRITE(stdout,'(" celldm(5) = ",f15.8)') celldm_internal(5)

IF( celldm_internal(6) /= 0._dp) WRITE(stdout,'(" celldm(6) = ",f15.8)') celldm_internal(6)

如果vc-relax中没有要求优化中ibrav不变，则不会输出ibrav以及celldm(i)

Notes2

对于类似于石墨烯超胞等原子应该满足严格的分数坐标时，采用vc-relax可能导致原子位置偏移。这是可以在vc-relax计算中，在&IONS中设置参数：trust_radius_min、trust_radius_ini等参数，以降低优化过程中原子的移动幅度。对优化后的结构，导入MS查看，可以更好的指导晶体结构的对称性。

Notes3

对于超胞的石墨烯结构，由于在优化过程中设置了cell_dofree = "ibrav"，会导致原子的受力总是对称的，并且不为零。该参数的设置也可能导致优化过程中，太多的能带计算不收敛，对于超胞的情况，需要谨慎使用该参数。

Forces acting on atoms (cartesian axes, Ry/au):

atom 1 type 1 force = 0.00000000 -0.00000553 0.00000000

atom 2 type 1 force = -0.00001351 -0.00001328 -0.00000000

atom 3 type 1 force = -0.00001826 -0.00000506 0.00000000

atom 4 type 1 force = -0.00000479 0.00000277 -0.00000000

atom 5 type 1 force = 0.00000864 0.00000499 0.00000000

atom 6 type 1 force = 0.00001351 -0.00001328 0.00000000

atom 7 type 1 force = 0.00000000 -0.00000000 0.00000000

atom 8 type 1 force = -0.00000475 0.00001834 0.00000000

atom 9 type 1 force = 0.00000000 0.00001551 0.00000000

atom 10 type 1 force = 0.00001343 -0.00000776 -0.00000000

atom 11 type 1 force = 0.00001826 -0.00000506 -0.00000000

atom 12 type 1 force = 0.00000475 0.00001834 0.00000000

atom 13 type 1 force = -0.00000864 0.00000499 -0.00000000

atom 14 type 1 force = -0.00001343 -0.00000776 -0.00000000

atom 15 type 1 force = -0.00000000 -0.00000997 0.00000000

atom 16 type 1 force = 0.00000479 0.00000277 0.00000000

atom 17 type 1 force = -0.00000479 -0.00000277 0.00000000

atom 18 type 1 force = -0.00000000 0.00000997 -0.00000000

atom 19 type 1 force = 0.00001343 0.00000776 0.00000000

atom 20 type 1 force = 0.00000864 -0.00000499 -0.00000000

atom 21 type 1 force = -0.00000475 -0.00001834 0.00000000

atom 22 type 1 force = -0.00001826 0.00000506 0.00000000

atom 23 type 1 force = -0.00001343 0.00000776 -0.00000000

atom 24 type 1 force = -0.00000000 -0.00001551 0.00000000

atom 25 type 1 force = 0.00000475 -0.00001834 0.00000000

atom 26 type 1 force = -0.00000000 -0.00000000 0.00000000

atom 27 type 1 force = -0.00001351 0.00001328 -0.00000000

atom 28 type 1 force = -0.00000864 -0.00000499 0.00000000

atom 29 type 1 force = 0.00000479 -0.00000277 0.00000000

atom 30 type 1 force = 0.00001826 0.00000506 0.00000000

atom 31 type 1 force = 0.00001351 0.00001328 -0.00000000

atom 32 type 1 force = 0.00000000 0.00000553 0.00000000

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Error in routine c_bands (1):

too many bands are not converged

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

stopping ...

为了使得原子受力满足较高的力收敛判据，需要将cell_dofree = "ibrav"取消。

QUANTUM ESPRESSO：scf

QUANTUM ESPRESSO：bands

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QUANTUM ESPRESSO：vc-relax - 谢华的博客

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