关注：

1） USPEX手册及版本更新

2）当前从手册中解决：变胞预测实现问题

   变组成结构预测-T7_varcomp_GULP算例分析 ......calculationType- 301

   变胞预测：1倍分子式，2倍分子式，3倍分子式等等.....calculationType 300 ?  仍然用301

You can also do fixed-composition calculations with a variable number of formula units【最常用的，但多少倍分子式上限如何确定？】;

in this
case set just one line (and calculationType=301), for example for compound A2BC4:
% numSpecies
2 1 4
% EndNumSpecies

http://han.ess.sunysb.edu/uspex_manual/

Manual解读

• variable calculationMethod（变量：计算方法/选择）
  Meaning: Species the method of calculation

 variability of chemical composition in the calculation:
" | fixed composition
1" | variable composition

Default: 300
Format:
301 : calculationType
Note: If calculationType=310, i.e., a prediction for a molecular crystal is to be performed,
then USPEX expects you to provide les MOL 1, MOL 2, . . . with molecular geometries for all
types of molecules, and these molecules will be placed in the newly generated structures as
whole objects.

Available options: 300, 301, 310, 000, 200, 201, {200 (and not yet released: 110,
311.)

• variable atomType （变量：原子种类）

Meaning: Describes the identities of each type of atom.
Default: none, must specify explicitly
Format:
If you prefer to use the atomic numbers from Mendeleev's Periodic Table of the Elements,
specify:
% atomType
12 14 8
% EndAtomType
Or, if you prefer to use atomic names, specify:
% atomType
Mg Si O
% EndAtomType
You can alternatively specify the full names of the elements, for example:
% atomType
Magnesium Silicon Oxygen
% EndAtomType

• variable numSpecies  （变量：每种原子个数）【！！变胞预测在此处有巧妙设置】

Meaning: Describes the number of atoms of each type.
Default: none, must specify explicitly
Format:

% numSpecies
4 4 12
% EndNumSpecies

This means there are 4 atoms of the first type, 4 of the second type, and 12 of the third type.

！！！Notes: For variable-composition calculations, you have to specify the compositional building
blocks as follows:

% numSpecies
2 0 3
0 1 1
% EndNumSpecies
This means that

   the first building block has formula A2C3 and

   the second building block has formula BC,

where A, B and C are described in the block atomType.

All structures will then
have the formula xA2C3 + yBC with x, y = (0,1,2,. . . ) | or A2xByC3x+y.【x,y的上限怎么确定？！】

If you want to do
prediction of all possible compositions in the A-B-C system, you should specify:

% numSpecies
1 0 0
0 1 0
0 0 1
% EndNumSpecies

[AxByCz?]

You can also do fixed-composition calculations with a variable number of formula units【最常用的，但多少倍分子式上限如何确定？】; in this
case set just one line (and calculationType=301), for example for compound A2BC4:
% numSpecies
2 1 4
% EndNumSpecies

5.2 Variable-composition code

To switch to the variable-composition mode, you have to:

1. Specify 301 or 311 or 201 : calculationType.

2. Specify compositional building blocks in numSpecies (see the description of numSpecies
variable).

3. Specify the approximate atomic volumes for each atom (or compositional block)
type using keyblock Latticevalues.

4. Specify the following varcomp-only options:

5.3 Variable-composition code  For  9.4.1 version

To switch on the variable-composition mode, you have to:

1. Specify 301 or 311 or 201 : calculationType.

2. Specify compositional building blocks in numSpecies (see the description of numSpecies variable，above).

3. Specify the approximate atomic volumes for each atom type (or for each compositional block[如何指定按原子种类还是按组成block给出体积]) using keyblock Latticevalues.

4. Specify the following varcomp-only options:

variable  firstGeneMax 【变量  第一代产生的different compositions数量】

Meaning: How many different compositions 【怎样确保产生自己想要的组成？！】are sampled in the first generation. If 0, then the number is equal to initialPopSize/4. For binaries, we recommend firstGeneMax=11, for ternaries a higher value is needed, e.g. 30.

Default: 11

Format:

10 : firstGeneMax

variable  minAt

Meaning: Minimum number of atoms (for calculationType=301/201/300) or molecules (for calculationType=311) in the unit cell for the first generation.

Default: No default

Format:

10 : minAt

variable  maxAt

Meaning: Maximum number of atoms (for calculationType=301/201/300 or in META calculations) or molecules (for calculationType=311) in the unit cell for the first generation.

Default: No default   【没有默认值，需自己指定】

Format:

20 : maxAt

variable   fracTrans

Meaning: Percentage of structures obtained by transmutation. In this operator, a randomly selected atom is transmuted into another chemical species present in the system — the new chemical identity is chosen randomly by default, or you can specify it in the block specificTrans, just like with specific permutation swaps.

Default: 0.1

Format:

0.1 : fracTrans

variable  howManyTrans

Meaning: Maximum percentage of atoms in the structure that are being transmuted (0.1 = 10%). The fraction of atoms that will be transmuted is drawn randomly from a homogeneous distribution bounded between 0 and the fractional parameter howManyTrans.

Default: 0.2

Format:

0.2 : howManyTrans

variables  pecificTrans

Meaning: Specifies allowed transmutations.

Default: blank line (no specific transmutations)

Format:

% specificTrans
1 2
% EndTransSpecific

Note: In this case, atoms of type 1 could be transmuted into atoms of type 2 and vice versa. If you want to try all possible transmutations, just leave a blank line inside this keyblock.【需理解结构预测算法的本质哈？】

In the case of variable-composition runs, parameter keepBestHM takes a new meaning — all structures on the convex hull (i.e., thermodynamically stable states of the multicomponent system) survive, along with a few metastable states closest to the convex hull — the total number is keepBestHM.

For variable-composition runs, it is particularly important to set up the first generation wisely. Choose a suitably large initial generation size initialPopSize.

    Choose a reasonably large number of different compositions firstGeneMax 【排列组合算法？】to be sampled in the first generation (but not too large — each composition needs to be sampled several times at least).

Finally, minAt and maxAt should not differ by more than 2 times, and you may need a few calculations with different system sizes: e.g., 4–8, 8–16, 16–30 atoms, etc.

Figure 12: Convex hull diagram for Na-Cl system at selected pressures. 
Solid circles represent stable compounds; open circles — metastable compounds.

An additional comment for VASP users — if you want to perform a variable-composition run, let’s say for the Na-Cl system, you should make sure the atomic types are given correctly in INPUT.txt, and put pseudopotential files POTCAR_Na and POTCAR_Cl in the folder /StructurePrediction/Specific.

USPEX will then recognize each atom and take each atom’s POTCAR file appropriately for the calculations.

Fig. 12 shows thermodynamics of stable sodium chlorides discovered using USPEX and confirmed by experiment³⁸.

[38]

W. Zhang, A.R. Oganov, A.F. Goncharov, Q. Zhu, S.E. Boulfelfel, A.O. Lyakhov, E. Stavrou, M. Somayazulu, V.B. Prakapenka, and Z. Konopkova. Unexpected stable stoichiometries of sodium chlorides. Science, 342(6165):1502–1505, 2013.

其他变量：

variableExternalPressure

Meaning: Specifies external pressure at which you want to find structures, in GPa.

Default: 0

Format:

100 : ExternalPressure

variable  valences

Meaning: Describes the valences of each type of atom. Used only to evaluate bond hardnesses, which are used for computing the approximate dynamical matrix (for softmutation) and hardness of the crystal.

Default: USPEX has a table of default valences (see Appendix 17). Beware, however, that for some elements (e.g., N, S, W, Fe, Cr, etc.) many valence states are possible. Unless you calculate hardness, this is not a problem and you can use the default values. If you do calculate the hardness, you need to carefully specify the valence explicitly.

Format:

% valences
2 4 2
% endValences

variable goodBonds

Meaning: Specifes, in the matrix form, the minimum bond valences for contacts that will be considered as important bonds. Like the IonDistances matrix (see below), this is a square matrix cast in an upper-triangular form. This is only used in calculations of hardness and in softmutation. One can estimate these values for a given bond type taking goodBonds= or slightly smaller.  

Default: USPEX can make a reasonable default estimation of goodBonds, you will see the values in OUTPUT.txt. This should be sufficient for most purposes, but for hardness calculations you may need to carefully examine these values and perhaps set them manually. More details, see Appendix 18

Format:

% goodBonds
10.0 10.0 0.2
0.0 10.0 0.5
0.0 0.0 10.0
% EndGoodBonds

Notes: The dimensions of this matrix must be equal to either the number of atomic species or unity. If only one number is used, the matrix is filled with this number. The matrix above reads as follows: to be considered a bond, the Mg–Mg distance should be short enough to have bond valence of 10 or more, the same for Mg–Si, Si–Si, and O–O bonds (by using such exclusive criteria, we effectively disregard these interactions from the softmutation and hardness calculations), whereas Mg–O bonds that will be considered for hardness and softmutation calculations will have a bond valence of 0.2 or more, and the Si–O bonds will have a bond valence of 0.5 or more.

4.6 Cell

It is useful to create all new structures (before relaxing them) with a unit cell volume appropriate for given conditions. This can be specified in the Latticevalues keyblock:

variable Latticevalues

Meaning: Specifies the initial volume of the unit cell or known lattice parameters.

Default: For cell volumes you don’t have to specify values — USPEX has a powerful algorithm to find reasonable estimates at any pressure.

Format:

% Latticevalues
125.00
% Endvalues

Notes: (1) This volume is only used as an initial guess and only influences the first generation, each structure is fully optimized and adopts the volume corresponding to the (free) energy minimum.

This keyblock also has another use: when you know the lattice parameters【也可指定晶格参数】 (e.g., from experiment), you can specify them in the Latticevalues keyblock instead of unit cell volume, e.g.:

% Latticevalues
7.49 0.0 0.0
0.0 9.71 0.0
0.0 0.0 7.07
% Endvalues

You can also specify unit cell parameters just by listing a, b, c, , , and values:

% Latticevalues
10.1 8.4 12.5 90.0 101.3 90.0
% Endvalues

Attention: if you do a calculation with a fixed monoclinic cell, please use setting with special angle (standard setting).

(2) For variable-composition calculations,

you have to specify the volume of end members 【什么意思？】of the compositional search space, e.g.:

% Latticevalues
12.5 14.0 11.0
% Endvalues

(3) Users no longer need to specify the unit cell or atomic volumes in the keyblock Latticevalues — a special algorithm has been implemented that accurately estimates it at the pressure of interest, without the need for the user to specify it.

This option works well and is available for any calculationType where input volumes are required: 3**, 2D-crystals, 110, 000. You can also use online program http://han.ess.sunysb.edu/volume_estimation. The users can also input the volumes manually.

(4) If you study molecular crystals under pressure, you might sometimes need to increase the initial volumes somewhat, in order to be able to generate structures by the random symmetric algorithm.

variable splitInto

Meaning: Defines the number of identical subcells or pseudosubcells in the unit cell. If you do not want to use splitting, just use the value 1, or delete the block. Use splitting only for systems with 25–30 atoms/cell.

Default: 1

Format:

% splitInto (number of subcells into which the unit cell is split)
1 2 4
% EndSplitInto

Subcells introduce extra translational (pseudo)symmetry. In addition to this, each subcell can be built using space groups, using a special algorithm developed by A.R. Oganov and H.T. Stokes and implemented by H.T. Stokes (see Reference¹⁴).