1. Histo_each

    该程序可以一步给出晶胞中每个原子所处的环境(即该原子周围有多少个近邻和非近邻原子，从而可知配位情况)。程序输出文件中：横坐标为所考察的距离隔断(从0开始，以0.1 A步长递增，直至离该原子最远的原子距离，如10或15 A等)，纵坐标给出与该原子间距为某一值的原子（无法区分是何种原子）的个数。

    When you want in one run have an idea of the environment of each atom in the unit cell.

    It gives the total number of neighbors of each atom in the unit cell at different distances.

    This script allows classifying the atoms of the unit cell in different subgroups characterized by different environments.

    It is for example useful when there are H atoms in the unit cell and that you

want to know which ones are involved in H2 molecules and which ones are not.

   
No difference is made between neighbors of one atom type and neighbors of another type. This can be problematic for binary systems. 【改程序不能区分neighbor是谁】

操作：修改CONTCAR为：

SiH4

1.00000000000000

 2.9508519718916211 0.0012886260557479 -0.0025855793652686

 1.4744524494492086 3.6573978539178742 0.0003171182082060

 0.0021628080341597 2.3819016084661113 5.4006789835736289

20   （原位16 4）

Direct

0.7198625771484012 0.3489401099245155 0.0549192913797349

0.7199442834495026 0.3490575092232764 0.5549441918129401

0.1937505883612986 0.0761356062444437 0.1629237830616464

0.9362874145060102 0.0760662832787076 0.4542490748698111

0.1371453032480722 0.3486944783146299 0.9259771793577048

0.1372277749291061 0.3486889264691041 0.4260099386795520

0.1936690531960621 0.0761762638674806 0.6629384760710715

0.9362479552825910 0.0759907360574122 0.9542937978505820

0.0236546863137832 0.5757474216262967 0.1191878767083718

0.5498218702572352 0.8485826690998743 0.0111664506747879

0.6063196306816949 0.5760893879294731 0.2480857444491285

0.5497638556115823 0.8486452049679729 0.5112002874396104

0.0237073608963271 0.5758667860762234 0.6191940731107033

0.8072870369522093 0.8487032734677908 0.2198647073371188

0.8072654359899124 0.8488058396894830 0.7197900556338696

0.6063677623943227 0.5760640230919675 0.7481334954392547

0.4969442007392463 0.2121792154581331 0.7746885361182054

0.4969374885195341 0.2121486732518044 0.2746885160415800

0.2466942975312079 0.7125316528059543 0.3993874070252186

0.2466144239919012 0.7124799391554487 0.8994031169391126

运行程序即可得到输出文件，如下所示。在输出文件列表中，纵列为距离，横列为晶胞中包含的所有原子的原子编号，数值即为与该编号原子间距为该数值的原子（无法区分原子种类）的个数。

distances    1 2 3 4 5 6 7 8 9 10  11 12 13 14 15 16 17 18 19 20

0.           0 0 0 0 0 0 0 0 0  0  0  0   0  0  0  0  0  0  0  0

0.100000001  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1.00000001   0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1.10000002   0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1.20000002   0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1.30000002   0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1.40000002   3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 0 0 0 0

1.50000002   2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 8 8 8 8

1.60000002   1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0

1.70000003   2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0

1.80000003   2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0

  It appears that the 16 H atoms have the same environment (3 neighbors at 1.4Å, 2 neighbors at 1.5 Å and …), as well as the 4 Si atoms with 8 neighbors at 1.5 Å.

  改程序不能区分neighbor是谁？！

2. Histo_average_spec

   相对于Histo_each程序，该程序可指出近邻原子的种类。

   When you want to study the distances between 2 subgroups of the unit cell.

   It gives the average number of neighbors of one type (specified by the user) at different distances of a set of atoms (specified by the user) in the unit cell.

    Contrary to Histo_each, Histo_average_spec allows to focus on neighbors of a particular kind, what is useful for binary systems.

  操作：

The program needs a modified CONTCAR file.

The line giving the number of atoms of each atom type has to be replaced by 6 lines:

1. The total number of atoms in the unit cell   20

2. The total number of atoms you want to know the average environment of  4

3. The labels of these atoms  17 18 19 20  【4个Si原子的编号】

4. The total number of atoms constituting the neighbors of interest  4

5. The labels of these atoms  17 18 19 20  【考察Si-Si之间的近邻和非近邻情况】

6. The step between 2 distances considered   0.1 【所考察的距离间隔】。

With this script, it is possible to study how far are:

· The Si neighbors of Si atoms (case A)

· The H neighbors of Si atoms (case B)

· The H neighbors of H atoms (case C)

· The Si neighbors of H atoms (case D)

In each case, a different CONTCAR file has to be used.

CASE A,修改后的CONTCAR文件为：

SiH4

1.00000000000000

 2.9508519718916211 0.0012886260557479 -0.0025855793652686

 1.4744524494492086 3.6573978539178742 0.0003171182082060

 0.0021628080341597 2.3819016084661113 5.4006789835736289

20

4

17 18 19 20

4

17 18 18 20

0.1

Direct

0.7198625771484012 0.3489401099245155 0.0549192913797349

0.7199442834495026 0.3490575092232764 0.5549441918129401

0.1937505883612986 0.0761356062444437 0.1629237830616464

0.9362874145060102 0.0760662832787076 0.4542490748698111

0.1371453032480722 0.3486944783146299 0.9259771793577048

0.1372277749291061 0.3486889264691041 0.4260099386795520

0.1936690531960621 0.0761762638674806 0.6629384760710715

0.9362479552825910 0.0759907360574122 0.9542937978505820

0.0236546863137832 0.5757474216262967 0.1191878767083718

0.5498218702572352 0.8485826690998743 0.0111664506747879

0.6063196306816949 0.5760893879294731 0.2480857444491285

0.5497638556115823 0.8486452049679729 0.5112002874396104

0.0237073608963271 0.5758667860762234 0.6191940731107033

0.8072870369522093 0.8487032734677908 0.2198647073371188

0.8072654359899124 0.8488058396894830 0.7197900556338696

0.6063677623943227 0.5760640230919675 0.7481334954392547

0.4969442007392463 0.2121792154581331 0.7746885361182054

0.4969374885195341 0.2121486732518044 0.2746885160415800

0.2466942975312079 0.7125316528059543 0.3993874070252186

0.2466144239919012 0.7124799391554487 0.8994031169391126

运行程序，得到输出文件为：

average made on atoms

         17          18          19          20

with respect to atoms

         17          18          18          20

distances  average frequency

 0.0000  1.0000

 0.1000  0.0000

 0.2000  0.0000

 0.3000  0.0000

 0.4000  0.0000

 0.5000  0.0000

 0.6000  0.0000

 0.7000  0.0000

 0.8000  0.0000

 0.9000  0.0000

 1.0000  0.0000

 1.1000  0.0000

 1.2000  0.0000

 1.3000  0.0000

 1.4000  0.0000

 1.5000  0.0000

 1.6000  0.0000

 1.7000  0.0000

 1.8000  0.0000

 1.9000  0.0000

 2.0000  0.0000

 2.1000  0.0000

  2.2000  4.0000

 2.3000  0.0000

 2.4000  0.0000

 2.5000  0.0000

 2.6000  0.0000

 2.7000  0.0000

 2.8000  0.0000

 2.9000  0.0000

 3.0000  4.0000

On average, each Si atoms has 4 Si neighbors at 2.2Å.

CASE B,修改后的CONTCAR文件为：

SiH4

1.00000000000000

 2.9508519718916211 0.0012886260557479 -0.0025855793652686

 1.4744524494492086 3.6573978539178742 0.0003171182082060

 0.0021628080341597 2.3819016084661113 5.4006789835736289

20

4

17 18 19 20

16   【在Si周围参与“配位”的总的H原子数，配位有可能是4或8或其他配位数】

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

0.1

Direct

0.7198625771484012 0.3489401099245155 0.0549192913797349

0.7199442834495026 0.3490575092232764 0.5549441918129401

0.1937505883612986 0.0761356062444437 0.1629237830616464

0.9362874145060102 0.0760662832787076 0.4542490748698111

0.1371453032480722 0.3486944783146299 0.9259771793577048

0.1372277749291061 0.3486889264691041 0.4260099386795520

0.1936690531960621 0.0761762638674806 0.6629384760710715

0.9362479552825910 0.0759907360574122 0.9542937978505820

0.0236546863137832 0.5757474216262967 0.1191878767083718

0.5498218702572352 0.8485826690998743 0.0111664506747879

0.6063196306816949 0.5760893879294731 0.2480857444491285

0.5497638556115823 0.8486452049679729 0.5112002874396104

0.0237073608963271 0.5758667860762234 0.6191940731107033

0.8072870369522093 0.8487032734677908 0.2198647073371188

0.8072654359899124 0.8488058396894830 0.7197900556338696

0.6063677623943227 0.5760640230919675 0.7481334954392547

0.4969442007392463 0.2121792154581331 0.7746885361182054

0.4969374885195341 0.2121486732518044 0.2746885160415800

0.2466942975312079 0.7125316528059543 0.3993874070252186

0.2466144239919012 0.7124799391554487 0.8994031169391126

运行程序得：

 average made on atoms

         17          18          19          20

with respect to atoms

          1           2           3           4           5           6           7           8           9          10          11          12          13          14          15          16

distances  average frequency

 0.0000  0.0000

 0.1000  0.0000

 0.2000  0.0000

 0.3000  0.0000

 0.4000  0.0000

 0.5000  0.0000

 0.6000  0.0000

 0.7000  0.0000

 0.8000  0.0000

 0.9000  0.0000

 1.0000  0.0000

 1.1000  0.0000

 1.2000  0.0000

 1.3000  0.0000

 1.4000  0.0000

 1.5000  8.0000

 1.6000  0.0000

 1.7000  0.0000

 1.8000  0.0000

 1.9000  0.0000

 2.0000  0.0000

 2.1000  4.0000

 2.2000  0.0000

On average, each Si atoms has 8 H neighbors at 1.5Å.

CASE C修改CONTCAR为：

SiH4

1.00000000000000

 2.9508519718916211 0.0012886260557479 -0.0025855793652686

 1.4744524494492086 3.6573978539178742 0.0003171182082060

 0.0021628080341597 2.3819016084661113 5.4006789835736289

20

16

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

16

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

0.1

Direct

0.7198625771484012 0.3489401099245155 0.0549192913797349

0.7199442834495026 0.3490575092232764 0.5549441918129401

0.1937505883612986 0.0761356062444437 0.1629237830616464

0.9362874145060102 0.0760662832787076 0.4542490748698111

0.1371453032480722 0.3486944783146299 0.9259771793577048

0.1372277749291061 0.3486889264691041 0.4260099386795520

0.1936690531960621 0.0761762638674806 0.6629384760710715

0.9362479552825910 0.0759907360574122 0.9542937978505820

0.0236546863137832 0.5757474216262967 0.1191878767083718

0.5498218702572352 0.8485826690998743 0.0111664506747879

0.6063196306816949 0.5760893879294731 0.2480857444491285

0.5497638556115823 0.8486452049679729 0.5112002874396104

0.0237073608963271 0.5758667860762234 0.6191940731107033

0.8072870369522093 0.8487032734677908 0.2198647073371188

0.8072654359899124 0.8488058396894830 0.7197900556338696

0.6063677623943227 0.5760640230919675 0.7481334954392547

0.4969442007392463 0.2121792154581331 0.7746885361182054

0.4969374885195341 0.2121486732518044 0.2746885160415800

0.2466942975312079 0.7125316528059543 0.3993874070252186

0.2466144239919012 0.7124799391554487 0.8994031169391126

运行程序得，

average made on atoms

          1           2           3           4           5           6           7           8           9          10          11          12          13          14          15          16

with respect to atoms

          1           2           3           4           5           6           7           8           9          10          11          12          13          14          15          16

distances  average frequency

 0.0000  1.0000

 0.1000  0.0000

 0.2000  0.0000

 0.3000  0.0000

 0.4000  0.0000

 0.5000  0.0000

 0.6000  0.0000

 0.7000  0.0000

 0.8000  0.0000

 0.9000  0.0000

 1.0000  0.0000

 1.1000  0.0000

 1.2000  0.0000

 1.3000  0.0000

 1.4000  3.0000

 1.5000  0.0000

 1.6000  1.0000

 1.7000  2.0000

 1.8000  2.0000

 1.9000  1.0000

 2.0000  1.0000

....

On average, each H atoms has 3 H neighbors at 1.3Å.

CASE D修改CONTCAR为

SiH4

1.00000000000000

 2.9508519718916211 0.0012886260557479 -0.0025855793652686

 1.4744524494492086 3.6573978539178742 0.0003171182082060

 0.0021628080341597 2.3819016084661113 5.4006789835736289

20

16

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

4

17 18 19 20

0.1

Direct

0.7198625771484012 0.3489401099245155 0.0549192913797349

0.7199442834495026 0.3490575092232764 0.5549441918129401

0.1937505883612986 0.0761356062444437 0.1629237830616464

0.9362874145060102 0.0760662832787076 0.4542490748698111

0.1371453032480722 0.3486944783146299 0.9259771793577048

0.1372277749291061 0.3486889264691041 0.4260099386795520

0.1936690531960621 0.0761762638674806 0.6629384760710715

0.9362479552825910 0.0759907360574122 0.9542937978505820

0.0236546863137832 0.5757474216262967 0.1191878767083718

0.5498218702572352 0.8485826690998743 0.0111664506747879

0.6063196306816949 0.5760893879294731 0.2480857444491285

0.5497638556115823 0.8486452049679729 0.5112002874396104

0.0237073608963271 0.5758667860762234 0.6191940731107033

0.8072870369522093 0.8487032734677908 0.2198647073371188

0.8072654359899124 0.8488058396894830 0.7197900556338696

0.6063677623943227 0.5760640230919675 0.7481334954392547

0.4969442007392463 0.2121792154581331 0.7746885361182054

0.4969374885195341 0.2121486732518044 0.2746885160415800

0.2466942975312079 0.7125316528059543 0.3993874070252186

0.2466144239919012 0.7124799391554487 0.8994031169391126

运行程序得，

average made on atoms

          1           2           3           4           5           6           7           8           9          10          11          12          13          14          15          16

with respect to atoms

         17          18          19          20

distances  average frequency

 0.0000  0.0000

 0.1000  0.0000

 0.2000  0.0000

 0.3000  0.0000

 0.4000  0.0000

 0.5000  0.0000

 0.6000  0.0000

 0.7000  0.0000

 0.8000  0.0000

 0.9000  0.0000

 1.0000  0.0000

 1.1000  0.0000

 1.2000  0.0000

 1.3000  0.0000

 1.4000  0.0000

 1.5000  2.0000

 1.6000  0.0000

 1.7000  0.0000

 1.8000  0.0000

 1.9000  0.0000

 2.0000  0.0000

 2.1000  1.0000

 2.2000  0.0000

On average, each H atom has 2 Si neighbors at 1.5Å.

注意：距离间隔步长是可以修改的。

Histo_average_spec.exe provides the possibility to modify the step between 2 distances considered.

To draw histograms, 0.1Å is just fine. But if one wants to evaluate the equalization function of H atoms, it is necessary to be more precise. In this latter case, 0.01Å is better.