update candela

MCresearch · Dec 13, 2023 · 7834b54 · 7834b54
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diff --git a/_book/abacus-candela.html b/_book/abacus-candela.html
diff --git a/_book/abacus-dcu.html b/_book/abacus-dcu.html
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diff --git a/_book/contribute.html b/_book/contribute.html
diff --git a/_book/develop-C++.html b/_book/develop-C++.html
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diff --git a/_book/develop-sm1.html b/_book/develop-sm1.html
diff --git a/_book/develop-sm2.html b/_book/develop-sm2.html
diff --git a/_book/develop-test1.html b/_book/develop-test1.html
diff --git a/_book/develop-test2.html b/_book/develop-test2.html
diff --git a/_book/examples/candela/MSD_ntype_2/INPUT b/_book/examples/candela/MSD_ntype_2/INPUT
@@ -0,0 +1,23 @@
+calculation   msd_multiple
+geo_in_type   ABACUS
+geo_directory MD_dump
+geo_1         0
+geo_2         100
+geo_interval  1
+geo_ignore    50
+
+ntype         2
+natom         17
+natom1        16
+natom2        1
+id1           C
+id2           Li
+
+msd_n         2
+msd_t0        0.003
+msd_t         0.0015
+msd_dt0       0.0015
+msd_dt        0.00006
+ele_select    C
+msd_natom     16
+
diff --git a/_book/examples/candela/MSD_ntype_2/MD_dump b/_book/examples/candela/MSD_ntype_2/MD_dump
diff --git a/_book/examples/candela/MSD_ntype_2/ref_MSD_each.txt b/_book/examples/candela/MSD_ntype_2/ref_MSD_each.txt
@@ -0,0 +1,24 @@
+6e-05 1.228e-05 9.32147e-06
+0.00012 4.86616e-05 3.62656e-05
+0.00018 0.000108149 7.91152e-05
+0.00024 0.000189406 0.000136004
+0.0003 0.000290858 0.000205047
+0.00036 0.00041079 0.000284473
+0.00042 0.000547443 0.00037274
+0.00048 0.000699106 0.000468633
+0.00054 0.000864194 0.000571325
+0.0006 0.00104131 0.000680418
+0.00066 0.0012293 0.00079593
+0.00072 0.00142726 0.000918272
+0.00078 0.00163455 0.00104822
+0.00084 0.00185078 0.00118686
+0.0009 0.00207575 0.00133544
+0.00096 0.00230936 0.00149524
+0.00102 0.00255172 0.00166748
+0.00108 0.00280316 0.00185322
+0.00114 0.00306414 0.00205328
+0.0012 0.00333497 0.0022683
+0.00126 0.00361551 0.00249871
+0.00132 0.00390511 0.00274474
+0.00138 0.00420274 0.00300638
+0.00144 0.00450696 0.0032833
diff --git a/_book/examples/candela/MSD_ntype_2/ref_MSD_total.txt b/_book/examples/candela/MSD_ntype_2/ref_MSD_total.txt
@@ -0,0 +1,24 @@
+6e-05 1.08007e-05 0.030002 2.09199e-06
+0.00012 4.24636e-05 0.0589772 8.76531e-06
+0.00018 9.36319e-05 0.0866962 2.05298e-05
+0.00024 0.000162705 0.112989 3.7761e-05
+0.0003 0.000247952 0.137751 6.06776e-05
+0.00036 0.000347631 0.16094 8.93195e-05
+0.00042 0.000460092 0.182576 0.000123534
+0.00048 0.000583869 0.202732 0.000162969
+0.00054 0.000717759 0.221531 0.000207089
+0.0006 0.000860864 0.239129 0.000255189
+0.00066 0.00101261 0.25571 0.000306436
+0.00072 0.00117276 0.271473 0.000359906
+0.00078 0.00134139 0.286621 0.000414597
+0.00084 0.00151882 0.301353 0.000469467
+0.0009 0.00170559 0.31585 0.000523481
+0.00096 0.0019023 0.33026 0.000575667
+0.00102 0.0021096 0.344706 0.00062525
+0.00108 0.00232819 0.359289 0.000671714
+0.00114 0.00255871 0.37408 0.000714783
+0.0012 0.00280163 0.389116 0.000754248
+0.00126 0.00305711 0.40438 0.000789698
+0.00132 0.00332493 0.419814 0.000820507
+0.00138 0.00360456 0.435333 0.000845959
+0.00144 0.00389513 0.450826 0.000865255
diff --git a/_book/index.html b/_book/index.html
diff --git a/_book/news.html b/_book/news.html
diff --git a/_book/search_plus_index.json b/_book/search_plus_index.json
diff --git a/abacus-candela.md b/abacus-candela.md
@@ -4,7 +4,7 @@
 
 <strong>审核：陈默涵，邮箱：[email protected]</strong>
 
-<strong>最后更新时间：2023/08/23</strong>
+<strong>最后更新时间：2023/12/13</strong>
 
 <strong>在Bohrium Notebook上快速学习：</strong><a href="https://nb.bohrium.dp.tech/detail/2912697542" target="_blank"><img src="https://cdn.dp.tech/bohrium/web/static/images/open-in-bohrium.svg" /></a>
 
@@ -40,7 +40,7 @@ git clone https://gitee.com/mcresearch/abacus-user-guide.git
 
 下载完成后解压，之后进入 `abacus-user-guide/examples/candela` 文件夹
 
-算例中包含 `RDF`、`SSF`、`DSF`、`MSD` 四个文件夹和 `MD_dump` 文件。其中 `MD_dump` 是 32 原子的铝的 MD 轨迹
+算例中包含 `RDF`、`SSF`、`DSF`、`MSD` 以及 `MSD_ntype_2` 五个文件夹和 `MD_dump` 文件。其中 `MD_dump` 是 32 原子的铝的 MD 轨迹
 
 # 三、流程
 
@@ -187,6 +187,8 @@ python PathtoCandela/examples/e3_dsf/onedsf.py 0.00006 0.0006
 
 ## 4 均方差位移
 
+### 4.1 单种原子
+
 进入 `MSD` 文件夹，`INPUT` 文件具体如下：
 
 ```bash
@@ -225,3 +227,40 @@ mpirun -n 2 candela
 ```
 
 即可得到 MSD，输出到 `MSD_each.txt` 和 `MSD_total.txt`。其中 `MSD_each.txt` 第一列为时间，单位为 ps，第二列到最后一列即为对应的每段的 MSD，单位为$$\mathrm{Angstrom^{2}}$$；`MSD_total.txt` 第一列为时间，单位为 ps，第二列为平均的每段的 MSD，单位为$$\mathrm{Angstrom^{2}}$$。
+
+### 4.2 多种原子
+
+进入 `MSD_ntype_2` 文件夹，`INPUT` 文件具体如下：
+
+```bash
+calculation   msd_multiple
+geo_in_type   ABACUS
+geo_directory MD_dump
+geo_1         0
+geo_2         100
+geo_interval  1
+geo_ignore    50
+
+ntype         2
+natom         17
+natom1        16
+natom2        1
+id1           C
+id2           Li
+
+msd_n         2
+msd_t0        0.003
+msd_t         0.0015
+msd_dt0       0.0015
+msd_dt        0.00006
+ele_select    C
+msd_natom     16
+```
+
+以上参数在 Candela 的[线上文档](https://candela-docs.readthedocs.io/en/latest/)中均有详细说明，与单种原子不同的参数如下：
+
+- natom1、natom2：不同种类原子的个数
+- id1、id2：不同种类原子的名称，需要与读入的 MD_dump 中原子名称一致
+- ele_select：计算 MSD 的原子名称，需要与 id1 或 id2 对应
+
+多种原子的计算过程与结果与单种原子并无区别。
diff --git a/examples/candela/MSD_ntype_2/INPUT b/examples/candela/MSD_ntype_2/INPUT
@@ -0,0 +1,23 @@
+calculation   msd_multiple
+geo_in_type   ABACUS
+geo_directory MD_dump
+geo_1         0
+geo_2         100
+geo_interval  1
+geo_ignore    50
+
+ntype         2
+natom         17
+natom1        16
+natom2        1
+id1           C
+id2           Li
+
+msd_n         2
+msd_t0        0.003
+msd_t         0.0015
+msd_dt0       0.0015
+msd_dt        0.00006
+ele_select    C
+msd_natom     16
+