[rsgrad gap] docs done, bump version

.gitignore

@@ -2,3 +2,4 @@
 
 Cargo.lock
 .DS_Store
+*.swp

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rsgrad"
-version = "0.4.2"
+version = "0.4.3"
 authors = ["Ionizing <PeterSmith_9@outlook.com>"]
 edition = "2018"
 

docs/src/Gap.md

@@ -0,0 +1,85 @@
+# Gap
+
+This command (`rsgrad gap`) calculates the band gap and prints positions of VBM and CBM.
+
+There are two ways to run this command:
+1. Use `WAVECAR` only. All required information can be extracted from `WAVECAR`.
+2. Or use `PROCAR` and `OUTCAR` instead. `PROCAR` is read for the band energies, band occupations and k-point coordinates;
+`OUTCAR` is read for the Fermi level only.
+
+Note: Usually it's faster to parse results from `WAVECAR`.
+
+If your system is a non-SCF calculation for band structure, you may need to specify the correct Fermi level by
+`rsgrad gap -e <put the correct E-fermi here>`, the correct Fermi level can be obtained from the OUTCAR of SCF calculation.
+
+
+## Help Message
+```shell
+$ rsgrad gap --help
+rsgrad-gap
+Find band gap and print positions of VBM and CBM
+
+USAGE:
+    rsgrad gap [OPTIONS]
+
+OPTIONS:
+    -e, --efermi <EFERMI>      Specify Fermi level, if left empty, this value would be read from
+                               WAVECAR or OUTCAR
+    -h, --help                 Print help information
+    -o, --outcar <OUTCAR>      OUTCAR file name, this file is parsed to get Fermi level only
+                               [default: OUTCAR]
+    -p, --procar <PROCAR>      PROCAR file name, OUTCAR is also needed to get Fermi level [default:
+                               PROCAR]
+    -w, --wavecar <WAVECAR>    WAVECAR file name, no more files needed [default: WAVECAR]
+```
+
+## Example
+
+1. For metal system:
+```shell
+[2022-12-01T11:30:49Z INFO  rsgrad::commands::gap] Trying to parse "WAVECAR" ...
+----------------------------------------
+ Current system is         Metal
+----------------------------------------
+[2022-12-01T11:30:49Z INFO  rsgrad] Time used: 166.251241ms
+```
+
+2. For non-spin-polarized direct gap system:
+```shell
+[2022-12-01T11:37:15Z INFO  rsgrad::commands::gap] Trying to parse "WAVECAR" ...
+--------------------------------------------------------------------------------
+ Current system has    Direct Gap    of   0.328    eV
+  CBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   819 of    0.322 eV
+  VBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   818 of   -0.006 eV
+--------------------------------------------------------------------------------
+[2022-12-01T11:37:15Z INFO  rsgrad] Time used: 253.556682ms
+```
+
+3. For spin-polarized direct gap system:
+```shell
+$ rsgrad gap
+[2022-12-01T11:38:16Z INFO  rsgrad::commands::gap] Trying to parse "WAVECAR" ...
+--------------------------------------------------------------------------------
+    ====================  Gap Info For     SPIN UP      ====================
+ Current system has    Direct Gap    of   0.976    eV
+  CBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   129 of    0.498 eV
+  VBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   128 of   -0.478 eV
+    ====================  Gap Info For    SPIN DOWN     ====================
+ Current system has    Direct Gap    of   0.980    eV
+  CBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   129 of    0.499 eV
+  VBM @ k-point     1 of ( 0.000, 0.000, 0.000) , band   128 of   -0.481 eV
+--------------------------------------------------------------------------------
+[2022-12-01T11:38:16Z INFO  rsgrad] Time used: 31.744371ms
+```
+
+4. For non-spin-polarized indirect gap system:
+```shell
+$ rsgrad gap
+[2022-12-01T11:40:52Z INFO  rsgrad::commands::gap] Trying to parse "WAVECAR" ...
+--------------------------------------------------------------------------------
+ Current system has   Indirect Gap   of   1.160    eV
+  CBM @ k-point    25 of ( 0.000, 0.444, 0.444) , band     5 of    1.097 eV
+  VBM @ k-point    17 of ( 0.000, 0.000, 0.000) , band     4 of   -0.062 eV
+--------------------------------------------------------------------------------
+[2022-12-01T11:40:52Z INFO  rsgrad] Time used: 22.565948ms
+```

docs/src/SUMMARY.md

@@ -17,6 +17,7 @@
 - [POSCAR](./POSCAR.md)
 - [POTCAR](./POTCAR.md)
 - [Transition Dipole Moment](./TransitionDipoleMoment.md)
+- [Gap](./Gap.md)
 
 ---
 

src/commands/gap.rs

@@ -135,7 +135,7 @@ impl OptProcess for Gap {
 
 
         // find vbm
-        let vbeigs = multizip((vbidx, eigs.lanes(Axis(2))))
+        let vbeigs = multizip((vbidx.clone(), eigs.lanes(Axis(2))))
             .map(|(i, v)| v[i])
             .collect::<Array1<f64>>()
             .into_shape((nspin, nkpts)).unwrap();
@@ -164,7 +164,7 @@ impl OptProcess for Gap {
                                      format!("{:8.3}", cbeigs[(0, cbmik[0])]).bright_blue()
                                      ));
             output.push_str(&format!("  VBM @ k-point {:5} of ({:6.3},{:6.3},{:6.3}) , band {:5} of {:8} eV\n",
-                                     vbmik[0]+1, kvbm[0], kvbm[1], kvbm[2], cbidx[(0,0)]+1,
+                                     vbmik[0]+1, kvbm[0], kvbm[1], kvbm[2], vbidx[(0,0)]+1,
                                      format!("{:8.3}", vbeigs[(0, vbmik[0])]).bright_blue()
                                      ));
         } else {
@@ -185,7 +185,7 @@ impl OptProcess for Gap {
                                          format!("{:8.3}", cbeigs[(ispin, cbmik[ispin])]).bright_blue()
                                          ));
                 output.push_str(&format!("  VBM @ k-point {:5} of ({:6.3},{:6.3},{:6.3}) , band {:5} of {:8} eV\n",
-                                         vbmik[ispin]+1, kvbm[0], kvbm[1], kvbm[2], cbidx[(ispin,0)]+1,
+                                         vbmik[ispin]+1, kvbm[0], kvbm[1], kvbm[2], vbidx[(ispin,0)]+1,
                                          format!("{:8.3}", vbeigs[(ispin, vbmik[ispin])]).bright_blue()
                                          ));
             }