chore(templates): make default parameters more clear, capitalize mole…

…cule in input (#37) * Modify default names for some configs * Modify annotations to description in molecule struct * Modify molecule reference in templates to Molecule(capitalized)
caprilesport · Jan 17, 2024 · 8c884ce · 8c884ce
1 parent 140d1a4
commit 8c884ce
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Showing 12 changed files with 40 additions and 41 deletions.
diff --git a/README.md b/README.md
@@ -219,7 +219,7 @@ Let's walk through an example using `gedent` to generate an input file for optim
    charge = 1
    basis_set = "def2svp"
    functional = "BP86"
-   dft_type = "GGA"
+   functional_class = "GGA"
    memory = 3000
    mult = 1
    nprocs = 8

diff --git a/gedent.toml b/gedent.toml
@@ -3,14 +3,13 @@ default_extension = "inp"
 
 [parameters]
 charge = 1
-dft_basis_set = "def2svp"
-dft_level = "PB86"
-dft_type = "GGA"
+basis_set = "def2svp"
+functional = "BP86"
+functional_class = "GGA" #required by adf
 memory = 3000
 mult = 1
 nprocs = 8
 solvation = false
 solvent = "water"
 split_index = 10
-start_hessian = true
-xyz_file = "init.xyz"
+start_hessian = false
diff --git a/src/main.rs b/src/main.rs
@@ -370,7 +370,7 @@ fn generate_input(
 
     for molecule in molecules {
         let mut mol_context = context.clone();
-        mol_context.insert("molecule", &molecule);
+        mol_context.insert("Molecule", &molecule);
         results.push(Input {
             filename: PathBuf::from(molecule.filename).with_extension(extension),
             content: template.render(&mol_context)?,

diff --git a/src/molecule.rs b/src/molecule.rs
@@ -5,15 +5,15 @@ use std::path::PathBuf;
 #[derive(PartialEq, Serialize, Deserialize, Debug, Clone)]
 pub struct Molecule {
     pub filename: String,
-    pub annotations: String,
+    pub description: String,
     pub atoms: Vec<String>,
 }
 
 impl Molecule {
     fn new() -> Molecule {
         Molecule {
             filename: "".to_string(),
-            annotations: "".to_string(),
+            description: "".to_string(),
             atoms: Vec::new(),
         }
     }
@@ -85,7 +85,7 @@ impl Molecule {
                 }
 
                 natoms += xyz_lines.next().unwrap().parse::<usize>()?;
-                mol.annotations = xyz_lines.next().unwrap_or("").to_string();
+                mol.description = xyz_lines.next().unwrap_or("").to_string();
                 mol.atoms.clear();
             } else {
                 mol.atoms.push(xyz_lines.next().unwrap().to_string());
@@ -131,7 +131,7 @@ H       -1.537653553     -0.759337000     -2.285220893"
 
         let ch4 = Molecule {
             filename: "./ch4".to_string(),
-            annotations: "symmetry c1".to_string(),
+            description: "symmetry c1".to_string(),
             atoms: vec![
                 "C       -0.702728547      0.000000000     -1.996862306".to_string(),
                 "H       -0.172294601     -0.951333822     -1.920672276".to_string(),
@@ -142,7 +142,7 @@ H       -1.537653553     -0.759337000     -2.285220893"
         };
         let h2o = Molecule {
             filename: "./ch4_h2o_1".to_string(),
-            annotations: "symmetry c1".to_string(),
+            description: "symmetry c1".to_string(),
             atoms: vec![
                 "O       -1.537653553      0.000000000     -2.881263893".to_string(),
                 "H       -1.537653553      0.759337000     -2.285220893".to_string(),
@@ -170,7 +170,7 @@ H       -1.537653553     -0.759337000     -2.285220893"
     fn molecule_split_works() {
         let ch4 = Molecule {
             filename: "./ch4".to_string(),
-            annotations: "symmetry c1".to_string(),
+            description: "symmetry c1".to_string(),
             atoms: vec![
                 "C       -0.702728547      0.000000000     -1.996862306".to_string(),
                 "H       -0.172294601     -0.951333822     -1.920672276".to_string(),
@@ -182,7 +182,7 @@ H       -1.537653553     -0.759337000     -2.285220893"
 
         let ch3 = Molecule {
             filename: "./ch4_split_1".to_string(),
-            annotations: "symmetry c1".to_string(),
+            description: "symmetry c1".to_string(),
             atoms: vec![
                 "C       -0.702728547      0.000000000     -1.996862306".to_string(),
                 "H       -0.172294601     -0.951333822     -1.920672276".to_string(),
@@ -192,7 +192,7 @@ H       -1.537653553     -0.759337000     -2.285220893"
         };
         let h = Molecule {
             filename: "./ch4_split_2".to_string(),
-            annotations: "symmetry c1".to_string(),
+            description: "symmetry c1".to_string(),
             atoms: vec!["H       -1.233162492      0.045629756     -2.950150766".to_string()],
         };
         match ch4.split(4) {

diff --git a/templates/adf/eda b/templates/adf/eda
@@ -6,7 +6,7 @@ AMS_JOBNAME=eda $AMSBIN/ams <<eor
 Task SinglePoint
 
 Engine adf
-	title {{ molecule.filename }}
+	title {{ Molecule.filename }}
 
 	ETSNOCV
 		RHOKmin 1e-3
@@ -26,15 +26,15 @@ Engine adf
 	end
 
 	Basis
-		type {{ dft_basis_set }}
+		type {{ basis_set }}
 		CORE none
 	end
 
 	Symmetry NoSYM
 
 	XC
 		Dispersion Grimme3 BJDAMP
-		{{ dft_type }} {{ dft_level }}
+		{{ functional_class }} {{ functional }}
 	end
 
 	Beckegrid
@@ -46,7 +46,7 @@ Engine adf
 		frag2 {{ get_env(name="PWD") }}/frag2.results/adf.rkf
 	end
 EndEngine
-{% set molecules = split_molecule(molecule=molecule, index=split_index) -%}
+{% set molecules = split_molecule(molecule=Molecule, index=split_index) -%}
 
 System
 	atoms

diff --git a/templates/adf/sp b/templates/adf/sp
@@ -1,15 +1,15 @@
 --@
 extension = "run"
 --@
-AMS_JOBNAME={{ molecule.filename }} $AMSBIN/ams <<eor
+AMS_JOBNAME={{ Molecule.filename }} $AMSBIN/ams <<eor
 
 Task SinglePoint
 
 Engine ADF
-	title {{ molecule.filename }}
+	title {{ Molecule.filename }}
 
 	BASIS
-		TYPE {{ dft_basis_set }}
+		TYPE {{ basis_set }}
 		CreateOutput yes
 	end
 
@@ -18,7 +18,7 @@ Engine ADF
 	end
 
 	XC
-		{{ dft_type }} {{ dft_level }}
+		{{ functional_class }} {{ functional }}
 		Dispersion Grimme3 BJDAMP
 	end
 
@@ -30,7 +30,7 @@ EndEngine
 
 System
 	atoms
-{{ print_molecule(molecule=molecule) }}
+{{ print_molecule(molecule=Molecule) }}
 	end
 		Charge {{ charge }}
 	end

diff --git a/templates/gaussian/nbo_del b/templates/gaussian/nbo_del
@@ -1,15 +1,15 @@
 --@
 extension = "gjf"
 --@
-%chk={{ molecule.filename }}.chk
+%chk={{ Molecule.filename }}.chk
 %nproc={{ nprocs }}
 %mem={{ memory }}GB
-# {{ dft_level }}/{{ dft_basis_set }} pop=nbo6del nosymm
+# {{ functional }}/{{ basis_set }} pop=nbo6del nosymm
 
-job title: {{ molecule.filename }}
+job title: {{ Molecule.filename }}
 
 {{ charge }} {{mult}}
-{{print_molecule(molecule=molecule)}}
+{{print_molecule(molecule=Molecule)}}
 
 $nbo  $end
 $del  lewis  $end

diff --git a/templates/gaussian/opt b/templates/gaussian/opt
@@ -6,13 +6,13 @@ extension = "gjf"
 {%else-%}
 {%set solvent=""-%}
 {%endif-%}
-%chk={{ molecule.filename }}.chk
+%chk={{ Molecule.filename }}.chk
 %nproc={{ nprocs }}
 %mem={{ memory }}GB
-# {{ dft_level }}/{{ dft_basis_set }} opt freq=noraman {{ solvent }}
+# {{ functional }}/{{ basis_set }} opt freq=noraman {{ solvent }}
 
-job title: {{ molecule.filename }}
+job title: {{ Molecule.filename }}
 
 {{ charge }} {{mult}}
-{{print_molecule(molecule=molecule)}}
+{{print_molecule(molecule=Molecule)}}
 
diff --git a/templates/gaussian/sp b/templates/gaussian/sp
@@ -8,10 +8,10 @@ extension = "gjf"
 {%endif-%}
 %nproc={{ nprocs }}
 %mem={{ memory }}GB
-# {{ dft_level }}/{{ dft_basis_set }} freq=noraman scrf=(smd,solvent=ethanol) temperature=353
+# {{ functional }}/{{ basis_set }} freq=noraman scrf=(smd,solvent=ethanol) temperature=353
 
-job title: {{ molecule.filename }}
+job title: {{ Molecule.filename }}
 
 {{ charge }} {{mult}}
-{{print_molecule(molecule=molecule)}}
+{{print_molecule(molecule=Molecule)}}
 
diff --git a/templates/orca/neb b/templates/orca/neb
@@ -1,4 +1,4 @@
-! {{ dft_level }} {{ dft_basis_set }} 
+! {{ functional }} {{ basis_set }} 
 ! NEB-TS NumFreq IRC
 
 *xyzfile {{ charge }} {{ mult }} {{ xyz_file }}

diff --git a/templates/orca/opt b/templates/orca/opt
@@ -1,7 +1,7 @@
 --@
 extension = "inp"
 --@
-! {{ dft_level }} {{ dft_basis_set }} 
+! {{ functional }} {{ basis_set }} 
 ! Opt freq D3BJ
 
 %pal
@@ -21,11 +21,11 @@ end
 {% if start_hessian -%}
 %Geom
  InHess Read
- InHessName "{{ molecule.filename }}.hess"
+ InHessName "{{ Molecule.filename }}.hess"
 end
 
 {% endif -%} 
 
 *xyz {{ charge }} {{ mult }}
-{{ print_molecule(molecule = molecule) }}
+{{ print_molecule(molecule = Molecule) }}
 *
diff --git a/templates/orca/scan b/templates/orca/scan
@@ -1,4 +1,4 @@
-! {{ dft_level }} {{ dft_basis_set }} 
+! {{ functional }} {{ basis_set }} 
 ! Opt
 
 {% if solvation -%}
@@ -16,5 +16,5 @@ end
 end
 
 *xyz {{ charge }} {{ mult }}
-{{ print_molecule(molecule="molecule") }}
+{{ print_molecule(molecule="Molecule") }}
 *