Add more flags (#46)

* Add more flags to gen command

* Fix templates

gedent.toml

@@ -4,12 +4,14 @@ default_extension = "inp"
 [parameters]
 basis_set = "def2svp"
 charge = 1
-functional = "BP86"
-functional_class = "GGA"
-memory = 3000
-multiplicity = 1
+method = "BP86"
+method_class = "GGA"
+mem = 3000
+mult = 1
 nprocs = 20
 solvation = false
 solvent = "water"
 split_index = 10
 hessian = false
+solvation_model = "CPCM"
+dispersion = "D3"

src/main.rs

@@ -42,22 +42,46 @@ enum Mode {
  Gen {
  /// The template to look for in ~/.config/gedent/templates
  template_name: String,
- // TODO: Make this a flag
  /// xyz files
  #[arg(value_name = "XYZ files")]
  xyz_files: Option<Vec<PathBuf>>,
  /// Print to screen and don't save file
  #[arg(short, long, default_value_t = false)]
  print: bool,
+ /// Set method
+ #[arg(long, default_value = None)]
+ method: Option<String>,
+ /// Set basis_set
+ #[arg(long, default_value = None)]
+ basis_set: Option<String>,
+ /// Set dispersion
+ #[arg(long, default_value = None)]
+ dispersion: Option<String>,
  /// Set solvent to value and solvation to true
  #[arg(short, long, default_value = None)]
  solvent: Option<Option<String>>,
+ /// Set solvation_model
+ #[arg(long, default_value = None)]
+ solvation_model: Option<String>,
  /// Set charge
  #[arg(short, long, default_value = None)]
  charge: Option<usize>,
- /// Set multiplicity
+ /// Set hessian
+ #[arg(long, default_value_t = false)]
+ hessian: bool,
  #[arg(short, long, default_value = None)]
- multiplicity: Option<usize>,
+ /// Set mult
+ #[arg(short, long, default_value = None)]
+ mult: Option<usize>,
+ /// Set nprocs
+ #[arg(long, default_value = None)]
+ nprocs: Option<usize>,
+ /// Set mem
+ #[arg(long, default_value = None)]
+ mem: Option<usize>,
+ /// Set split_index
+ #[arg(long, default_value = None)]
+ split_index: Option<usize>,
  },
  // Subcommand to deal with configurations
  /// Access gedent configuration
@@ -157,9 +181,17 @@ fn main() -> Result<()> {
  template_name,
  xyz_files,
  print,
+ method,
+ basis_set,
+ dispersion,
  solvent,
+ solvation_model,
  charge,
- multiplicity,
+ hessian,
+ mult,
+ nprocs,
+ mem,
+ split_index,
  } => {
  let mut molecules: Vec<Molecule> = vec![];
  if let Some(files) = xyz_files {
@@ -168,7 +200,21 @@ fn main() -> Result<()> {
  }
  };
  let template = Template::get(template_name)?;
- let results = generate_input(template, molecules, solvent, multiplicity, charge)?;
+ let results = generate_input(
+ template,
+ molecules,
+ solvent,
+ mult,
+ charge,
+ method,
+ basis_set,
+ dispersion,
+ solvation_model,
+ hessian,
+ nprocs,
+ mem,
+ split_index,
+ )?;
  for input in results {
  if print {
  println!("{}", input.content);
@@ -338,6 +384,14 @@ fn generate_input(
  solvation: Option<Option<String>>,
  mult: Option<usize>,
  charge: Option<usize>,
+ method: Option<String>,
+ basis_set: Option<String>,
+ dispersion: Option<String>,
+ solvation_model: Option<String>,
+ hessian: bool,
+ nprocs: Option<usize>,
+ mem: Option<usize>,
+ split_index: Option<usize>,
 ) -> Result<Vec<Input>, Error> {
  let mut context = tera::Context::new();
  let config = Config::get()?;
@@ -353,12 +407,31 @@ fn generate_input(
  }
  }
 
- if let Some(mult) = mult {
- context.insert("multiplicity", &mult);
+ if hessian {
+ context.insert("hessian", &hessian);
  }
 
- if let Some(charge) = charge {
- context.insert("charge", &charge);
+ for (k, v) in [
+ ("charge", charge),
+ ("mult", mult),
+ ("nprocs", nprocs),
+ ("mem", mem),
+ ("split_index", split_index),
+ ] {
+ if let Some(v) = v {
+ context.insert(k, &v);
+ }
+ }
+
+ for (k, v) in [
+ ("method", method),
+ ("basis_set", basis_set),
+ ("dispersion", dispersion),
+ ("solvation_model", solvation_model),
+ ] {
+ if let Some(v) = v {
+ context.insert(k, &v);
+ }
  }
 
  let extension = match &template.options.extension {

templates/adf/eda

@@ -34,7 +34,7 @@ Engine adf
 
  XC
  Dispersion Grimme3 BJDAMP
- {{ functional_class }} {{ functional }}
+ {{ method_class }} {{ functional }}
  end
 
  Beckegrid

templates/adf/sp

@@ -18,7 +18,7 @@ Engine ADF
  end
 
  XC
- {{ functional_class }} {{ functional }}
+ {{ method_class }} {{ functional }}
  Dispersion Grimme3 BJDAMP
  end
 

templates/gaussian/nbo_del

@@ -3,8 +3,8 @@ extension = "gjf"
 --@
 %chk={{ Molecule.filename }}.chk
 %nproc={{ nprocs }}
-%mem={{ memory }}GB
-# {{ functional }}/{{ basis_set }} pop=nbo6del nosymm
+%mem={{ mem }}GB
+# {{ method }}/{{ basis_set }} pop=nbo6del nosymm
 
 job title: {{ Molecule.filename }}
 

templates/gaussian/opt

@@ -8,8 +8,8 @@ extension = "gjf"
 {%endif-%}
 %chk={{ Molecule.filename }}.chk
 %nproc={{ nprocs }}
-%mem={{ memory }}GB
-# {{ functional }}/{{ basis_set }} opt freq=noraman {{ solvent }}
+%mem={{ mem }}GB
+# {{ method }}/{{ basis_set }} opt freq=noraman {{ solvent }}
 
 job title: {{ Molecule.filename }}
 

templates/gaussian/sp

@@ -7,8 +7,8 @@ extension = "gjf"
 {%set solvent=""-%}
 {%endif-%}
 %nproc={{ nprocs }}
-%mem={{ memory }}GB
-# {{ functional }}/{{ basis_set }} freq=noraman scrf=(smd,solvent=ethanol) temperature=353
+%mem={{ mem }}GB
+# {{ method }}/{{ basis_set }} freq=noraman scrf=(smd,solvent=ethanol) temperature=353
 
 job title: {{ Molecule.filename }}
 

templates/orca/neb

@@ -1,4 +1,4 @@
-! {{ functional }} {{ basis_set }} 
+! {{ method }} {{ basis_set }} 
 ! NEB-TS NumFreq IRC
 
 *xyzfile {{ charge }} {{ mult }} {{ xyz_file }}
@@ -7,7 +7,7 @@
  nprocs {{ nprocs }}
 end
 
-%maxcore {{ memory }} 
+%maxcore {{ mem }} 
 
 {% if solvation -%}
 %cpcm

templates/orca/opt

@@ -1,14 +1,14 @@
 --@
 extension = "inp"
 --@
-! {{ functional }} {{ basis_set }} 
+! {{ method }} {{ basis_set }} 
 ! Opt freq D3BJ
 
 %pal
  nprocs {{ nprocs }}
 end
 
-%maxcore {{ memory }} 
+%maxcore {{ mem }} 
 
 {% if solvation -%}
 %cpcm

templates/orca/scan

@@ -1,4 +1,4 @@
-! {{ functional }} {{ basis_set }} 
+! {{ method }} {{ basis_set }} 
 ! Opt
 
 {% if solvation -%}