import neb codes from gosh

Cargo.toml

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+# cargo
+
+# [[file:~/Workspace/Programming/gosh/nebrun/neb.note::*cargo][cargo:1]]
+[package]
+name = "neb"
+version = "0.0.1"
+edition = "2018"
+authors = ["Wenping Guo <[email protected]>"]
+
+[dependencies]
+quicli = "0.4"
+structopt = "0.2"
+#gosh = {git = "https://github.com/gosh-rs/gosh.git", tag="v0.0.17"}
+gosh = {path = "/home/ybyygu/Workspace/Programming/gosh"}
+
+[dev-dependencies]
+approx = "0.3"
+# cargo:1 ends here

src/bin/nebrun.rs

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+// entry
+
+use gosh::cmd_utils::*;
+use std::path::PathBuf;
+
+use gosh::gchemol::io;
+
+use neb::NEB;
+use gosh::models::*;
+
+/// An universal runner for Blackbox Model
+#[derive(Debug, StructOpt)]
+struct Cli {
+    /// Input molecule file
+    #[structopt(parse(from_os_str))]
+    molfile: PathBuf,
+
+    /// Template directory with all related files. The default is current directory.
+    #[structopt(short = "t", long = "template-dir", parse(from_os_str))]
+    tpldir: Option<PathBuf>,
+
+    /// Output the caputured structure. e.g.: -o foo.xyz
+    #[structopt(short = "o", long = "output", parse(from_os_str))]
+    output: Option<PathBuf>,
+
+    #[structopt(flatten)]
+    verbosity: Verbosity,
+}
+
+fn main() -> CliResult {
+    let args = Cli::from_args();
+    args.verbosity.setup_env_logger(&env!("CARGO_PKG_NAME"))?;
+
+    // 1. load molecules
+    info!("input molecule file: {}", &args.molfile.display());
+    let mut mols = io::read(args.molfile)?;
+    info!("loaded {} molecules.", mols.len());
+
+    let bbm = if let Some(d) = args.tpldir {
+        BlackBox::from_dotenv(&d)
+    } else {
+        BlackBox::default()
+    };
+
+    let mut neb = NEB::new(mols);
+
+    neb.run(&bbm)?;
+
+    // output molecules
+    if let Some(path) = args.output {
+        let mut mols = vec![];
+        for image in neb.images {
+            mols.push(image.mol.clone());
+        }
+
+        println!("file saved to: {:}", path.display());
+        io::write(path, &mols)?;
+    }
+
+    Ok(())
+}

src/lib.rs

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+// mods
+
+// [[file:~/Workspace/Programming/gosh/nebrun/neb.note::*mods][mods:1]]
+mod neb;
+
+pub use crate::neb::NEB;
+// mods:1 ends here
+
+// base
+
+// [[file:~/Workspace/Programming/gosh/nebrun/neb.note::*base][base:1]]
+pub(crate) mod common {
+    pub use quicli::prelude::*;
+    pub type Result<T> = ::std::result::Result<T, Error>;
+}
+// base:1 ends here