Add progress bar

Author: seatonullberg

Cargo.toml

@@ -36,6 +36,7 @@ hdf5-sys = { version = "0.7", optional = true }
 approx = "0.4"
 criterion = "0.3"
 nalgebra = "0.26"
+serial_test = "0.5"
 velvet-test-utils = { path = "crates/velvet-test-utils" }
 
 [features]
@@ -55,7 +56,10 @@ rayon = [
 ]
 
 [package.metadata.docs.rs]
-features = ["hdf5-sys/static", "hdf5-sys/zlib"]
+features = [
+    "hdf5-sys/static", 
+    "hdf5-sys/zlib"
+]
 
 [[bench]]
 name = "argon-benchmarks"

crates/velvet-core/Cargo.toml

@@ -8,6 +8,7 @@ repository = "https://github.com/seatonullberg/velvet"
 edition = "2018"
 
 [dependencies]
+indicatif = "0.15"
 nalgebra = "0.26"
 rand = "0.7"
 rand_distr = "0.3"

crates/velvet-core/src/simulation.rs

@@ -1,5 +1,7 @@
 //! High level abstraction for an atomistic simulation.
 
+use indicatif::{ProgressBar, ProgressStyle, ProgressDrawTarget};
+
 use crate::config::Configuration;
 use crate::potentials::Potentials;
 use crate::propagators::Propagator;
@@ -40,6 +42,11 @@ impl Simulation {
         // setup propagation
         self.propagator.setup(&mut self.system, &self.potentials);
 
+        // setup progress bar
+        let pb = ProgressBar::new(steps as u64);
+        pb.set_style(ProgressStyle::default_bar()
+            .template("[{eta_precise}] {bar:40.cyan/blue} {pos:>7} /{len:>7} steps"));
+
         // start iteration loop
         for i in 0..steps {
             // do one propagation step
@@ -72,8 +79,10 @@ impl Simulation {
                         }
                     }
                 }
-            }
+            }   
+            pb.inc(1);
         }
+        pb.finish();
     }
 
     /// Consume the simulation and return its [`System`] and [`Potentials`].

examples/argon.rs

@@ -26,16 +26,7 @@ fn main() {
     // Run MD with no thermostat to simulate the NVE ensemble.
     let md = MolecularDynamics::new(velocity_verlet, NullThermostat);
 
-    // Create an output group which writes scalar properties to stderr (the default destination).
-    let stderr_group = RawOutputGroupBuilder::new()
-        .interval(100)
-        .output(PotentialEnergy)
-        .output(KineticEnergy)
-        .output(TotalEnergy)
-        .output(Temperature)
-        .build();
-
-    // Write the same outputs to a file for post-processing.
+    // Create an output group which writes scalar properties to a file for post-processing.
     let file_group = RawOutputGroupBuilder::new()
         .destination(std::fs::File::create("argon.txt").unwrap())
         .interval(100)
@@ -47,7 +38,6 @@ fn main() {
 
     // Build the configuration.
     let config = ConfigurationBuilder::new()
-        .raw_output_group(stderr_group)
         .raw_output_group(file_group)
         .build();
 

examples/binary-gas.rs

@@ -36,16 +36,7 @@ fn main() {
     // Run MD with a Nose-Hoover thermostat to simulate the NVT ensemble.
     let md = MolecularDynamics::new(velocity_verlet, nose_hoover);
 
-    // Create an output group which writes scalar properties to stderr (the default destination).
-    let stderr_group = RawOutputGroupBuilder::new()
-        .interval(100)
-        .output(PotentialEnergy)
-        .output(KineticEnergy)
-        .output(TotalEnergy)
-        .output(Temperature)
-        .build();
-
-    // Write the same outputs to a file for post-processing.
+    // Create an output group which writes scalar properties to a file for post-processing.
     let file_group = RawOutputGroupBuilder::new()
         .destination(std::fs::File::create("binary-gas.txt").unwrap())
         .interval(100)
@@ -57,7 +48,6 @@ fn main() {
 
     // Build the configuration.
     let config = ConfigurationBuilder::new()
-        .raw_output_group(stderr_group)
         .raw_output_group(file_group)
         .build();
 

examples/magnesium-oxide.rs

@@ -39,16 +39,7 @@ fn main() {
     // Run MD with a Nose-Hoover thermostat to simulate the NVT ensemble.
     let md = MolecularDynamics::new(velocity_verlet, nose_hoover);
 
-    // Create an output group which writes scalar properties to stderr (the default destination).
-    let stderr_group = RawOutputGroupBuilder::new()
-        .interval(100)
-        .output(PotentialEnergy)
-        .output(KineticEnergy)
-        .output(TotalEnergy)
-        .output(Temperature)
-        .build();
-
-    // Write the same outputs to a file for post-processing.
+    // Create an output group which writes scalar properties to a file for post-processing.
     let file_group = RawOutputGroupBuilder::new()
         .destination(std::fs::File::create("magnesium-oxide.txt").unwrap())
         .interval(100)
@@ -60,7 +51,6 @@ fn main() {
 
     // Build the configuration.
     let config = ConfigurationBuilder::new()
-        .raw_output_group(stderr_group)
         .raw_output_group(file_group)
         .build();
 

tests/argon.rs

@@ -1,11 +1,13 @@
 use approx::*;
+use serial_test::serial;
 
 use velvet::prelude::*;
 use velvet_test_utils as test_utils;
 
 static ITERATIONS: usize = 10_000;
 
 #[test]
+#[serial]
 fn nve() {
     let system = test_utils::argon_system();
     let potentials = test_utils::argon_potentials();
@@ -37,6 +39,7 @@ fn nve() {
 }
 
 #[test]
+#[serial]
 fn nvt() {
     let system = test_utils::argon_system();
     let potentials = test_utils::argon_potentials();

tests/binary-gas.rs

@@ -1,11 +1,13 @@
 use approx::*;
+use serial_test::serial;
 
 use velvet::prelude::*;
 use velvet_test_utils as test_utils;
 
 static ITERATIONS: usize = 10_000;
 
 #[test]
+#[serial]
 fn nve() {
     let system = test_utils::binary_gas_system();
     let potentials = test_utils::binary_gas_potentials();
@@ -37,6 +39,7 @@ fn nve() {
 }
 
 #[test]
+#[serial]
 fn nvt() {
     let system = test_utils::binary_gas_system();
     let potentials = test_utils::binary_gas_potentials();

tests/xenon.rs

@@ -1,11 +1,13 @@
 use approx::*;
+use serial_test::serial;
 
 use velvet::prelude::*;
 use velvet_test_utils as test_utils;
 
 static ITERATIONS: usize = 10_000;
 
 #[test]
+#[serial]
 fn nve() {
     let system = test_utils::xenon_system();
     let potentials = test_utils::xenon_potentials();
@@ -37,6 +39,7 @@ fn nve() {
 }
 
 #[test]
+#[serial]
 fn nvt() {
     let system = test_utils::xenon_system();
     let potentials = test_utils::xenon_potentials();