From 15b055f3e33b7c5f5165161e444c9692d29810d7 Mon Sep 17 00:00:00 2001
From: Xavier Andrade <xavier@tddft.org>
Date: Tue, 9 Jul 2024 01:45:45 -0700
Subject: [PATCH] Add a subcommand to set the pseudopotential for a species.

---
 src/interface/species.hpp | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/src/interface/species.hpp b/src/interface/species.hpp
index 52ee5be4..9e14d20b 100644
--- a/src/interface/species.hpp
+++ b/src/interface/species.hpp
@@ -117,6 +117,16 @@ These are the options available:
    Python example: `pinq.species.pseudo-set("He", "sg15")`
 
 
+-  Shell:  `species <symbol> file <filename>`
+   Python: `species.file("symbol", "filename")`
+
+   Sets the pseudopotential file that will be used for the species
+   given by <symbol>.
+
+   Shell example:  `inq species Xe file Xe.upf`
+   Python example: `pinq.species.pseudo-set("Xe", "Xe.upf")`
+
+
 -  Shell:  `species <symbol> mass <value>`
    Python: `species.pseudo_set("symbol", value)`
 
@@ -212,6 +222,15 @@ These are the options available:
 		ions.save(input::environment::global().comm(), ".inq/default_ions");
 	}
 
+	static void file(std::string symbol, std::string const & file) {
+
+		symbol[0] = std::toupper(symbol[0]);
+		auto ions = systems::ions::load(".inq/default_ions");
+		if(not ions.species_list().contains(symbol)) ions.species_list().insert(string_to_species(symbol));
+		ions.species_list()[symbol].pseudo_file(file);
+		ions.save(input::environment::global().comm(), ".inq/default_ions");
+	}
+
 	static void mass(std::string symbol, double const & mass_value) {
 
 		symbol[0] = std::toupper(symbol[0]);
@@ -271,6 +290,12 @@ These are the options available:
 			actions::normal_exit();
 		}
 
+		if(args.size() == 3 and args[1] == "file") {
+			file(args[0], args[2]);
+			status();
+			actions::normal_exit();
+		}
+
 		if(args.size() == 3 and args[1] == "mass") {
 			mass(args[0], str_to<double>(args[2]));
 			status();