From 29835278f5112ab22de7788a1486b73cf7f7fa2b Mon Sep 17 00:00:00 2001
From: Subindev D <64056430+subindev-d@users.noreply.github.com>
Date: Mon, 24 Jun 2024 16:09:12 +0100
Subject: [PATCH 1/3] add iteration options

---
 mudirac/mudirac.xml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/mudirac/mudirac.xml b/mudirac/mudirac.xml
index 2f7c219..70c6dd0 100644
--- a/mudirac/mudirac.xml
+++ b/mudirac/mudirac.xml
@@ -38,6 +38,15 @@ write_spec: $generate_spectrum.generate_spectrum_selector
 #if $electronic_config:
 electronic_config: $electronic_config
 #end if
+#if $max_E_iter:
+max_E_iter: $max_E_iter
+#end if
+#if $max_nodes_iter:
+max_nodes_iter: $max_nodes_iter
+#end if
+#if $max_state_iter:
+max_state_iter: $max_state_iter
+#end if
 #if $generate_spectrum.generate_spectrum_selector=='true':
 #if $spec_step
 spec_step: $spec_step
@@ -188,6 +197,10 @@ spec_expdec: $spec_expdec
         <param name="uehling_correction" type="boolean" value="false" label="Uehling correction" help="whether to turn on the Uehling correction or not" optional="true"/>
         <param name="electronic_config" type="text" value="" label="electronic configuration to use in order to describe the negative charge background" help="Can be a full string describing the configuration (e.g. 1s2 2s2 2p2), 
         an element symbol to represent the default configuration of that atom when neutral (e.g. C) or a mix of the two (e.g. [He] 2s2 2p2)" optional="true"/>
+        <param name="max_E_iter" type="integer" value="" label="maximum number of iterations to perform when searching for the energy of a state." help="If exceeded, convergence will fail. Increase this value for slow convergences that are however progressing. Default is 100." optional="true"/>
+        <param name="max_nodes_iter" type="integer" value="" label="maximum number of iterations to perform when searching for a starting energy value that gives a state the expected number of nodes." help="If exceeded, convergence will fail. Should generally not need to be adjusted. Default is 100." optional="true"/>
+        <param name="max_state_iter" type="integer" value="" label=" maximum number of iterations to perform when searching for a state." help=" This loop encloses both node-based and energy-based search. Once a state is converged, the program checks again that it has the correct number of nodes. 
+        If it does not, the state is stored for future use and to provide an upper or lower limit to the energy of the searches and then the process is repeated. This number represents how much can the process be repeated before failing. Should not generally need to be adjusted. Default is 100." optional="true"/>
         <param name='output_level' type="boolean" value="false" falsevalue="1" truevalue="2" label="Produce states and transition matrices" help="Also produce each of the states in a separate file as well as the transition matrices for each line"/>
         <conditional name="generate_spectrum">
             <param name="generate_spectrum_selector" type="select" display="radio" value="false" label="Generate spectrum" help="Generate spectrum using the transition lines found broadened with Gaussian functions">
@@ -234,6 +247,20 @@ spec_expdec: $spec_expdec
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="3">
+            <param name="element" value="Au"/>
+            <param name="isotope" value="197"/>
+            <param name="xr_lines" value="K1-L2,K1-L3"/>
+            <param name="max_E_iter" value="100"/>
+            <param name="max_nodes_iter" value="100"/>
+            <param name="max_state_iter" value="100"/>
+            <output name="output" file="Au_basic.xr.out" ftype="tabular" compare="diff"/>
+            <output name="error_log">
+                <assert_contents>
+                    <has_size max="0"/>
+                </assert_contents>
+            </output>
+        </test>
         <test expect_num_outputs="3">
             <param name="element" value="Au"/>
             <param name="isotope" value="197"/>

From c4e042a7623ac68f0b71b71820ef6e17027b8945 Mon Sep 17 00:00:00 2001
From: Subindev D <64056430+subindev-d@users.noreply.github.com>
Date: Mon, 24 Jun 2024 18:01:57 +0100
Subject: [PATCH 2/3] add uehling correction parameters

---
 mudirac/mudirac.xml | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/mudirac/mudirac.xml b/mudirac/mudirac.xml
index 70c6dd0..6d30f67 100644
--- a/mudirac/mudirac.xml
+++ b/mudirac/mudirac.xml
@@ -31,7 +31,18 @@
         <configfile name="input_yaml">element: $element
 isotope: $isotope
 xr_lines: $xr_lines
-uehling_correction: $uehling_correction
+uehling_correction: $uehling_correction.uehling_correction
+#if $uehling_correction.uehling_correction=='true':
+#if $uehling_correction.uehling_steps:
+uehling_steps: $uehling_correction.uehling_steps
+#end if
+#if $uehling_correction.uehling_lowcut
+uehling_lowcut: $uehling_correction.uehling_lowcut
+#end if
+#if $uehling_correction.uehling_highcut:
+uehling_highcut: $uehling_correction.uehling_highcut
+#end if
+#end if
 nuclear_model: $nuclear_model
 output: $output_level
 write_spec: $generate_spectrum.generate_spectrum_selector
@@ -194,7 +205,18 @@ spec_expdec: $spec_expdec
             <option value="SPHERE"> finite size, uniformly charged spherical nucleus </option>
             <option value="FERMI2"> Fermi 2-term charge distribution </option>
         </param>
-        <param name="uehling_correction" type="boolean" value="false" label="Uehling correction" help="whether to turn on the Uehling correction or not" optional="true"/>
+        <conditional name="uehling_correction">
+            <param name="uehling_correction" type="select" display="radio" value="false" label="Uehling correction" help="whether to turn on the Uehling correction or not">
+                <option value="false" selected="true">False</option>
+                <option value="true">True</option>
+            </param>
+            <when value="false"/>
+            <when value="true">
+                <param name="uehling_steps" type="integer" value="" label="integration steps for the Uehling potential." help=" Higher numbers will make the Uehling energy more precise but increase computation times. Default is 100." optional="true"/>
+                <param name="uehling_lowcut" type="float" value="" label="low cutoff for Uehling potential" help="under low cutoff, the radius will be considered 0. Default is 0." optional="true"/>
+                <param name="uehling_highcut" type="float" value="" label="high cutoff for Uehling potential" help="over high cutoff, the radius will be considered r > > c . Default is INFINITY." optional="true"/>
+            </when>
+        </conditional>
         <param name="electronic_config" type="text" value="" label="electronic configuration to use in order to describe the negative charge background" help="Can be a full string describing the configuration (e.g. 1s2 2s2 2p2), 
         an element symbol to represent the default configuration of that atom when neutral (e.g. C) or a mix of the two (e.g. [He] 2s2 2p2)" optional="true"/>
         <param name="max_E_iter" type="integer" value="" label="maximum number of iterations to perform when searching for the energy of a state." help="If exceeded, convergence will fail. Increase this value for slow convergences that are however progressing. Default is 100." optional="true"/>
@@ -266,7 +288,9 @@ spec_expdec: $spec_expdec
             <param name="isotope" value="197"/>
             <param name="xr_lines" value="K1-L2,K1-L3"/>
             <param name="nuclear_model" value="FERMI2"/>
-            <param name="uehling_correction" value="true"/>
+            <conditional name="uehling_correction">
+                <param name="uehling_correction" value="true"/>
+            </conditional>
             <param name="electronic_config" value="Au"/>
             <output name="output" file="Au.xr.out" ftype="tabular" compare="diff"/>
             <output name="error_log">

From 09f2cebf9f0f32e1b5ddbb66874d2fc74f81fddf Mon Sep 17 00:00:00 2001
From: Subindev D <64056430+subindev-d@users.noreply.github.com>
Date: Tue, 2 Jul 2024 12:04:24 +0100
Subject: [PATCH 3/3] code review changes

Co-authored-by: patrick-austin <61705287+patrick-austin@users.noreply.github.com>

Update mudirac/mudirac.xml

Co-authored-by: patrick-austin <61705287+patrick-austin@users.noreply.github.com>

Update mudirac/mudirac.xml

Co-authored-by: patrick-austin <61705287+patrick-austin@users.noreply.github.com>

Update mudirac/mudirac.xml

Co-authored-by: patrick-austin <61705287+patrick-austin@users.noreply.github.com>

Update mudirac/mudirac.xml

Co-authored-by: patrick-austin <61705287+patrick-austin@users.noreply.github.com>
---
 mudirac/mudirac.xml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/mudirac/mudirac.xml b/mudirac/mudirac.xml
index 6d30f67..fd56f0c 100644
--- a/mudirac/mudirac.xml
+++ b/mudirac/mudirac.xml
@@ -206,23 +206,23 @@ spec_expdec: $spec_expdec
             <option value="FERMI2"> Fermi 2-term charge distribution </option>
         </param>
         <conditional name="uehling_correction">
-            <param name="uehling_correction" type="select" display="radio" value="false" label="Uehling correction" help="whether to turn on the Uehling correction or not">
+            <param name="uehling_correction" type="select" display="radio" label="Uehling correction" help="whether to turn on the Uehling correction or not">
                 <option value="false" selected="true">False</option>
                 <option value="true">True</option>
             </param>
             <when value="false"/>
             <when value="true">
-                <param name="uehling_steps" type="integer" value="" label="integration steps for the Uehling potential." help=" Higher numbers will make the Uehling energy more precise but increase computation times. Default is 100." optional="true"/>
-                <param name="uehling_lowcut" type="float" value="" label="low cutoff for Uehling potential" help="under low cutoff, the radius will be considered 0. Default is 0." optional="true"/>
-                <param name="uehling_highcut" type="float" value="" label="high cutoff for Uehling potential" help="over high cutoff, the radius will be considered r > > c . Default is INFINITY." optional="true"/>
+                <param name="uehling_steps" type="integer" value="100" min="0" label="integration steps for the Uehling potential." help=" Higher numbers will make the Uehling energy more precise but increase computation times. Default is 100."/>
+                <param name="uehling_lowcut" type="float" value="0" min="0" label="low cutoff for Uehling potential" help="under low cutoff, the radius will be considered 0. Default is 0."/>
+                <param name="uehling_highcut" type="float" value="" min="0" label="high cutoff for Uehling potential" help="over high cutoff, the radius will be considered r > > c . Default is INFINITY." optional="true"/>
             </when>
         </conditional>
         <param name="electronic_config" type="text" value="" label="electronic configuration to use in order to describe the negative charge background" help="Can be a full string describing the configuration (e.g. 1s2 2s2 2p2), 
         an element symbol to represent the default configuration of that atom when neutral (e.g. C) or a mix of the two (e.g. [He] 2s2 2p2)" optional="true"/>
-        <param name="max_E_iter" type="integer" value="" label="maximum number of iterations to perform when searching for the energy of a state." help="If exceeded, convergence will fail. Increase this value for slow convergences that are however progressing. Default is 100." optional="true"/>
-        <param name="max_nodes_iter" type="integer" value="" label="maximum number of iterations to perform when searching for a starting energy value that gives a state the expected number of nodes." help="If exceeded, convergence will fail. Should generally not need to be adjusted. Default is 100." optional="true"/>
-        <param name="max_state_iter" type="integer" value="" label=" maximum number of iterations to perform when searching for a state." help=" This loop encloses both node-based and energy-based search. Once a state is converged, the program checks again that it has the correct number of nodes. 
-        If it does not, the state is stored for future use and to provide an upper or lower limit to the energy of the searches and then the process is repeated. This number represents how much can the process be repeated before failing. Should not generally need to be adjusted. Default is 100." optional="true"/>
+        <param name="max_E_iter" type="integer" value="100" min="0" label="maximum number of iterations to perform when searching for the energy of a state." help="If exceeded, convergence will fail. Increase this value for slow convergences that are however progressing. Default is 100."/>
+        <param name="max_nodes_iter" type="integer" value="100" min="0" label="maximum number of iterations to perform when searching for a starting energy value that gives a state the expected number of nodes." help="If exceeded, convergence will fail. Should generally not need to be adjusted. Default is 100."/>
+        <param name="max_state_iter" type="integer" value="100" min="0" label=" maximum number of iterations to perform when searching for a state." help=" This loop encloses both node-based and energy-based search. Once a state is converged, the program checks again that it has the correct number of nodes. 
+        If it does not, the state is stored for future use and to provide an upper or lower limit to the energy of the searches and then the process is repeated. This number represents how much can the process be repeated before failing. Should not generally need to be adjusted. Default is 100."/>
         <param name='output_level' type="boolean" value="false" falsevalue="1" truevalue="2" label="Produce states and transition matrices" help="Also produce each of the states in a separate file as well as the transition matrices for each line"/>
         <conditional name="generate_spectrum">
             <param name="generate_spectrum_selector" type="select" display="radio" value="false" label="Generate spectrum" help="Generate spectrum using the transition lines found broadened with Gaussian functions">