Update Experiment descriptions, sample descriptions.

pyproject.toml

@@ -54,7 +54,7 @@ spm = "pynxtools_spm.reader:SPMReader"
 [project.entry-points."nomad.plugin"]
 sts_example = "pynxtools_spm.nomad.entrypoints:sts_example"
 stm_example = "pynxtools_spm.nomad.entrypoints:stm_example"
-afm_example = "pynxtools_spm.nomad.entrypoints:afm_example"   
+afm_example = "pynxtools_spm.nomad.entrypoints:afm_example"
 
 
 [tool.setuptools.packages.find]

src/pynxtools_spm/nomad/examples/afm/AFMExampleWithCustomization/AFMExampleWithCustomization.archive.json

@@ -1 +1 @@
-{"data":{"m_def":"../upload/raw/AFM.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXafm","input_files":["A151216.123306-02602.sxm","eln_data.yaml","config.json"],"default":"current_forward","definition":"NXafm","experiment_technique":"AFM","scan_mode":"contact mode","experiment_description":"<p>Experiment Description.</p>","experiment_identifier":{"identifier":"DemoExperimentIdentifier-12345"},"collection_identifier":{"identifier":"DemoCollectionIdentifier-12345"},"user":{"name":"Rubel Mozumder"},"experiment_instrument":{"hardware":{"vendor":"Nanonis","name":"Nanonis"},"software":{"vendor":"Nanonis","name":"Nanonis","model":"Generic 4","model/@version":"4"}},"Sample":{"name":"Demo Name","description":"<p>Description.</p>","sample_component_set":{"sample_component":{"name":"ComponentName"}},"History":{"notes":"<p>Sample History.</p>"}}}}
+{"data":{"m_def":"../upload/raw/AFM.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXafm","input_files":["A151216.123306-02602.sxm","eln_data.yaml","config.json"],"default":"current_forward","definition":"NXafm","experiment_technique":"AFM","scan_mode":"tapping mode","experiment_description":"<p>The experiment is performed with a cantilever that has a center frequency of 22.63 kHz</p>\n<p>The Lockin setup is off.<br />The setpoint for Z-controller is 50pA.</p>\n<p>Bias is -9.000E-4 V.</p>\n<p>&nbsp;</p>","experiment_identifier":{"identifier":"DemoExperimentIdentifier-1234"},"collection_identifier":{"identifier":"C:\\AFM\\_data\\201510"},"user":{"name":"Rubel Mozumder","affiliation":["HU"],"email":["rubel.mozumder@physik.hu-berlin.de","cojal@physik.hu-berlin.de"]},"experiment_instrument":{"hardware":{"vendor":"Nanonis","name":"Nanonis"},"software":{"vendor":"Nanonis","name":"Nanonis","model":"Generic 4","model/@version":"4"}},"Sample":{"name":"SampleName ","sample_component_set":{"sample_component":{"name":"DemoComponent","description":"<p>Description</p>"}},"History":{"notes":"<p>Sample History</p>"}}}}

src/pynxtools_spm/nomad/examples/afm/AFMExampleWithCustomization/eln_data.yaml

@@ -1,18 +1,25 @@
 Sample:
   History:
-    notes: <p>Sample History.</p>
-  description: <p>Description.</p>
-  name: Demo Name
+    notes: <p>Sample History</p>
+  name: 'SampleName '
   sample_component_set:
     sample_component:
-      name: ComponentName
+      description: <p>Description</p>
+      name: DemoComponent
 collection_identifier:
-  identifier: DemoCollectionIdentifier-12345
+  identifier: C:\AFM\_data\201510
 default: current_forward
 definition: NXafm
-experiment_description: <p>Experiment Description.</p>
+experiment_description: '<p>The experiment is performed with a cantilever that has
+  a center frequency of 22.63 kHz</p>
+
+  <p>The Lockin setup is off.<br />The setpoint for Z-controller is 50pA.</p>
+
+  <p>Bias is -9.000E-4 V.</p>
+
+  <p>&nbsp;</p>'
 experiment_identifier:
-  identifier: DemoExperimentIdentifier-12345
+  identifier: DemoExperimentIdentifier-1234
 experiment_instrument:
   hardware:
     name: Nanonis
@@ -23,6 +30,11 @@ experiment_instrument:
     name: Nanonis
     vendor: Nanonis
 experiment_technique: AFM
-scan_mode: contact mode
+scan_mode: tapping mode
 user:
+  affiliation:
+  - HU
+  email:
+  - rubel.mozumder@physik.hu-berlin.de
+  - cojal@physik.hu-berlin.de
   name: Rubel Mozumder

src/pynxtools_spm/nomad/examples/stm/STMExampleWithCustomization/STMExampleWithCustomization.archive.json

@@ -1 +1 @@
-{"data":{"m_def":"../upload/raw/STM.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXstm","input_files":["STM_nanonis_generic_4_5.sxm","config.json","eln_data.yaml"],"default":"current_forward","definition":"NXstm","experiment_technique":"STM","scan_mode":"constant current","experiment_description":"<p>The experiment description goes here.</p>","experiment_identifier":{"identifier":"DemoExperimentIdentifier-12"},"collection_identifier":{"identifier":"DemoCollectionIdentifier-12"},"user":{"name":"Rubel Mozumder","affiliation":["HU"],"email":["rubel.mozumder@physik.hu-berlin.de"]},"experiment_instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis"},"software":{"name":"Nanonis","vendor":"Nanonis","model":"Generic 4.5","model/@version":"4.5"},"scan_environment":{"tip_temp":100}},"Sample":{"name":"DemoSample","description":"<p>The sample description goes here.</p>","sample_component_set":{"sample_component":{"name":"DemoSample","description":"<p>Sample component description goes here.</p>"}},"History":{"notes":"<p>Sample History goes here.</p>"}}}}
+{"data":{"m_def":"../upload/raw/STM.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXstm","input_files":["STM_nanonis_generic_4_5.sxm","config.json","eln_data.yaml"],"default":"current_forward","definition":"NXstm","experiment_technique":"STM","scan_mode":"constant current","experiment_description":"<p>Experiment with</p>\n<p>Bias: 50mV</p>\n<p>Setpoint: 500pA</p>\n<p>Comment: &nbsp;</p>\n<p>&nbsp; &nbsp;Lockin:</p>\n<p>&nbsp; &nbsp; voltage: 10mV (Rms Frequency 831Hz, Phase -31.5deg) S 50mV Tcons 10mS</p>","experiment_identifier":{"identifier":"D:\\DATA\\nanonis V45_sessions\\Zurich PLL\\2023-03-31\\2023_03_31_oAu(111)__FeBr2_EP1_018.sxm"},"collection_identifier":{"identifier":"D:\\DATA\\nanonis V45_sessions\\Zurich PLL\\2023-03-31"},"user":{"name":"Rubel Mozumder","affiliation":["HU"],"email":["rubel,.mozumder@physik.hu-berlin.de","cojal@physik.hu-berlin.de"]},"experiment_instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis","model":"Generic 4.5","model/@version":"4.5"}},"Sample":{"name":"diPAMY","description":"<p>Sample description.</p>","sample_component_set":{"sample_component":{"name":"DemoComponent","description":"<p>Component Description goes here.</p>"}},"History":{"notes":"<p>Sample History goes here.</p>"}}}}

src/pynxtools_spm/nomad/examples/stm/STMExampleWithCustomization/eln_data.yaml

@@ -1,28 +1,32 @@
 Sample:
   History:
     notes: <p>Sample History goes here.</p>
-  description: <p>The sample description goes here.</p>
-  name: DemoSample
+  description: <p>Sample description.</p>
+  name: diPAMY
   sample_component_set:
     sample_component:
-      description: <p>Sample component description goes here.</p>
-      name: DemoSample
+      description: <p>Component Description goes here.</p>
+      name: DemoComponent
 collection_identifier:
-  identifier: DemoCollectionIdentifier-12
+  identifier: D:\DATA\nanonis V45_sessions\Zurich PLL\2023-03-31
 default: current_forward
 definition: NXstm
-experiment_description: <p>The experiment description goes here.</p>
+experiment_description: '<p>Experiment with</p>
+
+  <p>Bias: 50mV</p>
+
+  <p>Setpoint: 500pA</p>
+
+  <p>Comment: &nbsp;</p>
+
+  <p>&nbsp; &nbsp;Lockin:</p>
+
+  <p>&nbsp; &nbsp; voltage: 10mV (Rms Frequency 831Hz, Phase -31.5deg) S 50mV Tcons
+  10mS</p>'
 experiment_identifier:
-  identifier: DemoExperimentIdentifier-12
+  identifier: D:\DATA\nanonis V45_sessions\Zurich PLL\2023-03-31\2023_03_31_oAu(111)__FeBr2_EP1_018.sxm
 experiment_instrument:
   hardware:
-    name: Nanonis
-    vendor: Nanonis
-  scan_environment:
-    tip_temp:
-      unit: K
-      value: 100.0
-  software:
     model: Generic 4.5
     model/@version: '4.5'
     name: Nanonis
@@ -33,5 +37,6 @@ user:
   affiliation:
   - HU
   email:
-  - rubel.mozumder@physik.hu-berlin.de
+  - rubel,.mozumder@physik.hu-berlin.de
+  - cojal@physik.hu-berlin.de
   name: Rubel Mozumder

src/pynxtools_spm/nomad/examples/sts/STSExampleWithCustomization/STSExampleWithCustomization.archive.json

@@ -1 +1 @@
-{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXsts","input_files":["config.json","STS_nanonis_generic_5e_1.dat","eln_data.yaml"],"default":"current_grad","definition":"NXsts","experiment_technique":"STS","experiment_description":"<p>Experiment description is here.</p>","experiment_identifier":{"identifier":"STSExperimentIdentifier-1"},"collection_identifier":{"identifier":"STSCollectionIdentifier-1"},"user":{"name":"Rubel Mozumder","affiliation":["HU"],"email":["rubel.mozumder@physik.hu-berlin.de"]},"experiment_instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis"},"software":{"vendor":"Nanonis","name":"Nanonis","model":"Generic 5e"},"lockin_amplifier":{"modulation_signal":"current","lockin_current_flip_sign":-1},"scan_environment":{"tip_temp":100}},"Sample":{"name":"DemoName","description":"<p>Sample Description</p>","sample_component_set":{"sample_component":{"name":"Sample Component","description":"<p>Sample component description.</p>"}},"History":{"notes":"<p>Sample history goes here.</p>"}}}}
+{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","reader":"spm","nxdl":"NXsts","input_files":["config.json","STS_nanonis_generic_5e_1.dat","eln_data.yaml"],"default":"current_grad","definition":"NXsts","experiment_technique":"STS","experiment_description":"<p>Experiment with<br />Setpoints: 50pA</p>\n<p>Bias: 100mV</p>\n<p>Comment: SYNC &amp; Filter LP 8order WITHDRAW 600 steps, locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138 1st H, -84 2nd H</p>","experiment_identifier":{"identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin"},"collection_identifier":{"identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711"},"user":{"name":"Rubel Mozumer","affiliation":["HU"],"email":["rubel.mozumder@physik.hu-berlin.de"]},"experiment_instrument":{"hardware":{"name":"Nanonis","vendor":"Nanonis","model":"Generic 5e"},"software":{"vendor":"Nanonis","name":"Nanonis","model":"Generic 5e","model/@version":"5e"},"lockin_amplifier":{"modulation_signal":"current","lockin_current_flip_sign":-1}},"Sample":{"name":"Gold","sample_component_set":{"sample_component":{"name":"DemoSampleComponent","description":"<p>Description of the sample component</p>"}},"History":{"notes":"<p>Sample history goes here.</p>"},"chemical_formula":"Au"}}}

src/pynxtools_spm/nomad/examples/sts/STSExampleWithCustomization/eln_data.yaml

@@ -1,32 +1,35 @@
 Sample:
   History:
     notes: <p>Sample history goes here.</p>
-  description: <p>Sample Description</p>
-  name: DemoName
+  chemical_formula: Au
+  name: Gold
   sample_component_set:
     sample_component:
-      description: <p>Sample component description.</p>
-      name: Sample Component
+      description: <p>Description of the sample component</p>
+      name: DemoSampleComponent
 collection_identifier:
-  identifier: STSCollectionIdentifier-1
+  identifier: C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711
 default: current_grad
 definition: NXsts
-experiment_description: <p>Experiment description is here.</p>
+experiment_description: '<p>Experiment with<br />Setpoints: 50pA</p>
+
+  <p>Bias: 100mV</p>
+
+  <p>Comment: SYNC &amp; Filter LP 8order WITHDRAW 600 steps, locked Au(111), 50pA,
+  100 mV set point, 1mV DCA, 973Hz,138 1st H, -84 2nd H</p>'
 experiment_identifier:
-  identifier: STSExperimentIdentifier-1
+  identifier: C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin
 experiment_instrument:
   hardware:
+    model: Generic 5e
     name: Nanonis
     vendor: Nanonis
   lockin_amplifier:
     lockin_current_flip_sign: -1.0
     modulation_signal: current
-  scan_environment:
-    tip_temp:
-      unit: K
-      value: 100.0
   software:
     model: Generic 5e
+    model/@version: 5e
     name: Nanonis
     vendor: Nanonis
 experiment_technique: STS
@@ -35,4 +38,4 @@ user:
   - HU
   email:
   - rubel.mozumder@physik.hu-berlin.de
-  name: Rubel Mozumder
+  name: Rubel Mozumer