Fix #6187: new 3d crystal plot

sirepo/package_data/static/html/silas-thermal-transport.html

@@ -18,5 +18,8 @@
     <div class="col-md-6 col-xl-4" data-ng-if="crystal.simState.isStateCompleted()">
       <div data-report-panel="parameter" data-model-name="tempProfileAnimation"></div>
     </div>
+    <div class="col-md-6 col-xl-4" data-ng-if="crystal.hasCrystal3d()">
+      <div data-report-panel="crystal3d" data-model-name="crystal3dAnimation"></div>
+    </div>
   </div>
 </div>

sirepo/package_data/static/js/silas.js

@@ -5,11 +5,7 @@ var srdbg = SIREPO.srdbg;
 
 SIREPO.app.config(function() {
     SIREPO.INITIAL_INTENSITY_REPORT_TITLE = 'Initial Laser Pulse';
-    SIREPO.SINGLE_FRAME_ANIMATION = [
-        'plotAnimation',
-        'plot2Animation',
-        'crystal3dAnimation',
-    ];
+    SIREPO.SINGLE_FRAME_ANIMATION = [];
     SIREPO.appFieldEditors += `
         <div data-ng-switch-when="FloatArray" class="col-sm-7">
             <div data-num-array="" data-model="model" data-field-name="field" data-field="model[field]" data-info="info" data-num-type="Float"></div>
@@ -50,7 +46,7 @@ SIREPO.app.factory('silasService', function(appState) {
     const self = {};
 
     self.computeModel = (analysisModel) => {
-        if (['crystalAnimation', 'crystal3dAnimation', 'plotAnimation', 'plot2Animation', 'tempHeatMapAnimation', 'tempProfileAnimation'].indexOf(analysisModel) >= 0) {
+        if (['crystalAnimation', 'crystal3dAnimation', 'tempHeatMapAnimation', 'tempProfileAnimation'].indexOf(analysisModel) >= 0) {
             return 'crystalAnimation';
         }
         if (['laserPulseAnimation', 'laserPulse2Animation'].includes(analysisModel)) {
@@ -189,14 +185,6 @@ SIREPO.app.controller('CrystalController', function (appState, frameCache, persi
 
     self.simState = persistentSimulation.initSimulationState(self);
     self.simState.errorMessage = () => errorMessage;
-
-    appState.whenModelsLoaded($scope, () => {
-        $scope.$on('plotAnimation.summaryData', function (e, data) {
-            if (data.crystalLength && data.crystalLength != silasService.getThermalCrystal().length) {
-                frameCache.setFrameCount(0);
-            }
-        });
-    });
 });
 
 SIREPO.app.directive('appFooter', function(appState, silasService) {
@@ -677,11 +665,12 @@ SIREPO.app.directive('crystal3d', function(appState, plotting, silasService, plo
                 let len = [];
                 let indices = [];
                 let verts = data.vertices;
+                const c = appState.applicationState().thermalTransportCrystal.crystal;
                 let size = $scope.boundAxis == 'Z'
-                    ? silasService.getThermalCrystal().length
-                    : appState.applicationState().thermalTransportCrystal.crystal.inversion_mesh_extent * 2;
+                    ? c.length
+                    : c.inversion_mesh_extent * 2 * 100;
                 let axisIdx = $scope.axes.indexOf($scope.boundAxis);
-                $scope.bound = (size + 0.01) * ($scope.sliderValue - 50) / 100;
+                $scope.bound = (size + 0.01) * $scope.sliderValue / 100 - size / 2;
                 for (let i = 0; i < data.indices.length; i += 3) {
                     if (checkBounds(i, axisIdx)) {
                         indices.push(data.indices[i], data.indices[i + 1], data.indices[i + 2]);
@@ -732,7 +721,6 @@ SIREPO.app.directive('crystal3d', function(appState, plotting, silasService, plo
                     camera.setFocalPoint(0, 0, 0);
                     camera.setViewUp(0, -1, 0);
                     renderer.resetCamera();
-                    camera.zoom(1.3);
                     orientationMarker.updateMarkerOrientation();
                 }
                 fsRenderer.getRenderWindow().render();

sirepo/package_data/static/json/silas-schema.json

@@ -149,7 +149,7 @@
             "x": ["Horizontal Value to Plot", "ValueList", "x"],
             "y1": ["Vertical Value to Plot", "ValueList", "y"],
             "histogramBins": ["Histogram Bins", "Integer", 200],
-            "colorMap": ["Color Map", "ColorMap", "afmhot"]
+            "colorMap": ["Color Map", "ColorMap", "viridis"]
         },
         "crystal3dAnimation": {},
         "laserPulse": {
@@ -192,8 +192,6 @@
             "_super": ["_", "model", "beamElement"],
             "title": ["Element Name", "String", "Mirror"]
         },
-        "plotAnimation": {},
-        "plot2Animation": {},
         "simulation": {
             "distanceFromSource": ["", "Float", 0.0 , "", 0.0]
         },
@@ -297,7 +295,8 @@
         },
         "crystal3dAnimation": {
             "title": "Crystal 3D Mesh",
-            "advanced": []
+            "advanced": [],
+            "canFullScreen": false
         },
         "mirror2": {
             "title": "Two Mirrors",
@@ -364,14 +363,6 @@
                 "focalLength"
             ]
         },
-        "plotAnimation": {
-            "title": "Radial Temperature Profile",
-            "advanced": []
-        },
-        "plot2Animation": {
-            "title": "Longitudinal Temperature Profile",
-            "advanced": []
-        },
         "n0n2Plot": {
             "title": "",
             "advanced": []

sirepo/package_data/template/silas/crystal.py.jinja

@@ -10,32 +10,31 @@ crystal = Crystal(params=PKDict({{crystalParams}}))
 sim_type = "{{ thermalCrystal.calc_type }}"
 
 def thermo_optic_sim():
-    thermo = ThermoOptic(crystal, {{thermalCrystal.mesh_density}})
+    def _solve():
+        if sim_type == "analytical":
+            return thermo.{{ pump_pulse_profile }}_solution()
 
-    # Initialize a simulator with a crystal object set
-    # Set evaluation points & boundary conditions
+        elif sim_type == "fenics":
+            thermo.set_boundary(2*(crystal.radius*100.)**2./40.)
+            thermo.set_load('{{ pump_pulse_profile }}')
+            r = crystal.params.pop_inversion_pump_rep_rate
+            if r <= 1:
+                return thermo.slow_solution('{{ pump_pulse_profile }}')
+            elif r >= 100:
+                return thermo.solve_steady()
+            else:
+                raise AssertionError(f"Invalid rep rate for simulated solve heat_load={'{{ pump_pulse_profile }}'}")
+
+    thermo = ThermoOptic(crystal, {{ thermalCrystal.mesh_density }})
+
+    # prep for 2d solve
     thermo.set_points((
         {{thermalTransportSettings_grid_points_r}},
         {{thermalTransportSettings_grid_points_w}},
         {{thermalTransportSettings_grid_points_z}},
-    ), {{thermalTransportSettings_edge_fraction}})
-    thermo.set_boundary(2*(crystal.radius*100.)**2./40.)
-
-    if sim_type == "analytical":
-        Ts = thermo.{{ pump_pulse_profile }}_solution()
+    ))
+    res_2d = _solve()
 
-    elif sim_type == "fenics":
-        thermo.set_load('{{ pump_pulse_profile }}')
-        r = crystal.params.pop_inversion_pump_rep_rate
-        if r <= 1:
-            Ts = thermo.slow_solution('{{ pump_pulse_profile }}')
-        elif r >= 100:
-            Ts = thermo.solve_steady()
-        else:
-            raise AssertionError(f"Invalid rep rate for simulated solve heat_load={'{{ pump_pulse_profile }}'}")
-
-    nT, n0Fit, n2Fit = thermo.compute_indices(Ts)
-    # Positions of each evaluation point & sets of the unique values
     ptzs = thermo.eval_pts[:, 2]
     ptrs = (thermo.eval_pts[:, 0] ** 2 + thermo.eval_pts[:, 1] ** 2) ** 0.5
     zs = unique(ptzs)
@@ -44,37 +43,38 @@ def thermo_optic_sim():
     zface = zs.min() if crystal.params.pop_inversion_pump_type != "right" else zs.max()
 
     # Radial values reflected across axis & meshgrid with longitudinal values
-    rrs = array((-rs[::-1]).tolist() + rs[1:].tolist())
-    RZ, ZR = meshgrid(rrs, zs)
     temp_profile = PKDict(
-        radial=[rs, Ts[ptzs==zface]],
-        longitudinal=[zs, Ts[ptrs==rcenter]]
+        radial=[rs, res_2d[ptzs==zface]],
+        longitudinal=[zs, res_2d[ptrs==rcenter]]
     )
-    pTs = Ts.reshape((len(rs), len(zs)), order='F')
+    pTs = res_2d.reshape((len(rs), len(zs)), order='F')
     pTs = array((pTs[::-1]).tolist()+pTs[1:].tolist())
-    heat_map = pTs
+
+    # prep for 3d solve
+    mesh = thermo.mesh
+    inds = []
+    for item in dolfin.cpp.mesh.facets(mesh):
+        inds.append(item.entities(0).tolist())
+    vertices = mesh.coordinates()
+    thermo.eval_pts = vertices
+    res_3d = _solve()
     return PKDict(
         thermo=thermo,
-        heat_map=heat_map,
+        heat_map=pTs,
         temp_profile=temp_profile,
-        nT=nT,
-        n0Fit=n0Fit,
-        n2Fit=n2Fit,
+        intensity=res_3d,
+        vertices=vertices,
+        indices=numpy.array(inds),
     )
 
 
 res = thermo_optic_sim()
 
-# for 3D plots, get the facets, and build an array
-# containing the indices of their coordinates
-inds = []
-for item in dolfin.cpp.mesh.facets(res.thermo.mesh):
-    inds.append(item.entities(0).tolist())
 
 # we will provide these indices to plotly so it can draw proper surfaces
-inds = numpy.array(inds)
-numpy.save("indices.npy", inds)
-numpy.save("vertices.npy", res.thermo.mesh.coordinates())
+numpy.save("indices.npy", res.indices)
+numpy.save("intensity.npy", res.intensity)
+numpy.save("vertices.npy", res.vertices)
 template_common.write_dict_to_h5(
     res.temp_profile,
     "tempProfile.h5"

sirepo/package_data/template/silas/examples/bella.json

@@ -612,11 +612,8 @@
             "reportType": "3d",
             "watchpointPlot": "total_intensity"
         },
-        "plot2Animation": {},
-        "plotAnimation": {},
         "simulation": {
             "distanceFromSource": 0,
-            "documentationUrl": "",
             "folder": "/Examples",
             "name": "100TW amplifier with 3 crystals"
         }

sirepo/package_data/template/silas/examples/multiple-pass-single-crystal.json

@@ -318,12 +318,9 @@
             "sigy_waist": 0.003056,
             "wfs": ""
         },
-        "plot2Animation": {},
-        "plotAnimation": {},
         "simulation": {
             "distanceFromSource": 0,
             "folder": "/Examples",
-            "isExample": true,
             "name": "Multiple Passes Through Single Crystal"
         }
     },

sirepo/package_data/template/silas/examples/single-crystal.json

@@ -67,12 +67,9 @@
             "sigy_waist": 0.001,
             "wfs": ""
         },
-        "plot2Animation": {},
-        "plotAnimation": {},
         "simulation": {
             "distanceFromSource": 0,
             "folder": "/Examples",
-            "isExample": true,
             "name": "Single Crystal"
         },
         "watchpointReport3": {

sirepo/sim_data/silas.py

@@ -65,8 +65,6 @@ def _compute_model(cls, analysis_model, *args, **kwargs):
             "crystal3dAnimation",
             "tempProfileAnimation",
             "tempHeatMapAnimation",
-            "plotAnimation",
-            "plot2Animation",
         ):
             return "crystalAnimation"
         if "beamlineAnimation" in analysis_model:

sirepo/template/silas.py

@@ -19,7 +19,6 @@
 
 _SIM_DATA, SIM_TYPE, SCHEMA = sirepo.sim_data.template_globals()
 
-_CRYSTAL_CSV_FILE = "crystal.csv"
 _TEMP_PROFILE_FILE = "tempProfile.h5"
 _TEMP_HEATMAP_FILE = "tempHeatMap.h5"
 _RESULTS_FILE = "results{}.h5"
@@ -309,38 +308,6 @@ def _crystal_animation_percent_complete(run_dir, res, data):
     return res
 
 
-def _crystal_plot(frame_args):
-    x = None
-    plots = []
-    with open(str(frame_args.run_dir.join(_CRYSTAL_CSV_FILE))) as f:
-        for r in csv.reader(f):
-            if x is None and r[0] == x_column:
-                r.pop(0)
-                r.pop(0)
-                x = [float(v) * scale for v in r]
-            elif r[0] == y_column:
-                r.pop(0)
-                t = r.pop(0)
-                plots.append(
-                    PKDict(
-                        points=[float(v) for v in r],
-                        label="{:.1f} sec".format(float(t)),
-                    )
-                )
-    return PKDict(
-        title="",
-        x_range=[min(x), max(x)],
-        y_label="Temperature [°C]",
-        x_label=x_heading,
-        x_points=x,
-        plots=plots,
-        y_range=template_common.compute_plot_color_and_range(plots),
-        summaryData=PKDict(
-            crystalLength=_get_crystal(frame_args.sim_in).length,
-        ),
-    )
-
-
 def _generate_beamline_elements(data):
     def _callback(state, element, dz):
         if dz:
@@ -425,7 +392,7 @@ def _generate_parameters_file(data):
 
     res, v = template_common.generate_parameters_file(data)
     if data.report == "crystalAnimation":
-        c = _get_crystal(data)
+        c = data.models.thermalTransportCrystal.crystal
         if c.pump_rep_rate <= 1:
             c.calc_type = "fenics"
         v.crystalParams = PKDict(
@@ -445,7 +412,6 @@ def _generate_parameters_file(data):
         )
         v.pump_pulse_profile = c.pump_pulse_profile
         v.crystalLength = c.length
-        v.crystalCSV = _CRYSTAL_CSV_FILE
         v.thermalCrystal = c
         return res + template_common.render_jinja(SIM_TYPE, v, "crystal.py")
     if data.report in _SIM_DATA.SOURCE_REPORTS:
@@ -461,10 +427,6 @@ def _generate_parameters_file(data):
     return res + template_common.render_jinja(SIM_TYPE, v)
 
 
-def _get_crystal(data):
-    return data.models.thermalTransportCrystal.crystal
-
-
 def _initial_intensity_percent_complete(run_dir, res, data, model_names):
     res.outputInfo = []
     if run_dir.join(_RESULTS_FILE.format(0)).exists():
@@ -614,25 +576,6 @@ def gen(self):
         raise AssertionError("Report is unavailable")
 
 
-def _laser_pulse_report(value_index, filename, title, label):
-    values = numpy.load(filename)
-    return template_common.parameter_plot(
-        values[0].tolist(),
-        [
-            PKDict(
-                points=values[value_index].tolist(),
-                label=label,
-            ),
-        ],
-        PKDict(),
-        PKDict(
-            title=title,
-            y_label="",
-            x_label="s [m]",
-        ),
-    )
-
-
 def _parse_silas_log(run_dir):
     res = ""
     path = run_dir.join(template_common.RUN_LOG)