fix #5942 match silas notebook

sirepo/package_data/static/html/silas-source.html

@@ -18,3 +18,6 @@
     </div>
   </div>
 </div>
+<!-- required to have the intensityViewHandler update the SINGLE_FRAME_ANIMATION list -->
+<div data-modal-editor="" data-view-name="laserPulseAnimation" data-sr-laserpulseanimation-editor=""></div>
+<div data-modal-editor="" data-view-name="laserPulse2Animation" data-sr-laserpulse2animation-editor=""></div>

sirepo/package_data/static/js/sirepo-plotting.js

@@ -1822,19 +1822,14 @@ SIREPO.app.service('layoutService', function(panelState, plotting, utilities) {
             const v0 = applyUnit(tickValues[0], base, unit);
             const v1 = applyUnit(tickValues[1], base, unit);
             const vn = applyUnit(tickValues[tickValues.length - 1], base, unit);
-            let decimals;
-            if (Math.abs(v0) > Math.abs(vn)) {
-                decimals = d3_precisionRound(v1 - v0, Math.abs(v0));
-            }
-            else {
-                decimals = d3_precisionRound(v1 - v0, vn);
-            }
+            const max = Math.abs(v0) > Math.abs(vn) ? Math.abs(v0) : vn;
+            let decimals = d3_precisionRound(v1 - v0, max);
             if (decimals > 1) {
                 decimals -= 1;
             }
             if (useFloatFormat(v0) && useFloatFormat(vn)) {
                 code = 'f';
-                decimals -= valuePrecision(vn);
+                decimals -= valuePrecision(max);
                 if (decimals < 0) {
                     decimals = 0;
                 }

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

@@ -123,7 +123,10 @@
             "pump_gaussian_order": ["Pump Gaussian Order", "Float", 2.0],
             "pump_type": ["Pump Type", "PumpType", "dual"],
             "origin": ["Crystal", "CrystalOrigin", "new"],
-            "reuseCrystal": ["Select Crystal", "SelectCrystal", 0]
+            "reuseCrystal": ["Select Crystal", "SelectCrystal", 0],
+            "pump_offset_x": ["Pump Offset X [m]", "Float", 0],
+            "pump_offset_y": ["Pump Offset X [m]", "Float", 0],
+            "pump_rep_rate": ["Pump Rep Rate", "Float", 1.0]
         },
         "crystalAnimation": {},
         "crystalSettings": {
@@ -160,7 +163,8 @@
             "pulseE": ["Total Laser Pulse Energy [J]", "Float", 0.001],
             "distribution": ["Distribution Type", "DistributionType", "gaussian"],
             "sigx_waist": ["Horizontal RMS Waist Size [m]", "Float", 0.001],
-            "sigy_waist": ["Vertical RMS Waist Size [m]", "Float", 0.001]
+            "sigy_waist": ["Vertical RMS Waist Size [m]", "Float", 0.001],
+            "phase_flatten_cutoff": ["Phase Flatten Cutoff", "Float", 0.85]
         },
         "laserPulseAnimation": {
             "_super": ["_", "model", "initialIntensityReport"]
@@ -171,7 +175,7 @@
         },
         "initialIntensityReport": {
             "colorMap": ["Color Map", "ColorMap", "viridis"],
-            "watchpointPlot": ["Value to Plot", "WatchpointPlot", "intensity"]
+            "watchpointPlot": ["Value to Plot", "WatchpointPlot", "total_intensity"]
         },
         "lens": {
             "_super": ["_", "model", "beamElement"],
@@ -218,18 +222,21 @@
                     "C",
                     "D",
                     "l_scale",
-                    "pump_type",
                     "radial_n2",
                     "calc_gain"
                 ]],
                 ["Pump Pulse", [
+                    "pump_type",
                     "inversion_n_cells",
                     "inversion_mesh_extent",
                     "crystal_alpha",
                     "pump_waist",
                     "pump_wavelength",
                     "pump_energy",
-                    "pump_gaussian_order"
+                    "pump_gaussian_order",
+                    "pump_rep_rate",
+                    "pump_offset_x",
+                    "pump_offset_y"
                 ]]
             ]
         },
@@ -281,7 +288,8 @@
             "basic": [
                 ["Energy", [
                     "photon_e_ev",
-                    "pulseE"
+                    "pulseE",
+                    "phase_flatten_cutoff"
                 ]],
                 ["Transverse", [
                     "num_sig_trans",

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

@@ -114,6 +114,7 @@ pulse = LaserPulse(
             'sigx_waist',
             'sigy_waist',
             'tau_fwhm',
+            'phase_flatten_cutoff',
             'tau_0',
         ) %}
         {{ f }}={{ laserPulse[f] }},

sirepo/template/silas.py

@@ -14,15 +14,14 @@
 import numpy
 import re
 import sirepo.sim_data
-
-# TODO(pjm): currently aligned with rslaser version
-# git checkout `git rev-list -n 1 --first-parent --before="2023-04-24 13:37" main`
+import time
 
 _SIM_DATA, SIM_TYPE, SCHEMA = sirepo.sim_data.template_globals()
 
 _CRYSTAL_CSV_FILE = "crystal.csv"
 _RESULTS_FILE = "results{}.h5"
 _CRYSTAL_FILE = "crystal{}.h5"
+_MAX_H5_READ_TRIES = 3
 
 
 def background_percent_complete(report, run_dir, is_running):
@@ -134,8 +133,7 @@ def write_parameters(data, run_dir, is_parallel):
 
 
 def _beamline_animation_percent_complete(run_dir, res, data):
-    def _output_append(frame_count, filename, count, element, res, total_count):
-        total_count += 1
+    def _output_append(frame_count, filename, count, element, res):
         if run_dir.join(filename).exists():
             res.outputInfo.append(
                 PKDict(
@@ -170,15 +168,14 @@ def _frames(element, data):
     total_count = 1
     for e in data.models.beamline:
         if e.type in ("watch", "crystal"):
+            total_count += 1
             _output_append(
                 _frames(e, data),
                 _file(e, count),
                 count,
                 e,
                 res,
-                total_count,
             )
-
     res.percentComplete = res.frameCount * 100 / total_count
     return res
 
@@ -308,6 +305,9 @@ def _generate_crystal(crystal):
                 pop_inversion_pump_gaussian_order={crystal.pump_gaussian_order},
                 pop_inversion_pump_energy={crystal.pump_energy},
                 pop_inversion_pump_type="{crystal.pump_type}",
+                pop_inversion_pump_rep_rate={crystal.pump_rep_rate},
+                pop_inversion_pump_offset_x={crystal.pump_offset_x},
+                pop_inversion_pump_offset_y={crystal.pump_offset_y},
             ),
         ),
         ["{crystal.propagationType}", {crystal.calc_gain == "1"}, {crystal.radial_n2 == "1"}],
@@ -382,6 +382,11 @@ def _fname(element):
             return _CRYSTAL_FILE
         return _RESULTS_FILE
 
+    def _index(index, plot_type):
+        if plot_type == "longitudinal_photons":
+            return index
+        return index + 1
+
     def _is_crystal(element):
         return element and element.type == "crystal"
 
@@ -407,6 +412,13 @@ def _title(plot_type, slice_index):
             return plot_type.replace("_", " ").title()
         return plot_type.replace("_", " ").title() + " Slice #" + str(slice_index + 1)
 
+    def _x_label(plot_type):
+        return PKDict(
+            excited_states_longitudinal="Crystal Slice",
+            longitudinal_photons="Crystal width [cm]",
+            longitudinal_intensity="Pulse Slice",
+        )[plot_type]
+
     def _y_value(element, index, file, cell_volume):
         if _is_crystal(element):
             return numpy.sum(numpy.array(file[f"{index}/excited_states"]) * cell_volume)
@@ -425,53 +437,48 @@ def _z_label(plot_type):
             excited_states="Number [1/m³]",
         )[plot_type]
 
-    def _x_label(plot_type):
-        return PKDict(
-            excited_states_longitudinal="Crystal Slice",
-            longitudinal_photons="Crystal width [cm]",
-            longitudinal_intensity="Pulse Slice",
-        )[plot_type]
-
-    def _index(index, plot_type):
-        if plot_type == "longitudinal_photons":
-            return index
-        return index + 1
-
-    with h5py.File(run_dir.join(_fname(element).format(element_index)), "r") as f:
-        if _is_longitudinal_plot(plot_type):
-            x = []
-            y = []
-            nslice = _nslice(element, f)
-            if element:
-                element.nslice = nslice
-            for idx in range(nslice):
-                x.append(_index(idx, plot_type))
-                y.append(_y_value(element, idx, f, _cell_volume(element)))
-            return template_common.parameter_plot(
-                x,
-                [
-                    PKDict(
-                        points=y,
-                        label=_label(plot_type, slice_index),
-                    ),
-                ],
-                PKDict(),
-                PKDict(
-                    x_label=_x_label(plot_type),
-                ),
-            )
-        d = template_common.h5_to_dict(f, str(slice_index))
-        r = d.ranges
-        z = d[plot_type]
-        return PKDict(
-            title=_title(plot_type, slice_index),
-            x_range=[r.x[0], r.x[1], len(z)],
-            y_range=[r.y[0], r.y[1], len(z[0])],
-            x_label="Horizontal Position [m]",
-            y_label="Vertical Position [m]",
-            z_label=_z_label(plot_type),
-            z_matrix=z,
-        )
+    for _ in range(_MAX_H5_READ_TRIES):
+        try:
+            with h5py.File(
+                run_dir.join(_fname(element).format(element_index)), "r"
+            ) as f:
+                if _is_longitudinal_plot(plot_type):
+                    x = []
+                    y = []
+                    nslice = _nslice(element, f)
+                    if element:
+                        element.nslice = nslice
+                    for idx in range(nslice):
+                        x.append(_index(idx, plot_type))
+                        y.append(_y_value(element, idx, f, _cell_volume(element)))
+                    return template_common.parameter_plot(
+                        x,
+                        [
+                            PKDict(
+                                points=y,
+                                label=_label(plot_type, 0),
+                            ),
+                        ],
+                        PKDict(),
+                        PKDict(
+                            x_label=_x_label(plot_type),
+                        ),
+                    )
+                d = template_common.h5_to_dict(f, str(slice_index))
+                r = d.ranges
+                z = d[plot_type]
+                return PKDict(
+                    title=_title(plot_type, slice_index),
+                    x_range=[r.x[0], r.x[1], len(z)],
+                    y_range=[r.y[0], r.y[1], len(z[0])],
+                    x_label="Horizontal Position [m]",
+                    y_label="Vertical Position [m]",
+                    z_label=_z_label(plot_type),
+                    z_matrix=z,
+                )
+        except BlockingIOError as e:
+            time.sleep(3)
+    raise AssertionError("Report is unavailable")
 
 
 def _laser_pulse_report(value_index, filename, title, label):

tests/karma/plotAxis_test.js

@@ -111,7 +111,14 @@ describe('plotting: plotAxis', function() {
             tickValues('', [-0.0002, -0.0018], {width: 315, height: 200}, 'y', 'left'),
             ['-1.5e-3', '-1.0e-3', '-5.0e-4'],
         );
-
+        assertTicks(
+            tickValues('', [-0.02, 0], {width: 350, height: 180}, 'y', 'left'),
+            ['-0.02', '-0.01', '0'],
+        );
+        assertTicks(
+            tickValues('', [0, 0.02], {width: 350, height: 180}, 'y', 'left'),
+            ['0', '0.01', '0.02'],
+        );
     }));
     it('should format units', inject(function(layoutService) {
         expect(layoutService.formatUnits('m')).toEqual('[m]');