Merge pull request #318 from jinyan1214/master

JZ - Capacity Spectrum method in R2D and parallel site creation of EQ Tool in R2D

conanfile.py

@@ -2,6 +2,7 @@
 
 from conans import CMake, ConanFile
 
+
 class simCenterBackendApps(ConanFile):  # noqa: D101
     name = 'SimCenterBackendApplications'
     version = '1.2.2'
@@ -30,8 +31,8 @@ class simCenterBackendApps(ConanFile):  # noqa: D101
         'jsonformoderncpp/3.7.0',
         'nanoflann/1.3.2',
         'nlopt/2.7.1',
-        "boost/1.71.0",
-        'kissfft/131.1.0'
+        'boost/1.71.0',
+        'kissfft/131.1.0',
     ]
 
     # Custom attributes for Bincrafters recipe conventions

modules/Workflow/WorkflowApplications.json

@@ -974,6 +974,10 @@
         "Name": "IMasEDP",
         "ExecutablePath": "applications/performSIMULATION/IMasEDP/IMasEDP.py"
       },
+      {
+        "Name": "CapacitySpectrumMethod",
+        "ExecutablePath": "applications/performSIMULATION/capacitySpectrum/runCMS.py"
+      },
       {
         "Name": "SurrogateSimulation",
         "ExecutablePath": "applications/performSIMULATION/surrogateSimulation/SurrogateSimulation.py"

modules/createAIM/GeoJSON_to_ASSET/GeoJSON_to_ASSET.py

@@ -1,4 +1,4 @@
-import argparse  # noqa: INP001, D100
+import argparse  # noqa: D100, INP001
 import importlib
 import json
 import os
@@ -8,7 +8,8 @@
 import warnings
 
 import geopandas as gpd
-import momepy
+
+# import momepy
 import numpy as np
 import pandas as pd
 import shapely
@@ -179,10 +180,10 @@ def defineConnectivities(  # noqa: N802, D102
         # Convert find connectivity and add start_node, end_node attributes
         edges = self.gdf
         datacrs = edges.crs
-        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')
+        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')  # noqa: F821
         with warnings.catch_warnings():  # Suppress the warning of disconnected components in the graph
             warnings.simplefilter('ignore')
-            nodes, edges, sw = momepy.nx_to_gdf(
+            nodes, edges, sw = momepy.nx_to_gdf(  # noqa: F821
                 graph, points=True, lines=True, spatial_weights=True
             )
         # edges = edges.set_index('ind')

modules/createAIM/INP_FILE/INP_FILE.py

@@ -1,4 +1,4 @@
-import argparse  # noqa: INP001, D100
+import argparse  # noqa: D100, INP001
 import importlib
 import json
 import os
@@ -8,7 +8,8 @@
 import warnings
 
 import geopandas as gpd
-import momepy
+
+# import momepy
 import numpy as np
 import pandas as pd
 import shapely
@@ -179,10 +180,10 @@ def defineConnectivities(  # noqa: N802, D102
         # Convert find connectivity and add start_node, end_node attributes
         edges = self.gdf
         datacrs = edges.crs
-        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')
+        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')  # noqa: F821
         with warnings.catch_warnings():  # Suppress the warning of disconnected components in the graph
             warnings.simplefilter('ignore')
-            nodes, edges, sw = momepy.nx_to_gdf(
+            nodes, edges, sw = momepy.nx_to_gdf(  # noqa: F821
                 graph, points=True, lines=True, spatial_weights=True
             )
         # edges = edges.set_index('ind')

modules/createAIM/JSON_to_AIM/JSON_to_AIM_transport.py

@@ -48,7 +48,8 @@
 import warnings
 
 import geopandas as gpd
-import momepy
+
+# import momepy
 import numpy as np
 import pandas as pd
 import shapely
@@ -358,10 +359,10 @@ def create_asset_files(  # noqa: C901, D103, PLR0915
         roadDF['geometry'] = LineStringList
         roadDF = roadDF[['ID', 'roadType', 'lanes', 'maxMPH', 'geometry']]  # noqa: N806
         roadGDF = gpd.GeoDataFrame(roadDF, geometry='geometry', crs=datacrs)  # noqa: N806
-        graph = momepy.gdf_to_nx(roadGDF.to_crs('epsg:6500'), approach='primal')
+        graph = momepy.gdf_to_nx(roadGDF.to_crs('epsg:6500'), approach='primal')  # noqa: F821
         with warnings.catch_warnings():  # Suppress the warning of disconnected components in the graph
             warnings.simplefilter('ignore')
-            nodes, edges, sw = momepy.nx_to_gdf(
+            nodes, edges, sw = momepy.nx_to_gdf(  # noqa: F821
                 graph, points=True, lines=True, spatial_weights=True
             )
         # Oneway or twoway is not considered in D&L, remove duplicated edges

modules/createEVENT/common/smelt/dabaghi_der_kiureghian.cc

@@ -406,7 +406,7 @@ utilities::JsonObject stochastic::DabaghiDerKiureghian::generate(
         }
       }
 
-      // Baseline correct trunacted non-pulse-like motions
+      // Baseline correct truncated non-pulse-like motions
       for (unsigned int i = 0; i < num_sims_nopulse_; ++i) {
         for (unsigned int j = 0; j < num_realizations_; ++j) {
           baseline_correct_time_history(nopulse_motions_comp1[i][j], gfactor,
@@ -787,7 +787,7 @@ void stochastic::DabaghiDerKiureghian::transform_parameters_from_normal_space(
                        params_fitted1_(17), params_fitted2_(17),
                        params_fitted3_(17), params_lower_bound_(17));
 
-    // Calculate depth_to_rupture compenent 2
+    // Calculate depth_to_rupture component 2
     beta_dist =
         Factory<stochastic::Distribution, double, double>::instance()->create(
             "BetaDist", std::move(params_fitted1_(18)),
@@ -1203,7 +1203,7 @@ double stochastic::DabaghiDerKiureghian::calc_time_to_intensity(
 std::vector<double> stochastic::DabaghiDerKiureghian::calc_linear_filter(
     unsigned int num_steps, const Eigen::VectorXd& filter_params, double t01,
     double tmid, double t99) const {
-  // Mininum frequency in Hz
+  // Minimum frequency in Hz
   double min_freq = 0.3;
   std::vector<double> filter_func(num_steps);
   // Frequency at tmid, in Hz  
@@ -1458,7 +1458,7 @@ void stochastic::DabaghiDerKiureghian::baseline_correct_time_history(
     std::vector<double>& time_history, double gfactor,
     unsigned int order) const {
 
-  // Calculate velocity and displacment time histories
+  // Calculate velocity and displacement time histories
   std::vector<double> vel_series(time_history.size());
   std::vector<double> disp_series(time_history.size());
 

modules/createEVENT/common/smelt/dabaghi_der_kiureghian.h

@@ -218,7 +218,7 @@ class DabaghiDerKiureghian : public StochasticModel {
       unsigned int num_gms = 1) const;
 
   /**
-   * Backcalculate modulating parameters given Arias Intesity and duration parameters
+   * Backcalculate modulating parameters given Arias Intensity and duration parameters
    * @param[in] q_params Vector containing Ia, D595, D05, and D030
    * @param[in] t0 Initial time. Defaults to 0.0.
    * @return Vector containing parameters alpha, beta, tmaxq, and c
@@ -256,7 +256,7 @@ class DabaghiDerKiureghian : public StochasticModel {
    * @param[in] d095_target Time from t0 to time of 95% Arias intensity of
    *                        target motion
    * @param[in] t0 Start time of modulating function and of target ground motion
-   * @return ERrro in modulating function
+   * @return error in modulating function
    */
   double calc_parameter_error(const std::vector<double>& parameters,
                               double d05_target, double d030_target,
@@ -399,8 +399,8 @@ class DabaghiDerKiureghian : public StochasticModel {
   Eigen::VectorXd std_dev_nopulse_; /**< No-pulse-like parameter standard deviation */
   Eigen::MatrixXd corr_matrix_pulse_; /**< Pulse-like parameter correlation matrix */
   Eigen::MatrixXd corr_matrix_nopulse_; /**< No-pulse-like parameter correlation matrix */
-  Eigen::MatrixXd beta_distribution_pulse_; /**< Beta distrubution parameters for pulse-like motion */
-  Eigen::MatrixXd beta_distribution_nopulse_; /**< Beta distrubution parameters for no-pulse-like motion */
+  Eigen::MatrixXd beta_distribution_pulse_; /**< Beta distribution parameters for pulse-like motion */
+  Eigen::MatrixXd beta_distribution_nopulse_; /**< Beta distribution parameters for no-pulse-like motion */
   Eigen::VectorXd params_lower_bound_;        /**< Lower bound for marginal distributions fitted to params
 						 (Table 5 in Dabaghi & Der Kiureghian, 2017) */
   Eigen::VectorXd params_upper_bound_;        /**< Upper bound for marginal distributions fitted to params

modules/createEVENT/common/smelt/json_object.h

@@ -101,7 +101,7 @@ class JsonObject {
 
   /**
    * Get underlying JSON library object
-   * @return Copy of interal JSON implementation
+   * @return Copy of internal JSON implementation
    */
   json get_library_json() const {
     return json_object_;

modules/createEVENT/common/smelt/nelder_mead.cc

@@ -10,7 +10,7 @@ std::vector<double> optimization::NelderMead::minimize(
     std::function<double(const std::vector<double>&)>& objective_function) {
   // Create vector of deltas with length equal to the number of dimensions
   std::vector<double> deltas(initial_point.size(), delta);
-  // Call minmize with vector of deltas
+  // Call minimize with vector of deltas
   return minimize(initial_point, deltas, objective_function);
 }
 
@@ -33,7 +33,7 @@ std::vector<double> optimization::NelderMead::minimize(
     }
   }
 
-  // Call minimize with matrix definining initial simplex
+  // Call minimize with matrix defining initial simplex
   return minimize(simplex, objective_function);
 }
 

modules/createEVENT/common/smelt/numeric_utils.cc

@@ -55,7 +55,7 @@ bool convolve_1d(const std::vector<double>& input_x,
   // conv_status = vsldConvExec1D(conv_task, input_x.data(), 1, input_y.data(), 1,
   //                              response.data(), 1);
 
-  // // Check if convolution exectution was successful
+  // // Check if convolution execution was successful
   // if (conv_status != VSL_STATUS_OK) {
   //   throw std::runtime_error(
   //       "\nERROR: in numeric_utils::convolve_1d: Error in convolution "
@@ -159,7 +159,7 @@ bool inverse_fft(std::vector<std::complex<double>> input_vector,
   // }
 
   // // Set the backward scale factor to be 1 divided by the size of the input vector
-  // // to make the backward tranform the inverse of the forward transform
+  // // to make the backward transform the inverse of the forward transform
   // fft_status = DftiSetValue(fft_descriptor, DFTI_BACKWARD_SCALE,
   //                           static_cast<double>(1.0 / input_vector.size()));
   // if (fft_status != DFTI_NO_ERROR) {

modules/createEVENT/common/smelt/vlachos_et_al.cc

@@ -721,7 +721,7 @@ Eigen::VectorXd stochastic::VlachosEtAl::identify_parameters(
     energy[i] = energy[i - 1] + 0.05;
   }
 
-  // Initialze mode 1 parameters and frequencies
+  // Initialize mode 1 parameters and frequencies
   std::vector<double> mode_1_params = {initial_params(2),
 				       initial_params(3),
 				       initial_params(4)};

modules/createEVENT/common/smelt/vlachos_et_al.h

@@ -116,7 +116,7 @@ class VlachosEtAl : public StochasticModel {
    * @param[in, out] time_histories Location where time histories should be
    *                                stored
    * @param[in] parameters Set of model parameters to use for calculating power
-   *                       specturm and time histories
+   *                       spectrum and time histories
    * @return Returns true if successful, false otherwise
    */
   bool time_history_family(std::vector<std::vector<double>>& time_histories,
@@ -263,7 +263,7 @@ class VlachosEtAl : public StochasticModel {
   Eigen::VectorXd means_; /**< Mean values of model parameters */
   Eigen::MatrixXd covariance_; /**< Covariance matrix for model parameters */
   std::vector<std::shared_ptr<stochastic::Distribution>>
-      model_parameters_; /**< Distrubutions for 18-parameter model */
+      model_parameters_; /**< Distributions for 18-parameter model */
   Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic>
       parameter_realizations_; /**< Random realizations of normal model parameters */
   Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic>

modules/createEVENT/multiplePEER/MultiplePEER_Events.cpp

@@ -174,30 +174,30 @@ int main(int argc, char **argv)
       const char *eventType = json_string_value(type);
 
       if (strcmp(eventType,"Seismic") == 0) {
-	json_t *subType = json_object_get(value,"subtype");  
-	if ((subType != NULL) && (strcmp("MultiplePEER_Event",json_string_value(subType)) ==0)) {
-
-	  json_t *index = json_object_get(value,"index"); 
-
-	  if (json_is_integer(index) == false) {
-	    const char *eventName = json_string_value(index);
-
-	    // we need to replace the EVENT with another event
-	    json_t *inputEvent = json_array_get(inputEventsArray,count);
-	    json_t *events = json_object_get(inputEvent,"Events");
-	    for (int i=0; i<json_array_size(events); i++) {
-	      json_t *theEvent = json_array_get(events, i);
-	      const char * name = json_string_value(json_object_get(theEvent,"name"));
-
-	      if (strcmp(eventName, name) == 0) {
-		addEvent(name, value);
-		
-		i = json_array_size(events);
-	      }
-	    }
-	  }
-	  json_t *eventObj = json_object();
-	}	  
+        json_t *subType = json_object_get(value,"subtype");  
+        if ((subType != NULL) && (strcmp("MultiplePEER_Event",json_string_value(subType)) ==0)) {
+
+          json_t *index = json_object_get(value,"index"); 
+
+          if (json_is_integer(index) == false) {
+            const char *eventName = json_string_value(index);
+
+            // we need to replace the EVENT with another event
+            json_t *inputEvent = json_array_get(inputEventsArray,count);
+            json_t *events = json_object_get(inputEvent,"Events");
+            for (int i=0; i<json_array_size(events); i++) {
+              json_t *theEvent = json_array_get(events, i);
+              const char * name = json_string_value(json_object_get(theEvent,"name"));
+
+              if (strcmp(eventName, name) == 0) {
+          addEvent(name, value);
+          
+          i = json_array_size(events);
+              }
+            }
+          }
+          json_t *eventObj = json_object();
+        }	  
       }
     }
     // write rootEvent

modules/createSAM/openSeesInput/OpenSeesInput.c

@@ -67,23 +67,23 @@ main(int argc, char **argv) {
     if (fileName == 0) { // not passed in input, should be in AIM
       json_t *theApplications = json_object_get(rootAIM,"Applications");
       if (theApplications == NULL) {
-	fprintf(stderr, "AIM file missing Applications");
-	exit(-1);
+        fprintf(stderr, "AIM file missing Applications");
+        exit(-1);
       }
       json_t *theModeling = json_object_get(theApplications,"Modeling");
       if (theModeling == NULL) {
-	fprintf(stderr, "AIM file Applications missing Modeling");
-	exit(-1);
+        fprintf(stderr, "AIM file Applications missing Modeling");
+        exit(-1);
       }
       json_t *theAppData = json_object_get(theModeling,"ApplicationData");
       if (theAppData == NULL) {
-	fprintf(stderr, "AIM file Applications missing AppData");
-	exit(-1);
+        fprintf(stderr, "AIM file Applications missing AppData");
+        exit(-1);
       }
       json_t *theFileName = json_object_get(theAppData,"fileName");
       if (theFileName == NULL && !json_is_string(theFileName)) {
-	fprintf(stderr, "AIM file AppData missing fileName");
-	exit(-1);
+        fprintf(stderr, "AIM file AppData missing fileName");
+        exit(-1);
       }
       const char *fileName2 = json_string_value(theFileName);
       length = json_string_length(theFileName);
@@ -130,14 +130,14 @@ main(int argc, char **argv) {
       floor = 0;  // ground floor floor 0
 
       json_array_foreach(theCentroidNodes, index, intObj) {
-	json_t *nodeEntry =json_object();
-	int tag = json_integer_value(intObj);
-	json_object_set(nodeEntry,"node",json_integer(tag));
-	json_object_set(nodeEntry,"cline",json_string("centroid"));
-	sprintf(floorString,"%d",floor);
-	json_object_set(nodeEntry,"floor",json_string(floorString));
-	floor++;
-	json_array_append(mappingArray, nodeEntry);
+        json_t *nodeEntry =json_object();
+        int tag = json_integer_value(intObj);
+        json_object_set(nodeEntry,"node",json_integer(tag));
+        json_object_set(nodeEntry,"cline",json_string("centroid"));
+        sprintf(floorString,"%d",floor);
+        json_object_set(nodeEntry,"floor",json_string(floorString));
+        floor++;
+        json_array_append(mappingArray, nodeEntry);
       }
     }
 

modules/performRegionalEventSimulation/regionalGroundMotion/CMakeLists.txt

@@ -15,3 +15,4 @@ simcenter_add_python_script(SCRIPT ScenarioForecast.py)
 simcenter_add_python_script(SCRIPT liquefaction.py)
 simcenter_add_python_script(SCRIPT landslide.py)
 simcenter_add_python_script(SCRIPT GMSimulators.py)
+simcenter_add_python_script(SCRIPT GlobalVariable.py)