diff --git a/Stochastic/Tests/statstest.cpp b/Stochastic/Tests/statstest.cpp
index 94de1ccc..73c40ab2 100644
--- a/Stochastic/Tests/statstest.cpp
+++ b/Stochastic/Tests/statstest.cpp
@@ -7,6 +7,8 @@
#include <iostream>
#include <cstdio>
+#include "VCELL/SimulationMessaging.h"
+
const char* input_file_contents = R"INPUT_FILE(
<control>
STARTING_TIME 0.0
@@ -98,70 +100,68 @@ const std::map<int, double> expected_S0 = {
TEST(statstest,test1) {
std::cout << "Checkpoint 0" << std::endl;
- char *temp_input_file_name = new char[1000] {0};
- char *temp_output_file_name = new char[1000] {0};
- std::string in_prefix = testing::TempDir() + "input_XXXXXX";
- std::string out_prefix = testing::TempDir() + "output_XXXXXX";
- strncpy(temp_input_file_name, in_prefix.c_str(), in_prefix.length());
- strncpy(temp_output_file_name, out_prefix.c_str(), out_prefix.length());
+ //std::string inputFileName = std::tmpnam(nullptr);
+ std::string inputFileName {R"(C:\CustomTemp\testme_vcell.txt)"};
+ std::string outputFileName = std::tmpnam(nullptr);
+ std::map<int,double> results;
+ std::fstream inputFileStream{inputFileName};
+ ASSERT_TRUE(inputFileStream.fail());
+ std::cout << std::system_category().message(::GetLastError()) << std::endl;
+ std::cout << "Supposed file: " << inputFileName << std::endl;
+ return;
+ std::fstream outputFileStream{outputFileName};
+ ASSERT_FALSE(outputFileStream.fail());
+
+ // Setup the Gibson Solver input file
std::cout << "Checkpoint 1" << std::endl;
- assert(mkstemp(temp_input_file_name) != -1);
- assert(mkstemp(temp_output_file_name) != -1);
- std::ofstream input_file (temp_input_file_name);
- bool bWroteFile = false;
- if (input_file.is_open()){
- input_file << input_file_contents;
- input_file.close();
- bWroteFile = true;
- }
- ASSERT_TRUE(bWroteFile);
+ std::cout << " >> " << "Input: <" << inputFileName << ">;"<< std::endl;
+ std::cout << " >> " << "Output: <" << outputFileName << ">;"<< std::endl;
+ if (outputFileStream.is_open()) outputFileStream.close();
+ inputFileStream << input_file_contents;
+ inputFileStream.close();
+ return;
+
+ // Create the Gibson Solver
std::cout << "Checkpoint 2" << std::endl;
- Gibson *gb= new Gibson(temp_input_file_name, temp_output_file_name);
+ auto *gb = new Gibson(inputFileName.c_str(), outputFileName.c_str());
+
+ // Launch the test
std::cout << "Checkpoint 3" << std::endl;
gb->march();
+ // Verify file contents
std::cout << "Checkpoint 4" << std::endl;
- // verify file contents
- std::ifstream outfile(temp_output_file_name);
- string line;
- getline(outfile, line); // remove header line
-// std::cout << line << std::endl;
-// std::cout.flush();
-
+ outputFileStream.open(outputFileName);
+ std::string line;
+ std::getline(outputFileStream, line); // remove header line
+ for (int i = 0; !outputFileStream.eof(); i++) {
+ std::getline(outputFileStream, line);
+ // if index found in expected_S0 map, store in results map
+ if (expected_S0.find(i) != expected_S0.end()){
+ float t, s0, s1, s2;
+ // extract space separated values for t, s0, s1 and s2 from line
+ std::stringstream line_stream(line);
+ line_stream >> t >> s0 >> s1 >> s2;
+ results[i] = s0;
+ }
+ }
+ outputFileStream.close();
+
+ // compare the expected and actual values
std::cout << "Checkpoint 5" << std::endl;
- std::map<int,double> results;
- int i = 0;
- while (getline(outfile, line)){
- // if index found in expected_S0 map, store in results map
- if (expected_S0.find(i) != expected_S0.end()){
- float t, s0, s1, s2;
- // extract space separated values for t, s0, s1 and s2 from line
- std::stringstream line_stream(line);
- line_stream >> t >> s0 >> s1 >> s2;
- results[i] = s0;
-// std::cout << line << std::endl;
-// std::cout.flush();
- }
- i++;
- }
- std::cout << "Checkpoint 6" << std::endl;
- // compare the expected and actual values
- double accum_error = 0.0;
- double max_error = 0.0;
+ double accumulatedError = 0.0, maxIndividualError = 0.0;
for (auto const& expected : expected_S0){
- double s0_given = expected.second;
- double s0_computed = results[expected.first];
- double abserr = std::abs(s0_given - s0_computed);
-// std::cout << "t=" << expected.first << " expected=" << s0_given << " computed=" << s0_computed << " abserr=" << abserr << std::endl;
- accum_error += abserr;
- max_error = std::max(max_error, abserr);
+ double absoluteError = std::abs(expected.second - results[expected.first]);
+ // std::cout << "t=" << expected.first << " expected=" << expected.second << " computed=" << results[expected.first] << " abserr=" << abserr << std::endl;
+ accumulatedError += absoluteError;
+ maxIndividualError = std::max(maxIndividualError, absoluteError);
}
- assert(accum_error < 0.015);
- assert(max_error < 0.005);
+ assert(accumulatedError < 0.015);
+ assert(maxIndividualError < 0.005);
std::cout << "Checkpoint 7" << std::endl;
delete gb;
- delete[] temp_input_file_name;
- delete[] temp_output_file_name;
+ if (inputFileStream.is_open()) inputFileStream.close();
+ if (outputFileStream.is_open()) outputFileStream.close();
std::cout << "Checkpoint 8" << std::endl;
}
\ No newline at end of file
diff --git a/Stochastic/VCellStoch/src/Gibson.cpp b/Stochastic/VCellStoch/src/Gibson.cpp
index 9f50aa25..4a677209 100644
--- a/Stochastic/VCellStoch/src/Gibson.cpp
+++ b/Stochastic/VCellStoch/src/Gibson.cpp
@@ -10,13 +10,13 @@
#include <string>
#include <iomanip>
#include <vector>
-#include <stdint.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cstdint>
+#include <cmath>
+#include <cstdlib>
#include <random>
using namespace std;
-#include <time.h>
+#include <ctime>
#include "../include/IndexedTree.h"
#ifdef USE_MESSAGING
@@ -26,14 +26,12 @@ using namespace std;
const double double_infinity = numeric_limits<double>::infinity();
const double EPSILON = 1E-12;
const string Gibson::MY_T_STR = "t";
+
/*
*Empty constructor of Gibson. It will use the defalt settings in StochModel.
*/
Gibson::Gibson()
- :StochModel(),
- savedSampleCount(1),
- lastTime (std::numeric_limits<long>::min( ))
-{
+ : savedSampleCount(1), lastTime (std::numeric_limits<long>::min()) {
Tree=NULL;
currvals=NULL;
generator = new std::mt19937_64();
@@ -47,16 +45,13 @@ Gibson::Gibson()
* string, the output file(name), where the results are saved.
*/
Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
- :StochModel(),
- savedSampleCount(1),
- lastTime (std::numeric_limits<long>::min( ))
-{
- Tree=NULL;
- currvals=NULL;
- generator = new std::mt19937_64();
- distribution = new std::uniform_real_distribution<double>(0.0,1.0);
-
- outfilename=arg_outfilename;
+ : savedSampleCount(1), lastTime (std::numeric_limits<long>::min( )) {
+ // TODO: Call basic constructor rather than duplicate lines
+ this->Tree = NULL;
+ this->currvals = NULL;
+ this->generator = new std::mt19937_64();
+ this->distribution = new std::uniform_real_distribution<>(0.0,1.0);
+ this->outfilename = arg_outfilename;
ifstream infile;
string instring;
@@ -69,56 +64,33 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
while(infile >> instring)
{
//load control info.
- if (instring == "STARTING_TIME")
- {
+ if (instring == "STARTING_TIME"){
infile >> STARTING_TIME;
- }
- else if (instring == "BMULTIBUTNOTHISTO")
- {
+ } else if (instring == "BMULTIBUTNOTHISTO"){
infile >> bMultiButNotHisto;
- }
- else if (instring == "ENDING_TIME")
- {
+ } else if (instring == "ENDING_TIME"){
infile >> ENDING_TIME;
- }
- else if (instring == "SAVE_PERIOD")
- {
+ } else if (instring == "SAVE_PERIOD"){
infile >> SAVE_PERIOD;
flag_savePeriod=true;
- }
- else if (instring == "MAX_ITERATION")
- {
+ } else if (instring == "MAX_ITERATION"){
infile >> MAX_ITERATION;
- }
- else if (instring == "TOLERANCE")
- {
+ } else if (instring == "TOLERANCE"){
infile >> TOLERANCE;
- }
- else if (instring == "SAMPLE_INTERVAL")
- {
+ } else if (instring == "SAMPLE_INTERVAL"){
infile >> SAMPLE_INTERVAL;
- }
- else if (instring == "MAX_SAVE_POINTS")
- {
+ } else if (instring == "MAX_SAVE_POINTS"){
infile >> MAX_SAVE_POINTS;
- }
- else if (instring == "NUM_TRIAL")
- {
+ } else if (instring == "NUM_TRIAL"){
infile >> NUM_TRIAL;
- }
- else if (instring == "SEED")
- {
+ } else if (instring == "SEED"){
infile >> SEED;
- }
- //load listofvars
- else if (instring == "TotalVars")
- {
+ } else if (instring == "TotalVars"){ //load listofvars
int varCount;
infile >> varCount;
string name;
double amount;
- for(int i=0;i<varCount;i++)
- {
+ for(int i=0;i<varCount;i++){
infile >> name;
infile >> amount;
listOfVarNames.push_back(name);
@@ -126,10 +98,7 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
StochVar *var=new StochVar((uint64_t)amount);
listOfVars.push_back(var);
}
- }
- //load listOfProcesses
- else if (instring == "TotalProcesses")
- {
+ } else if (instring == "TotalProcesses"){ //load listOfProcesses
int pCount;
infile >> pCount;
string name;
@@ -140,15 +109,11 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
Jump *jp=new Jump();
listOfProcesses.push_back(jp);
}
- }
- //load process description to set up processes
- else if (instring == "TotalDescriptions")
- {
+ } else if (instring == "TotalDescriptions") { //load process description to set up processes
int dCount,idx;
infile >> dCount;
string name,str;
- for(int i=0;i<dCount;i++)//loop through each process description
- {
+ for(int i=0;i<dCount;i++){ //loop through each process description
infile >> name >> name;// "process name"
//find the process in listOfProcesses using it's name
idx=getProcessIndex(name);
@@ -201,10 +166,9 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
}
}
//setup IndexedTree
- Tree=new IndexedTree();
- for(int i=0;i<listOfProcesses.size();i++)
- {
- Tree->addProcess(listOfProcesses[i]);
+ Tree = new IndexedTree();
+ for(auto & listOfProcesse : listOfProcesses){
+ Tree->addProcess(listOfProcesse);
}
infile.close();
if (NUM_TRIAL > MAX_ALLOWED_POINTS) {
@@ -214,7 +178,6 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
VCELL_EXCEPTION(invalid_argument,"Stochastic initialization: Server save points " << MAX_SAVE_POINTS << " exceeds limit of " << MAX_ALLOWED_POINTS);
}
-
if(NUM_TRIAL > 1 && !bMultiButNotHisto){
//this must be a gibson 'histogram' sim,
//java gui not allow setting of MAX_SAVE_POINTS and default is too low
@@ -270,12 +233,12 @@ Gibson::~Gibson()
//delete indexedTree
delete Tree;
//delete variables
- for(int i=0;i<listOfVars.size();i++)
- delete listOfVars[i];
+ for(auto & listOfVar : listOfVars)
+ delete listOfVar;
listOfVars.clear();
//delete proccesses
- for(int i=0;i<listOfProcesses.size();i++)
- delete listOfProcesses[i];
+ for(auto & listOfProcesse : listOfProcesses)
+ delete listOfProcesse;
listOfProcesses.clear();
//delete vectors
listOfVarNames.clear();