mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 16:44:49 +01:00
Rewrote run_cells to do all of the calculations that would be
done if a series of USE and SAVE. Modified the logic when time step is defined in run_cells. Equivalent to time_step in nmax steps, where nmax is max steps in kinetics, reaction, reaction_temperature. Wrote dump for chart and chart_handler. chart_handler calls dump for all user_graph. Fixed bug in chart_object with log definition. Had wrong logic when looking for t/T/l/L. initial_total_time initialized twice in mainsubs and twice in phreeqc.cpp. Fixed heading logic for mixing graph_x, graph_y, graph_sy with plot_xy. Moved NA to header file. git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@5431 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
David L Parkhurst
parent
41a6354f1e
commit
2b11772777
@ -162,5 +162,16 @@ ChartHandler::End_timer(PHREEQC_PTR_ARG)
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return true;
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}
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bool
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ChartHandler::dump(std::ostream & oss, unsigned int indent)
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{
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std::map<int, ChartObject *>::iterator it = this->chart_map.begin();
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for ( ; it != chart_map.end(); it++)
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{
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size_t i = 0;
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it->second->dump(oss, indent);
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}
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return true;
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}
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#endif
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@ -29,7 +29,7 @@ public:
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bool Read(PHREEQC_PTR_ARG_COMMA CParser &parser);
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void Punch_user_graph(PHREEQC_PTR_ARG);
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bool End_timer(PHREEQC_PTR_ARG);
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bool dump(std::ostream & oss, unsigned int indent);
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protected:
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std::map<int, ChartObject *> chart_map;
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int current_chart_n_user;
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180
ChartObject.cpp
180
ChartObject.cpp
@ -205,7 +205,7 @@ ChartObject::Set_axis_scale(CParser & parser)
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if (string_vector.size() == 6)
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{
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std::string s = string_vector[5];
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if (s[0] != 't' || s[0] != 'T' || s[0] != 'l' || s[0] != 'L')
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if (s[0] == 't' || s[0] == 'T' || s[0] == 'l' || s[0] == 'L')
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{
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scale_ptr[4] = 10.0;
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if (((fabs(scale_ptr[0] - NA) > 1e-3) && scale_ptr[0] <=0) ||
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@ -330,7 +330,7 @@ ChartObject::Read(CParser & parser)
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{
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this->new_headings.push_back(token);
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}
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this->headings_original = this->new_headings;
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break;
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case 4: /* chart title */
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{
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@ -407,6 +407,7 @@ ChartObject::Read(CParser & parser)
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parser.get_rest_of_line(file_name);
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file_name = trim(file_name);
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this->OpenCSVFile(file_name);
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this->csv_file_names.push_back(file_name);
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}
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break;
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case 13: /* clear */
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@ -423,11 +424,13 @@ ChartObject::Read(CParser & parser)
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if (!new_command_lines)
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{
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this->rate_command_list.clear();
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this->rate_command_list_original.clear();
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new_command_lines = true;
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}
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this->rate_new_def = true;
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/* read command */
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std::string cmd(parser.line());
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this->rate_command_list_original.push_back(cmd);
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std::string cmd_lower = cmd;
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Utilities::str_tolower(cmd_lower);
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if ((cmd_lower.find("graph_y") != std::string::npos) ||
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@ -1097,4 +1100,177 @@ ChartObject::Set_rate_new_def(bool tf)
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}
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}
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}
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void
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ChartObject::dump(std::ostream & oss, unsigned int indent)
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{
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size_t i;
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oss.precision(DBL_DIG - 1);
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std::string indent0(""), indent1("");
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for (i = 0; i < indent; ++i)
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indent0.append(Utilities::INDENT);
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for (i = 0; i < indent + 1; ++i)
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indent1.append(Utilities::INDENT);
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oss << indent0 << "USER_GRAPH " << this->n_user << " " << this->description << std::endl;
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// chart title
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oss << indent1 << "-chart_title \"" << this->chart_title << "\"" << std::endl;
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// axis titles
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if (this->axis_titles.size() > 0)
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{
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oss << indent1 << "-axis_titles ";
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for (i = 0; i < this->axis_titles.size(); i++)
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{
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oss << "\"" << axis_titles[i] << "\" ";
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}
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oss << std::endl;
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}
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// axis_scale_x
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double *scale_ptr = this->axis_scale_x;
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{
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oss << indent1 << "-axis_scale x_axis ";
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for (i = 0; i < 4; i++)
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{
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if (scale_ptr[i] == NA)
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{
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oss << " auto";
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}
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else
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{
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oss << " " << scale_ptr[i];
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}
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}
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if (scale_ptr[4] == 10.0)
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{
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oss << " log";
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}
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oss << std::endl;
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}
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// axis_scale_y
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scale_ptr = this->axis_scale_y;
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{
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oss << indent1 << "-axis_scale y_axis ";
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for (i = 0; i < 4; i++)
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{
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if (scale_ptr[i] == NA)
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{
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oss << " auto";
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}
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else
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{
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oss << " " << scale_ptr[i];
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}
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}
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if (scale_ptr[4] == 10.0)
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{
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oss << " log";
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}
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oss << std::endl;
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}
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// axis_scale_sy
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scale_ptr = this->axis_scale_y2;
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{
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oss << indent1 << "-axis_scale sy_axis ";
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for (i = 0; i < 4; i++)
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{
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if (scale_ptr[i] == NA)
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{
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oss << " auto";
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}
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else
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{
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oss << " " << scale_ptr[i];
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}
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}
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if (scale_ptr[4] == 10.0)
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{
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oss << " log";
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}
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oss << std::endl;
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}
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// chart type
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if (this->chart_type == 0)
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{
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oss << indent1 << "-plot_concentration_vs x" << std::endl;
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}
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else
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{
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oss << indent1 << "-plot_concentration_vs t" << std::endl;
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}
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// graph_initial_solutions
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if (this->graph_initial_solutions)
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{
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oss << indent1 << "-initial_solutions true" << std::endl;
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}
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else
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{
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oss << indent1 << "-initial_solutions false" << std::endl;
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}
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// connect_simulations
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if (this->connect_simulations)
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{
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oss << indent1 << "-connect_simulations true" << std::endl;
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}
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else
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{
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oss << indent1 << "-connect_simulations false" << std::endl;
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}
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// csv files
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for (i = 0; i < this->csv_file_names.size(); i++)
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{
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oss << indent1 << "-plot_csv_file " << this->csv_file_names[i] << std::endl;
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}
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// headings
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if (this->headings_original.size() > 0)
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{
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oss << indent1 << "-headings ";
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for (i = 0; i < this->headings_original.size(); i++)
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{
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oss << this->headings_original[i] << " ";
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}
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oss << std::endl;
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}
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// commands
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oss << indent1 << "-start" << std::endl;
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std::list<std::string>::iterator it = rate_command_list_original.begin();
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for (; it != rate_command_list_original.end(); it++)
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{
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oss << *it << std::endl;
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}
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oss << indent1 << "-end" << std::endl;
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/*
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struct rate *user_graph;
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// C++ for rate struct
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std::string rate_name;
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std::list<std::string> rate_command_list;
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bool rate_new_def;
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int default_symbol;
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int default_symbol_csv;
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int default_color;
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int default_color_csv;
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// temporary storage before stored graph_x/y/sy data are stored in curves
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// Initialize_graph_pts and Finalize_graph_pts use this storage.
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double graph_x;
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std::map<int, double> graph_y;
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std::map<int, bool> secondary_y;
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// temporary plotxy curve definitions before stored in curves
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// a plotxy curve is copied to Curves when cmdplotxy is encountered
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// this keeps order correct between plotxy and graph_x/y/sy
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std::vector<CurveObject> new_plotxy_curves;
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// temporary headings until stored during basic_run
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std::vector<std::string> new_headings;
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bool active;
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bool detach;
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bool form_started;
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*/
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}
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#endif // MULTICHART
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@ -309,6 +309,7 @@ class ChartObject:public cxxNumKeyword
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double symbol_size = 6.0,
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int y_axis = 1,
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std::string color = "");
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void dump(std::ostream & s_oss, unsigned int indent);
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protected:
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bool new_ug;
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@ -341,6 +342,7 @@ class ChartObject:public cxxNumKeyword
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bool end_timer;
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bool done;
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std::vector<std::string> csv_file_names;
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std::vector<CurveObject *> CurvesCSV;
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std::vector<CurveObject *> Curves;
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bool curve_added;
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@ -350,6 +352,7 @@ class ChartObject:public cxxNumKeyword
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// C++ for rate struct
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std::string rate_name;
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std::list<std::string> rate_command_list;
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std::list<std::string> rate_command_list_original;
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bool rate_new_def;
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int default_symbol;
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@ -370,6 +373,7 @@ class ChartObject:public cxxNumKeyword
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// temporary headings until stored during basic_run
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std::vector<std::string> new_headings;
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std::vector<std::string> headings_original;
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bool active;
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bool detach;
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bool form_started;
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@ -377,6 +381,7 @@ class ChartObject:public cxxNumKeyword
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class Phreeqc * p_instance1;
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#endif
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public:
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int usingResource;
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@ -875,7 +875,6 @@ void Phreeqc::init(void)
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rate_sim_time_end = 0;
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rate_sim_time = 0;
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rate_moles = 0;
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initial_total_time = 0;
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/*
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* user_print, user_punch
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209
ReadClass.cxx
209
ReadClass.cxx
@ -2383,6 +2383,7 @@ run_as_cells(void)
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return (OK);
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}
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#endif
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#ifdef SKIP2
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/* ---------------------------------------------------------------------- */
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int CLASS_QUALIFIER
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run_as_cells(void)
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@ -2456,7 +2457,215 @@ run_as_cells(void)
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/* last_model.force_prep = TRUE; */
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return (OK);
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}
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#endif
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/* ---------------------------------------------------------------------- */
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int CLASS_QUALIFIER
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run_as_cells(void)
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/* ---------------------------------------------------------------------- */
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{
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struct save save_data;
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LDBLE kin_time;
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int count_steps, use_mix, m;
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char token[2 * MAX_LENGTH];
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struct kinetics *kinetics_ptr;
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state = REACTION;
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if (run_info.Get_cells().Get_numbers().size() == 0 ||
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!(run_info.Get_cells().Get_defined())) return(OK);
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// running cells
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run_info.Set_run_cells(true);
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dup_print("Beginning of run as cells.", TRUE);
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double initial_total_time_save;
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if (run_info.Get_start_time() != NA)
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{
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initial_total_time_save = run_info.Get_start_time();
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}
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else
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{
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initial_total_time_save = initial_total_time;
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}
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std::set < int >::iterator it = run_info.Get_cells().Get_numbers().begin();
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for ( ; it != run_info.Get_cells().Get_numbers().end(); it++)
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{
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int i = *it;
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if (i < 0) continue;
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initial_total_time = initial_total_time_save;
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set_advection(i, TRUE, TRUE, i);
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/*
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* Run reaction step
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*/
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/*
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* Find maximum number of steps
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*/
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dup_print("Beginning of batch-reaction calculations.", TRUE);
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count_steps = 1;
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if (use.irrev_in == TRUE && use.irrev_ptr != NULL)
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{
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if (abs(use.irrev_ptr->count_steps) > count_steps)
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count_steps = abs(use.irrev_ptr->count_steps);
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}
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if (use.kinetics_in == TRUE && use.kinetics_ptr != NULL)
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{
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if (abs(use.kinetics_ptr->count_steps) > count_steps)
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count_steps = abs(use.kinetics_ptr->count_steps);
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}
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if (use.temperature_in == TRUE && use.temperature_ptr != NULL)
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{
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if (abs(use.temperature_ptr->count_t) > count_steps)
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count_steps = abs(use.temperature_ptr->count_t);
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}
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count_total_steps = count_steps;
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/*
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* save data for saving solutions
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*/
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memcpy(&save_data, &save, sizeof(struct save));
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/*
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*Copy everything to -2
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*/
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copy_use(-2);
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rate_sim_time_start = 0;
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rate_sim_time = 0;
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for (reaction_step = 1; reaction_step <= count_steps; reaction_step++)
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{
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sprintf(token, "Reaction step %d.", reaction_step);
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if (reaction_step > 1 && incremental_reactions == FALSE)
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{
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copy_use(-2);
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}
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set_initial_moles(-2);
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dup_print(token, FALSE);
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/*
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* Determine time step for kinetics
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*/
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kin_time = 0.0;
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if (use.kinetics_in == TRUE)
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{
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// runner kin_time
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// equivalent to kin_time in count_steps
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if (run_info.Get_time_step() != NA)
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{
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if (incremental_reactions == FALSE)
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{
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/* not incremental reactions */
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kin_time = reaction_step * run_info.Get_time_step() / ((LDBLE) count_steps);
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}
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else
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{
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/* incremental reactions */
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kin_time = run_info.Get_time_step() / ((LDBLE) count_steps);
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}
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}
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// runner kin_time not defined
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else
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{
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kinetics_ptr = kinetics_bsearch(-2, &m);
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if (incremental_reactions == FALSE)
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{
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if (kinetics_ptr->count_steps > 0)
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{
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if (reaction_step > kinetics_ptr->count_steps)
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{
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kin_time = kinetics_ptr->steps[kinetics_ptr->count_steps - 1];
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}
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else
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{
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kin_time = kinetics_ptr->steps[reaction_step - 1];
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}
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}
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else if (kinetics_ptr->count_steps < 0)
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{
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if (reaction_step > -kinetics_ptr->count_steps)
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{
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kin_time = kinetics_ptr->steps[0];
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}
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else
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{
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kin_time = reaction_step * kinetics_ptr->steps[0] / ((LDBLE) (-kinetics_ptr->count_steps));
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}
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}
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}
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else
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{
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/* incremental reactions */
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if (kinetics_ptr->count_steps > 0)
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{
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if (reaction_step > kinetics_ptr->count_steps)
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{
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kin_time = kinetics_ptr->steps[kinetics_ptr->count_steps - 1];
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}
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else
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{
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kin_time = kinetics_ptr->steps[reaction_step - 1];
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}
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}
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else if (kinetics_ptr->count_steps < 0)
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{
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if (reaction_step > -kinetics_ptr->count_steps)
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{
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kin_time = 0;
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}
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else
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{
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kin_time =
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kinetics_ptr->steps[0] / ((LDBLE) (-kinetics_ptr->count_steps));
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}
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}
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}
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}
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}
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if (incremental_reactions == FALSE ||
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(incremental_reactions == TRUE && reaction_step == 1))
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{
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use_mix = TRUE;
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}
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else
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{
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use_mix = FALSE;
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}
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/*
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* Run reaction step
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*/
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run_reactions(-2, kin_time, use_mix, 1.0);
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if (incremental_reactions == TRUE)
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{
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rate_sim_time_start += kin_time;
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rate_sim_time = rate_sim_time_start;
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}
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else
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{
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rate_sim_time = kin_time;
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}
|
||||
if (state != ADVECTION)
|
||||
{
|
||||
punch_all();
|
||||
print_all();
|
||||
}
|
||||
/* saves back into -2 */
|
||||
if (reaction_step < count_steps)
|
||||
{
|
||||
saver();
|
||||
}
|
||||
}
|
||||
/*
|
||||
* save end of reaction
|
||||
*/
|
||||
memcpy(&save, &save_data, sizeof(struct save));
|
||||
if (use.kinetics_in == TRUE)
|
||||
{
|
||||
kinetics_duplicate(-2, use.n_kinetics_user);
|
||||
}
|
||||
saver();
|
||||
}
|
||||
initial_total_time += rate_sim_time;
|
||||
run_info.Get_cells().Set_defined(false);
|
||||
// not running cells
|
||||
run_info.Set_run_cells(false);
|
||||
return (OK);
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
void CLASS_QUALIFIER
|
||||
dump_ostream(std::ostream& os)
|
||||
|
||||
28
runner.cpp
28
runner.cpp
@ -1,14 +1,18 @@
|
||||
#include "runner.h"
|
||||
#include "Parser.h"
|
||||
#include "NA.h"
|
||||
runner::runner(void)
|
||||
{
|
||||
this->time_step = 0;
|
||||
this->start_time = 0;
|
||||
this->time_step = NA;
|
||||
this->start_time = NA;
|
||||
this->run_cells = false;
|
||||
|
||||
}
|
||||
runner::runner(CParser & parser)
|
||||
{
|
||||
this->time_step = 0;
|
||||
this->start_time = 0;
|
||||
this->time_step = NA;
|
||||
this->start_time = NA;
|
||||
this->run_cells = false;
|
||||
this->Read(parser);
|
||||
}
|
||||
|
||||
@ -27,6 +31,9 @@ bool runner::Read(CParser & parser)
|
||||
vopts.push_back("cells");
|
||||
vopts.push_back("start_time");
|
||||
vopts.push_back("time_step");
|
||||
vopts.push_back("time_steps");
|
||||
vopts.push_back("step");
|
||||
vopts.push_back("steps");
|
||||
}
|
||||
|
||||
std::istream::pos_type ptr;
|
||||
@ -52,13 +59,11 @@ bool runner::Read(CParser & parser)
|
||||
opt_save = opt;
|
||||
}
|
||||
|
||||
//// Read dump entity list of numbers or number ranges for line, store in item
|
||||
//if (opt >= 0 && opt <= 1)
|
||||
//{
|
||||
|
||||
|
||||
// Read dump entity list of numbers or number ranges for line, store in item
|
||||
if (opt >= 0 && opt <= 1)
|
||||
{
|
||||
|
||||
}
|
||||
//}
|
||||
|
||||
// Process other identifiers
|
||||
std::set < int >::iterator it;
|
||||
@ -99,6 +104,9 @@ bool runner::Read(CParser & parser)
|
||||
}
|
||||
break;
|
||||
case 3: //time_step
|
||||
case 4: //time_steps
|
||||
case 5: //step
|
||||
case 6: //steps
|
||||
if (!(parser.get_iss() >> this->time_step))
|
||||
{
|
||||
parser.error_msg("Expected time_step for RUN_CELLS.",
|
||||
|
||||
3
runner.h
3
runner.h
@ -16,10 +16,13 @@ public:
|
||||
StorageBinListItem & Get_cells(void) { return(this->cells); };
|
||||
double Get_time_step() { return(this->time_step); };
|
||||
double Get_start_time() { return(this->start_time); };
|
||||
bool Get_run_cells() { return(this->run_cells); };
|
||||
void Set_run_cells(bool tf) { this->run_cells = tf; };
|
||||
|
||||
protected:
|
||||
double time_step;
|
||||
double start_time;
|
||||
StorageBinListItem cells;
|
||||
bool run_cells;
|
||||
};
|
||||
#endif // !defined(RUNNER_H_INCLUDED)
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user