diff --git a/ALLLoadBalancer_8cpp.html b/ALLLoadBalancer_8cpp.html index 6036dac2c8..dbd336eede 100644 --- a/ALLLoadBalancer_8cpp.html +++ b/ALLLoadBalancer_8cpp.html @@ -77,7 +77,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ALLLoadBalancer_8h.html b/ALLLoadBalancer_8h.html index 5537508ef8..911f3bdd1b 100644 --- a/ALLLoadBalancer_8h.html +++ b/ALLLoadBalancer_8h.html @@ -74,6 +74,7 @@
#include <ALL.hpp>
#include "LoadBalancer.h"
+#include <tuple>

Go to the source code of this file.

@@ -88,7 +89,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ALLLoadBalancer_8h_source.html b/ALLLoadBalancer_8h_source.html index 1a92af75de..ca3d284601 100644 --- a/ALLLoadBalancer_8h_source.html +++ b/ALLLoadBalancer_8h_source.html @@ -76,38 +76,39 @@
9#include <ALL.hpp>
10#include "LoadBalancer.h"
11
-
12class ALLLoadBalancer : public LoadBalancer {
-
13public:
-
14 ALLLoadBalancer(std::array<double, 3> boxMin, std::array<double, 3> boxMax, double gamma, MPI_Comm comm,
-
15 std::array<size_t, 3> globalSize, std::array<size_t, 3> localCoordinates,
-
16 std::array<double, 3> minimalPartitionSize);
-
17
-
18 ~ALLLoadBalancer() override = default;
-
19 std::tuple<std::array<double, 3>, std::array<double, 3>> rebalance(double work) override;
-
20 void readXML(XMLfileUnits& xmlconfig) override {
-
21 // nothing yet.
-
22 }
-
23
-
24 std::array<bool, 3> getCoversWholeDomain() override { return _coversWholeDomain; }
-
25
-
26private:
-
27 ALL<double, double> _all;
-
28 using Point = ALL_Point<double>;
-
29 std::array<double, 3> _minimalPartitionSize{};
-
30 std::array<bool, 3> _coversWholeDomain{};
-
31};
-
32#endif
+
12#include <tuple>
+
13class ALLLoadBalancer : public LoadBalancer {
+
14public:
+
15 ALLLoadBalancer(std::array<double, 3> boxMin, std::array<double, 3> boxMax, double gamma, MPI_Comm comm,
+
16 std::array<size_t, 3> globalSize, std::array<size_t, 3> localCoordinates,
+
17 std::array<double, 3> minimalPartitionSize);
+
18
+
19 ~ALLLoadBalancer() override = default;
+
20 std::tuple<std::array<double, 3>, std::array<double, 3>> rebalance(double work) override;
+
21 void readXML(XMLfileUnits& xmlconfig) override {
+
22 // nothing yet.
+
23 }
+
24
+
25 std::array<bool, 3> getCoversWholeDomain() override { return _coversWholeDomain; }
+
26
+
27private:
+
28 ALL<double, double> _all;
+
29 using Point = ALL_Point<double>;
+
30 std::array<double, 3> _minimalPartitionSize{};
+
31 std::array<bool, 3> _coversWholeDomain{};
+
32};
+
33#endif
LoadBalancer.h
-
ALLLoadBalancer
Definition: ALLLoadBalancer.h:12
+
ALLLoadBalancer
Definition: ALLLoadBalancer.h:13
ALLLoadBalancer::rebalance
std::tuple< std::array< double, 3 >, std::array< double, 3 > > rebalance(double work) override
Definition: ALLLoadBalancer.cpp:27
-
ALLLoadBalancer::getCoversWholeDomain
std::array< bool, 3 > getCoversWholeDomain() override
Definition: ALLLoadBalancer.h:24
-
ALLLoadBalancer::readXML
void readXML(XMLfileUnits &xmlconfig) override
Definition: ALLLoadBalancer.h:20
+
ALLLoadBalancer::getCoversWholeDomain
std::array< bool, 3 > getCoversWholeDomain() override
Definition: ALLLoadBalancer.h:25
+
ALLLoadBalancer::readXML
void readXML(XMLfileUnits &xmlconfig) override
Definition: ALLLoadBalancer.h:21
LoadBalancer
Definition: LoadBalancer.h:15
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ASCIIReader_8h_source.html b/ASCIIReader_8h_source.html index ae2477cedf..c4e86ef04f 100644 --- a/ASCIIReader_8h_source.html +++ b/ASCIIReader_8h_source.html @@ -117,7 +117,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Accumulator_8h_source.html b/Accumulator_8h_source.html index 5affe674a5..a67b241a14 100644 --- a/Accumulator_8h_source.html +++ b/Accumulator_8h_source.html @@ -181,7 +181,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AdaptivePseudoParticleContainer_8h_source.html b/AdaptivePseudoParticleContainer_8h_source.html index 1f19834526..ed5621181b 100644 --- a/AdaptivePseudoParticleContainer_8h_source.html +++ b/AdaptivePseudoParticleContainer_8h_source.html @@ -170,7 +170,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Adios2Reader_8h_source.html b/Adios2Reader_8h_source.html index 18f0aded66..403897aef7 100644 --- a/Adios2Reader_8h_source.html +++ b/Adios2Reader_8h_source.html @@ -91,246 +91,247 @@
19#include "molecules/FullMolecule.h"
20#endif
21
-
22#include <errno.h>
-
23#include <chrono>
-
24#include <iomanip>
-
25#include <map>
-
26#include <memory>
-
27#include <set>
-
28#include <sstream>
-
29#include <string>
-
30#include <variant>
-
31#include <vector>
-
32
-
33#include "adios2.h"
-
34#ifdef ENABLE_MPI
-
35#include <mpi.h>
-
36#endif
-
37
-
38class Adios2Reader : public InputBase {
-
39public:
-
40 Adios2Reader() = default;
-
41 ~Adios2Reader() override = default;
-
42
-
43 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain);
-
44
-
60 void readXML(XMLfileUnits& xmlconfig) override;
-
61
-
62 void testInit(std::string infile = "mardyn.bp", int step = 0, std::string adios2enginetype = "BP4",
-
63 std::string mode = "rootOnly");
-
64
-
65 void readPhaseSpaceHeader(Domain* domain, double timestep) override;
-
66
-
67 std::string getPluginName() { return std::string("Adios2Reader"); }
-
68
-
69 unsigned long readPhaseSpace(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp) override;
-
70
-
71private:
-
72 void initAdios2();
-
73 void rootOnlyRead(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
-
74 void parallelRead(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
-
75
-
76 // input filename, from XML
-
77 std::string _inputfile;
-
78
-
79 std::string _adios2enginetype;
-
80 std::string _mode;
-
81 int _step;
-
82 uint64_t particle_count;
-
83 std::vector<Component> _dcomponents;
-
84 double _simtime = 0.0;
-
85 bool _single_precision = false;
-
86 // main instance
-
87 std::shared_ptr<adios2::ADIOS> mainInstance;
-
88 std::shared_ptr<adios2::Engine> engine;
-
89 std::shared_ptr<adios2::IO> io;
-
90
-
91 template <typename T>
-
92 void doTheRead(std::string var_name, std::vector<T>& container) {
-
93 uint64_t num = 1;
-
94 auto advar = io->InquireVariable<T>(var_name);
-
95 advar.SetStepSelection({_step, 1});
-
96 auto info = engine->BlocksInfo(advar, 0);
-
97 auto shape = info[0].Count;
-
98 std::for_each(shape.begin(), shape.end(), [&](decltype(num) n) { num *= n; });
-
99 container.resize(num);
-
100 engine->Get<T>(advar, container);
-
101 }
-
102
-
113 template <typename T>
-
114 void doTheRead(const std::string var_name, std::vector<T>& container, const uint64_t bufferSize, const uint64_t offset) {
-
115 adios2::Dims readsize({bufferSize});
-
116 adios2::Dims offs({offset});
-
117
-
118 Log::global_log->debug() << "[Adios2Reader]: Var name " << var_name << std::endl;
-
119 auto advar = io->InquireVariable<T>(var_name);
-
120 advar.SetStepSelection({_step, 1});
-
121 Log::global_log->debug() << "[Adios2Reader]: buffer " << bufferSize << " offset " << offset << std::endl;
-
122 for (auto entry : advar.Shape()) Log::global_log->debug() << "[Adios2Reader]: shape " << entry << std::endl;
-
123 advar.SetSelection(adios2::Box<adios2::Dims>(offs, readsize));
-
124 container.resize(bufferSize);
-
125 engine->Get<T>(advar, container);
-
126 }
-
127
-
128 template <typename T>
-
129 void doTheRead(std::string var_name, T& value) {
-
130 auto advar = io->InquireVariable<T>(var_name);
-
131 advar.SetStepSelection({_step, 1});
-
132 engine->Get<T>(advar, value);
-
133 }
-
134
-
135 template <typename T>
-
136 Molecule fillMolecule(int i_, std::vector<uint64_t>& mol_id_, std::vector<uint64_t>& comp_id_, T& rx_, T& ry_,
-
137 T& rz_, T& vx_, T& vy_, T& vz_, T& qw_, T& qx_, T& qy_, T& qz_, T& Lx_, T& Ly_, T& Lz_) {
-
138 Molecule m1;
-
139 if (qw_.empty()) {
-
140 m1 = Molecule(mol_id_[i_], &_dcomponents[comp_id_[i_]], rx_[i_], ry_[i_], rz_[i_], vx_[i_], vy_[i_],
-
141 vz_[i_], 1, 0, 0, 0, 0, 0, 0);
-
142 } else {
-
143 m1 = Molecule(mol_id_[i_], &_dcomponents[comp_id_[i_]], rx_[i_], ry_[i_], rz_[i_], vx_[i_], vy_[i_],
-
144 vz_[i_], qw_[i_], qx_[i_], qy_[i_], qz_[i_], Lx_[i_], Ly_[i_], Lz_[i_]);
-
145 }
-
146 return m1;
-
147 }
-
148
-
149 template <typename T>
-
150 void performInquire(std::map<std::string, adios2::Params> variables, uint64_t buffer, uint64_t offset,
-
151 std::vector<T>& rx, std::vector<T>& ry, std::vector<T>& rz, std::vector<T>& vx,
-
152 std::vector<T>& vy, std::vector<T>& vz, std::vector<T>& qw, std::vector<T>& qx,
-
153 std::vector<T>& qy, std::vector<T>& qz, std::vector<T>& Lx, std::vector<T>& Ly,
-
154 std::vector<T>& Lz, std::vector<uint64_t>& mol_id, std::vector<uint64_t>& comp_id) {
-
155 for (auto var : variables) {
-
156 if (var.first == "rx") {
-
157 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
158 doTheRead(var.first, rx, buffer, offset);
-
159 } else {
-
160 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
-
161 << std::endl;
-
162 }
-
163 }
-
164 if (var.first == "ry") {
-
165 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
166 doTheRead(var.first, ry, buffer, offset);
-
167 } else {
-
168 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
-
169 << std::endl;
-
170 }
-
171 }
-
172 if (var.first == "rz") {
-
173 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
174 doTheRead(var.first, rz, buffer, offset);
-
175 } else {
-
176 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
-
177 << std::endl;
-
178 }
-
179 }
-
180 if (var.first == "vx") {
-
181 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
182 doTheRead(var.first, vx, buffer, offset);
-
183 } else {
-
184 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
-
185 << std::endl;
-
186 }
-
187 }
-
188 if (var.first == "vy") {
-
189 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
190 doTheRead(var.first, vy, buffer, offset);
-
191 } else {
-
192 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
-
193 << std::endl;
-
194 }
-
195 }
-
196 if (var.first == "vz") {
-
197 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
198 doTheRead(var.first, vz, buffer, offset);
-
199 } else {
-
200 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
-
201 << std::endl;
-
202 }
-
203 }
-
204 if (var.first == "qw") {
-
205 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
206 doTheRead(var.first, qw, buffer, offset);
-
207 } else {
-
208 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
-
209 << std::endl;
-
210 }
-
211 }
-
212 if (var.first == "qx") {
-
213 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
214 doTheRead(var.first, qx, buffer, offset);
-
215 } else {
-
216 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
-
217 << std::endl;
-
218 }
-
219 }
-
220 if (var.first == "qy") {
-
221 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
222 doTheRead(var.first, qy, buffer, offset);
-
223 } else {
-
224 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
-
225 << std::endl;
-
226 }
-
227 }
-
228 if (var.first == "qz") {
-
229 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
230 doTheRead(var.first, qz, buffer, offset);
-
231 } else {
-
232 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
-
233 << std::endl;
-
234 }
-
235 }
-
236 if (var.first == "Lx") {
-
237 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
238 doTheRead(var.first, Lx, buffer, offset);
-
239 } else {
-
240 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
-
241 << std::endl;
-
242 }
-
243 }
-
244 if (var.first == "Ly") {
-
245 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
246 doTheRead(var.first, Ly, buffer, offset);
-
247 } else {
-
248 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
-
249 << std::endl;
-
250 }
-
251 }
-
252 if (var.first == "Lz") {
-
253 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
254 doTheRead(var.first, Lz, buffer, offset);
-
255 } else {
-
256 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
-
257 << std::endl;
-
258 }
-
259 }
-
260 if (var.first == "component_id") {
-
261 if (var.second["Type"] == "uint64_t") {
-
262 doTheRead(var.first, comp_id, buffer, offset);
-
263 } else {
-
264 Log::global_log->error() << "[Adios2Reader] Component ids should be uint64_t (for now)." << std::endl;
-
265 }
-
266 }
-
267 if (var.first == "molecule_id") {
-
268 if (var.second["Type"] == "uint64_t") {
-
269 doTheRead(var.first, mol_id, buffer, offset);
-
270 } else {
-
271 Log::global_log->error() << "[Adios2Reader] Molecule ids should be uint64_t (for now)." << std::endl;
-
272 }
-
273 }
-
274 if (var.first == "simulationtime") {
-
275 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
-
276 doTheRead(var.first, _simtime);
-
277 } else {
-
278 Log::global_log->error() << "[Adios2Reader] Simulation time should be double or float (for now)."
-
279 << std::endl;
-
280 }
-
281 }
-
282 }
-
283 }
-
284};
-
285#endif // ENABLE_ADIOS2
-
286#endif /* ADIOS2_READER_H_*/
+
22#include <algorithm>
+
23#include <errno.h>
+
24#include <chrono>
+
25#include <iomanip>
+
26#include <map>
+
27#include <memory>
+
28#include <set>
+
29#include <sstream>
+
30#include <string>
+
31#include <variant>
+
32#include <vector>
+
33
+
34#include "adios2.h"
+
35#ifdef ENABLE_MPI
+
36#include <mpi.h>
+
37#endif
+
38
+
39class Adios2Reader : public InputBase {
+
40public:
+
41 Adios2Reader() = default;
+
42 ~Adios2Reader() override = default;
+
43
+
44 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain);
+
45
+
61 void readXML(XMLfileUnits& xmlconfig) override;
+
62
+
63 void testInit(std::string infile = "mardyn.bp", int step = 0, std::string adios2enginetype = "BP4",
+
64 std::string mode = "rootOnly");
+
65
+
66 void readPhaseSpaceHeader(Domain* domain, double timestep) override;
+
67
+
68 std::string getPluginName() { return std::string("Adios2Reader"); }
+
69
+
70 unsigned long readPhaseSpace(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp) override;
+
71
+
72private:
+
73 void initAdios2();
+
74 void rootOnlyRead(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
+
75 void parallelRead(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
+
76
+
77 // input filename, from XML
+
78 std::string _inputfile;
+
79
+
80 std::string _adios2enginetype;
+
81 std::string _mode;
+
82 int _step;
+
83 uint64_t particle_count;
+
84 std::vector<Component> _dcomponents;
+
85 double _simtime = 0.0;
+
86 bool _single_precision = false;
+
87 // main instance
+
88 std::shared_ptr<adios2::ADIOS> mainInstance;
+
89 std::shared_ptr<adios2::Engine> engine;
+
90 std::shared_ptr<adios2::IO> io;
+
91
+
92 template <typename T>
+
93 void doTheRead(std::string var_name, std::vector<T>& container) {
+
94 uint64_t num = 1;
+
95 auto advar = io->InquireVariable<T>(var_name);
+
96 advar.SetStepSelection({_step, 1});
+
97 auto info = engine->BlocksInfo(advar, 0);
+
98 auto shape = info[0].Count;
+
99 std::for_each(shape.begin(), shape.end(), [&](decltype(num) n) { num *= n; });
+
100 container.resize(num);
+
101 engine->Get<T>(advar, container);
+
102 }
+
103
+
114 template <typename T>
+
115 void doTheRead(const std::string var_name, std::vector<T>& container, const uint64_t bufferSize, const uint64_t offset) {
+
116 adios2::Dims readsize({bufferSize});
+
117 adios2::Dims offs({offset});
+
118
+
119 Log::global_log->debug() << "[Adios2Reader]: Var name " << var_name << std::endl;
+
120 auto advar = io->InquireVariable<T>(var_name);
+
121 advar.SetStepSelection({_step, 1});
+
122 Log::global_log->debug() << "[Adios2Reader]: buffer " << bufferSize << " offset " << offset << std::endl;
+
123 for (auto entry : advar.Shape()) Log::global_log->debug() << "[Adios2Reader]: shape " << entry << std::endl;
+
124 advar.SetSelection(adios2::Box<adios2::Dims>(offs, readsize));
+
125 container.resize(bufferSize);
+
126 engine->Get<T>(advar, container);
+
127 }
+
128
+
129 template <typename T>
+
130 void doTheRead(std::string var_name, T& value) {
+
131 auto advar = io->InquireVariable<T>(var_name);
+
132 advar.SetStepSelection({_step, 1});
+
133 engine->Get<T>(advar, value);
+
134 }
+
135
+
136 template <typename T>
+
137 Molecule fillMolecule(int i_, std::vector<uint64_t>& mol_id_, std::vector<uint64_t>& comp_id_, T& rx_, T& ry_,
+
138 T& rz_, T& vx_, T& vy_, T& vz_, T& qw_, T& qx_, T& qy_, T& qz_, T& Lx_, T& Ly_, T& Lz_) {
+
139 Molecule m1;
+
140 if (qw_.empty()) {
+
141 m1 = Molecule(mol_id_[i_], &_dcomponents[comp_id_[i_]], rx_[i_], ry_[i_], rz_[i_], vx_[i_], vy_[i_],
+
142 vz_[i_], 1, 0, 0, 0, 0, 0, 0);
+
143 } else {
+
144 m1 = Molecule(mol_id_[i_], &_dcomponents[comp_id_[i_]], rx_[i_], ry_[i_], rz_[i_], vx_[i_], vy_[i_],
+
145 vz_[i_], qw_[i_], qx_[i_], qy_[i_], qz_[i_], Lx_[i_], Ly_[i_], Lz_[i_]);
+
146 }
+
147 return m1;
+
148 }
+
149
+
150 template <typename T>
+
151 void performInquire(std::map<std::string, adios2::Params> variables, uint64_t buffer, uint64_t offset,
+
152 std::vector<T>& rx, std::vector<T>& ry, std::vector<T>& rz, std::vector<T>& vx,
+
153 std::vector<T>& vy, std::vector<T>& vz, std::vector<T>& qw, std::vector<T>& qx,
+
154 std::vector<T>& qy, std::vector<T>& qz, std::vector<T>& Lx, std::vector<T>& Ly,
+
155 std::vector<T>& Lz, std::vector<uint64_t>& mol_id, std::vector<uint64_t>& comp_id) {
+
156 for (auto var : variables) {
+
157 if (var.first == "rx") {
+
158 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
159 doTheRead(var.first, rx, buffer, offset);
+
160 } else {
+
161 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
162 << std::endl;
+
163 }
+
164 }
+
165 if (var.first == "ry") {
+
166 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
167 doTheRead(var.first, ry, buffer, offset);
+
168 } else {
+
169 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
170 << std::endl;
+
171 }
+
172 }
+
173 if (var.first == "rz") {
+
174 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
175 doTheRead(var.first, rz, buffer, offset);
+
176 } else {
+
177 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
178 << std::endl;
+
179 }
+
180 }
+
181 if (var.first == "vx") {
+
182 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
183 doTheRead(var.first, vx, buffer, offset);
+
184 } else {
+
185 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
186 << std::endl;
+
187 }
+
188 }
+
189 if (var.first == "vy") {
+
190 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
191 doTheRead(var.first, vy, buffer, offset);
+
192 } else {
+
193 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
194 << std::endl;
+
195 }
+
196 }
+
197 if (var.first == "vz") {
+
198 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
199 doTheRead(var.first, vz, buffer, offset);
+
200 } else {
+
201 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
202 << std::endl;
+
203 }
+
204 }
+
205 if (var.first == "qw") {
+
206 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
207 doTheRead(var.first, qw, buffer, offset);
+
208 } else {
+
209 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
210 << std::endl;
+
211 }
+
212 }
+
213 if (var.first == "qx") {
+
214 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
215 doTheRead(var.first, qx, buffer, offset);
+
216 } else {
+
217 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
218 << std::endl;
+
219 }
+
220 }
+
221 if (var.first == "qy") {
+
222 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
223 doTheRead(var.first, qy, buffer, offset);
+
224 } else {
+
225 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
226 << std::endl;
+
227 }
+
228 }
+
229 if (var.first == "qz") {
+
230 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
231 doTheRead(var.first, qz, buffer, offset);
+
232 } else {
+
233 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
234 << std::endl;
+
235 }
+
236 }
+
237 if (var.first == "Lx") {
+
238 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
239 doTheRead(var.first, Lx, buffer, offset);
+
240 } else {
+
241 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
242 << std::endl;
+
243 }
+
244 }
+
245 if (var.first == "Ly") {
+
246 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
247 doTheRead(var.first, Ly, buffer, offset);
+
248 } else {
+
249 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
250 << std::endl;
+
251 }
+
252 }
+
253 if (var.first == "Lz") {
+
254 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
255 doTheRead(var.first, Lz, buffer, offset);
+
256 } else {
+
257 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
258 << std::endl;
+
259 }
+
260 }
+
261 if (var.first == "component_id") {
+
262 if (var.second["Type"] == "uint64_t") {
+
263 doTheRead(var.first, comp_id, buffer, offset);
+
264 } else {
+
265 Log::global_log->error() << "[Adios2Reader] Component ids should be uint64_t (for now)." << std::endl;
+
266 }
+
267 }
+
268 if (var.first == "molecule_id") {
+
269 if (var.second["Type"] == "uint64_t") {
+
270 doTheRead(var.first, mol_id, buffer, offset);
+
271 } else {
+
272 Log::global_log->error() << "[Adios2Reader] Molecule ids should be uint64_t (for now)." << std::endl;
+
273 }
+
274 }
+
275 if (var.first == "simulationtime") {
+
276 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
+
277 doTheRead(var.first, _simtime);
+
278 } else {
+
279 Log::global_log->error() << "[Adios2Reader] Simulation time should be double or float (for now)."
+
280 << std::endl;
+
281 }
+
282 }
+
283 }
+
284 }
+
285};
+
286#endif // ENABLE_ADIOS2
+
287#endif /* ADIOS2_READER_H_*/
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:46
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
@@ -345,7 +346,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Adios2Writer_8h_source.html b/Adios2Writer_8h_source.html index 88190cc882..7de894908b 100644 --- a/Adios2Writer_8h_source.html +++ b/Adios2Writer_8h_source.html @@ -179,7 +179,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArrayTriplet_8h_source.html b/AlignedArrayTriplet_8h_source.html index e302ea774d..43cdbde2ff 100644 --- a/AlignedArrayTriplet_8h_source.html +++ b/AlignedArrayTriplet_8h_source.html @@ -255,7 +255,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArray_8h.html b/AlignedArray_8h.html index f94d2ea5ba..5b9bc9cc9f 100644 --- a/AlignedArray_8h.html +++ b/AlignedArray_8h.html @@ -102,7 +102,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArray_8h_source.html b/AlignedArray_8h_source.html index 1bec797460..8170586404 100644 --- a/AlignedArray_8h_source.html +++ b/AlignedArray_8h_source.html @@ -284,7 +284,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Array2D_8h_source.html b/Array2D_8h_source.html index c6c5c2f6e8..5acd8a17f5 100644 --- a/Array2D_8h_source.html +++ b/Array2D_8h_source.html @@ -154,7 +154,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasClass_8cpp.html b/AutoPasClass_8cpp.html index bb598c35cf..57da50ece3 100644 --- a/AutoPasClass_8cpp.html +++ b/AutoPasClass_8cpp.html @@ -78,7 +78,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8cpp.html b/AutoPasContainer_8cpp.html index cc088a6184..36388fa10f 100644 --- a/AutoPasContainer_8cpp.html +++ b/AutoPasContainer_8cpp.html @@ -151,7 +151,7 @@

-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8h.html b/AutoPasContainer_8h.html index a191f5d1c9..911f968f59 100644 --- a/AutoPasContainer_8h.html +++ b/AutoPasContainer_8h.html @@ -89,7 +89,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8h_source.html b/AutoPasContainer_8h_source.html index ca5a05ba07..e51fe73212 100644 --- a/AutoPasContainer_8h_source.html +++ b/AutoPasContainer_8h_source.html @@ -245,7 +245,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasSimpleMolecule_8h_source.html b/AutoPasSimpleMolecule_8h_source.html index 6e6243b55b..7324f1bf16 100644 --- a/AutoPasSimpleMolecule_8h_source.html +++ b/AutoPasSimpleMolecule_8h_source.html @@ -398,7 +398,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Basis_8h_source.html b/Basis_8h_source.html index 00358e96e5..71f3e90c05 100644 --- a/Basis_8h_source.html +++ b/Basis_8h_source.html @@ -117,7 +117,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/BinaryReader_8h_source.html b/BinaryReader_8h_source.html index 42660c3bd1..20abb3d9a4 100644 --- a/BinaryReader_8h_source.html +++ b/BinaryReader_8h_source.html @@ -131,7 +131,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/BoxDomain_8h_source.html b/BoxDomain_8h_source.html index 3fb34f9a1c..0aa3101a47 100644 --- a/BoxDomain_8h_source.html +++ b/BoxDomain_8h_source.html @@ -100,7 +100,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C04CellPairTraversal_8h_source.html b/C04CellPairTraversal_8h_source.html index d3bc188663..7fe2100723 100644 --- a/C04CellPairTraversal_8h_source.html +++ b/C04CellPairTraversal_8h_source.html @@ -322,7 +322,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C08BasedTraversals_8h_source.html b/C08BasedTraversals_8h_source.html index b4b6e043b6..381d0e56f3 100644 --- a/C08BasedTraversals_8h_source.html +++ b/C08BasedTraversals_8h_source.html @@ -233,7 +233,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C08CellPairTraversal_8h_source.html b/C08CellPairTraversal_8h_source.html index 4c6486cf06..8168c0b5e6 100644 --- a/C08CellPairTraversal_8h_source.html +++ b/C08CellPairTraversal_8h_source.html @@ -309,7 +309,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/COMaligner_8h_source.html b/COMaligner_8h_source.html index 3344f60f23..277eaecb5e 100644 --- a/COMaligner_8h_source.html +++ b/COMaligner_8h_source.html @@ -170,7 +170,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellDataSoABase_8h_source.html b/CellDataSoABase_8h_source.html index 95db5677ba..90d26b32bf 100644 --- a/CellDataSoABase_8h_source.html +++ b/CellDataSoABase_8h_source.html @@ -100,7 +100,7 @@
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellPairTraversals_8h_source.html b/CellPairTraversals_8h_source.html index 1399d2c684..8c85771d70 100644 --- a/CellPairTraversals_8h_source.html +++ b/CellPairTraversals_8h_source.html @@ -130,7 +130,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellProcessor_8h_source.html b/CellProcessor_8h_source.html index 21c84d3a9a..aa21b5835a 100644 --- a/CellProcessor_8h_source.html +++ b/CellProcessor_8h_source.html @@ -133,7 +133,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Cell_8h_source.html b/Cell_8h_source.html index 6ab2ac82ce..5dc29ffe29 100644 --- a/Cell_8h_source.html +++ b/Cell_8h_source.html @@ -112,7 +112,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommBaseInterface_8h_source.html b/CollectiveCommBaseInterface_8h_source.html index 57cd4bc486..56051b10a5 100644 --- a/CollectiveCommBaseInterface_8h_source.html +++ b/CollectiveCommBaseInterface_8h_source.html @@ -139,7 +139,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommBase_8h_source.html b/CollectiveCommBase_8h_source.html index b1db38aa6a..11fd17c230 100644 --- a/CollectiveCommBase_8h_source.html +++ b/CollectiveCommBase_8h_source.html @@ -199,7 +199,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationInterface_8h_source.html b/CollectiveCommunicationInterface_8h_source.html index 1df29241b2..bc21ef5e03 100644 --- a/CollectiveCommunicationInterface_8h_source.html +++ b/CollectiveCommunicationInterface_8h_source.html @@ -103,7 +103,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationNonBlocking_8h_source.html b/CollectiveCommunicationNonBlocking_8h_source.html index 4e97be8c44..07af506250 100644 --- a/CollectiveCommunicationNonBlocking_8h_source.html +++ b/CollectiveCommunicationNonBlocking_8h_source.html @@ -247,7 +247,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationSingleNonBlocking_8h_source.html b/CollectiveCommunicationSingleNonBlocking_8h_source.html index dba585d20f..1bdb6438ed 100644 --- a/CollectiveCommunicationSingleNonBlocking_8h_source.html +++ b/CollectiveCommunicationSingleNonBlocking_8h_source.html @@ -227,7 +227,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunication_8h_source.html b/CollectiveCommunication_8h_source.html index f5095159b0..6a12d302a9 100644 --- a/CollectiveCommunication_8h_source.html +++ b/CollectiveCommunication_8h_source.html @@ -434,7 +434,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommVar_8h_source.html b/CommVar_8h_source.html index a6221fa2b6..964c412352 100644 --- a/CommVar_8h_source.html +++ b/CommVar_8h_source.html @@ -93,7 +93,7 @@
-Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Common_8h_source.html b/Common_8h_source.html index c641d2f9ff..b5b43a1515 100644 --- a/Common_8h_source.html +++ b/Common_8h_source.html @@ -98,7 +98,7 @@
-Generated on Sat Dec 7 2024 15:20:37 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:05 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommunicationBuffer_8h_source.html b/CommunicationBuffer_8h_source.html index 314d85a0fc..74ff920e46 100644 --- a/CommunicationBuffer_8h_source.html +++ b/CommunicationBuffer_8h_source.html @@ -200,7 +200,7 @@
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diff --git a/DomainDecompBase_8h_source.html b/DomainDecompBase_8h_source.html index ef2d2d6182..1fe67432dd 100644 --- a/DomainDecompBase_8h_source.html +++ b/DomainDecompBase_8h_source.html @@ -259,50 +259,50 @@
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
DirectNeighbourCommunicationScheme
Definition: NeighbourCommunicationScheme.h:128
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
-
DomainDecompBase::collCommAppendFloat
virtual void collCommAppendFloat(float floatValue)
has to call appendFloat method of a CollComm class
Definition: DomainDecompBase.cpp:560
-
DomainDecompBase::handleDomainLeavingParticlesDirect
void handleDomainLeavingParticlesDirect(const HaloRegion &haloRegion, ParticleContainer *moleculeContainer, std::vector< Molecule > &invalidParticles) const
Definition: DomainDecompBase.cpp:222
-
DomainDecompBase::collCommGetDouble
virtual double collCommGetDouble()
has to call getDouble method of a CollComm class
Definition: DomainDecompBase.cpp:584
-
DomainDecompBase::collCommAppendInt
virtual void collCommAppendInt(int intValue)
has to call appendInt method of a CollComm class
Definition: DomainDecompBase.cpp:552
+
DomainDecompBase::collCommAppendFloat
virtual void collCommAppendFloat(float floatValue)
has to call appendFloat method of a CollComm class
Definition: DomainDecompBase.cpp:561
+
DomainDecompBase::handleDomainLeavingParticlesDirect
void handleDomainLeavingParticlesDirect(const HaloRegion &haloRegion, ParticleContainer *moleculeContainer, std::vector< Molecule > &invalidParticles) const
Definition: DomainDecompBase.cpp:223
+
DomainDecompBase::collCommGetDouble
virtual double collCommGetDouble()
has to call getDouble method of a CollComm class
Definition: DomainDecompBase.cpp:585
+
DomainDecompBase::collCommAppendInt
virtual void collCommAppendInt(int intValue)
has to call appendInt method of a CollComm class
Definition: DomainDecompBase.cpp:553
DomainDecompBase::_numProcs
int _numProcs
total number of processes in the simulation
Definition: DomainDecompBase.h:339
-
DomainDecompBase::writeMoleculesToMPIFileBinary
void writeMoleculesToMPIFileBinary(const std::string &filename, ParticleContainer *moleculeContainer) const
appends molecule data to the file. The format is the same as that of the input file This version uses...
Definition: DomainDecompBase.cpp:448
+
DomainDecompBase::writeMoleculesToMPIFileBinary
void writeMoleculesToMPIFileBinary(const std::string &filename, ParticleContainer *moleculeContainer) const
appends molecule data to the file. The format is the same as that of the input file This version uses...
Definition: DomainDecompBase.cpp:449
DomainDecompBase::_rank
int _rank
the id of the current process
Definition: DomainDecompBase.h:336
-
DomainDecompBase::balanceAndExchange
virtual void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain)
balance the load (and optimize communication) and exchange boundary particles
Definition: DomainDecompBase.cpp:399
-
DomainDecompBase::collCommInit
virtual void collCommInit(int numValues, int key=0)
has to call init method of a CollComm class
Definition: DomainDecompBase.cpp:544
-
DomainDecompBase::queryBalanceAndExchangeNonBlocking
virtual bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime)
Checks whether the balance and exchange step can be performed non-blocking.
Definition: DomainDecompBase.cpp:395
-
DomainDecompBase::getIOCutoffRadius
double getIOCutoffRadius(int dim, Domain *domain, ParticleContainer *moleculeContainer)
returns an cutoff radius for a dimension for a global linked cells datastructure
Definition: DomainDecompBase.cpp:612
-
DomainDecompBase::collCommGetUnsLong
virtual unsigned long collCommGetUnsLong()
has to call getUnsLong method of a CollComm class
Definition: DomainDecompBase.cpp:576
-
DomainDecompBase::collCommBroadcast
virtual void collCommBroadcast(int root=0)
has to call broadcast method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:608
-
DomainDecompBase::collCommGetInt
virtual int collCommGetInt()
has to call getInt method of a CollComm class
Definition: DomainDecompBase.cpp:572
-
DomainDecompBase::collCommAppendDouble
virtual void collCommAppendDouble(double doubleValue)
has to call appendDouble method of a CollComm class
Definition: DomainDecompBase.cpp:564
-
DomainDecompBase::getBoundingBoxMinMax
void getBoundingBoxMinMax(Domain *domain, double *min, double *max)
get the minimum and maximum coordinate of the bounding box of this process' domain
Definition: DomainDecompBase.cpp:537
-
DomainDecompBase::getTime
virtual double getTime() const
returns the time in seconds since some time in the past
Definition: DomainDecompBase.cpp:417
-
DomainDecompBase::collCommAllreduceSum
virtual void collCommAllreduceSum()
has to call allreduceSum method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:592
-
DomainDecompBase::collCommGetLongDouble
virtual long double collCommGetLongDouble()
has to call getLongDouble method of a CollComm class
Definition: DomainDecompBase.cpp:588
-
DomainDecompBase::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension, Domain *domain)
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecompBase.cpp:409
-
DomainDecompBase::assertIntIdentity
virtual void assertIntIdentity(int IX)
checks identity of random number generators
Definition: DomainDecompBase.cpp:427
-
DomainDecompBase::barrier
virtual void barrier() const
synchronizes all processes
Definition: DomainDecompBase.cpp:445
-
DomainDecompBase::getNumProcs
virtual int getNumProcs() const
returns the number of processes
Definition: DomainDecompBase.cpp:441
-
DomainDecompBase::getRank
virtual int getRank() const
returns the own rank
Definition: DomainDecompBase.cpp:437
-
DomainDecompBase::handleDomainLeavingParticles
void handleDomainLeavingParticles(unsigned dim, ParticleContainer *moleculeContainer) const
Definition: DomainDecompBase.cpp:170
-
DomainDecompBase::handleForceExchange
void handleForceExchange(unsigned dim, ParticleContainer *moleculeContainer) const
Does the force exchange for each dimension. Will be called for dim=0, 1 and 2.
Definition: DomainDecompBase.cpp:93
-
DomainDecompBase::writeMoleculesToFile
void writeMoleculesToFile(const std::string &filename, ParticleContainer *moleculeContainer, bool binary=false) const
appends molecule data to the file. The format is the same as that of the input file If MPI is enabled...
Definition: DomainDecompBase.cpp:499
-
DomainDecompBase::printDecomp
virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer)
writes information about the current decomposition into the given file
Definition: DomainDecompBase.cpp:433
-
DomainDecompBase::collCommScanSum
virtual void collCommScanSum()
has to call scanSum method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:604
-
DomainDecompBase::exchangeMolecules
void exchangeMolecules(ParticleContainer *moleculeContainer, Domain *domain)
exchange molecules between processes
Definition: DomainDecompBase.cpp:51
-
DomainDecompBase::collCommGetFloat
virtual float collCommGetFloat()
has to call getFloat method of a CollComm class
Definition: DomainDecompBase.cpp:580
-
DomainDecompBase::Ndistribution
virtual unsigned Ndistribution(unsigned localN, float *minrnd, float *maxrnd)
returns total number of molecules
Definition: DomainDecompBase.cpp:421
-
DomainDecompBase::collCommFinalize
virtual void collCommFinalize()
has to call finalize method of a CollComm class
Definition: DomainDecompBase.cpp:548
-
DomainDecompBase::collCommAppendLongDouble
virtual void collCommAppendLongDouble(long double longDoubleValue)
has to call appendLongDouble method of a CollComm class
Definition: DomainDecompBase.cpp:568
-
DomainDecompBase::collCommAllreduceCustom
virtual void collCommAllreduceCustom(ReduceType type)
has to call allreduceCustom method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:600
-
DomainDecompBase::collCommAppendUnsLong
virtual void collCommAppendUnsLong(unsigned long unsLongValue)
has to call appendUnsLong method of a CollComm class
Definition: DomainDecompBase.cpp:556
-
DomainDecompBase::exchangeForces
virtual void exchangeForces(ParticleContainer *moleculeContainer, Domain *domain)
Exchanges forces at the domain boundaries if it's required by the cell container.
Definition: DomainDecompBase.cpp:87
-
DomainDecompBase::DomainDecompBase
DomainDecompBase()
The Constructor determines the own rank and the number of the neighbours *‍/.
Definition: DomainDecompBase.cpp:18
-
DomainDecompBase::getNonBlockingStageCount
virtual int getNonBlockingStageCount()
Definition: DomainDecompBase.cpp:391
-
DomainDecompBase::procOwnsPos
virtual bool procOwnsPos(double x, double y, double z, Domain *domain) final
find out whether the given position belongs to the domain of this process
Definition: DomainDecompBase.cpp:403
-
DomainDecompBase::getBoundingBoxMax
virtual double getBoundingBoxMax(int dimension, Domain *domain)
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecompBase.cpp:413
-
DomainDecompBase::handleForceExchangeDirect
virtual void handleForceExchangeDirect(const HaloRegion &haloRegion, ParticleContainer *moleculeContainer) const
Definition: DomainDecompBase.cpp:140
-
DomainDecompBase::~DomainDecompBase
~DomainDecompBase() override
The Destructor finalizes MPI.
Definition: DomainDecompBase.cpp:21
-
DomainDecompBase::collCommAllreduceSumAllowPrevious
virtual void collCommAllreduceSumAllowPrevious()
has to call allreduceSum method of a CollComm class (none in sequential version), allows for values o...
Definition: DomainDecompBase.cpp:596
+
DomainDecompBase::balanceAndExchange
virtual void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain)
balance the load (and optimize communication) and exchange boundary particles
Definition: DomainDecompBase.cpp:400
+
DomainDecompBase::collCommInit
virtual void collCommInit(int numValues, int key=0)
has to call init method of a CollComm class
Definition: DomainDecompBase.cpp:545
+
DomainDecompBase::queryBalanceAndExchangeNonBlocking
virtual bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime)
Checks whether the balance and exchange step can be performed non-blocking.
Definition: DomainDecompBase.cpp:396
+
DomainDecompBase::getIOCutoffRadius
double getIOCutoffRadius(int dim, Domain *domain, ParticleContainer *moleculeContainer)
returns an cutoff radius for a dimension for a global linked cells datastructure
Definition: DomainDecompBase.cpp:613
+
DomainDecompBase::collCommGetUnsLong
virtual unsigned long collCommGetUnsLong()
has to call getUnsLong method of a CollComm class
Definition: DomainDecompBase.cpp:577
+
DomainDecompBase::collCommBroadcast
virtual void collCommBroadcast(int root=0)
has to call broadcast method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:609
+
DomainDecompBase::collCommGetInt
virtual int collCommGetInt()
has to call getInt method of a CollComm class
Definition: DomainDecompBase.cpp:573
+
DomainDecompBase::collCommAppendDouble
virtual void collCommAppendDouble(double doubleValue)
has to call appendDouble method of a CollComm class
Definition: DomainDecompBase.cpp:565
+
DomainDecompBase::getBoundingBoxMinMax
void getBoundingBoxMinMax(Domain *domain, double *min, double *max)
get the minimum and maximum coordinate of the bounding box of this process' domain
Definition: DomainDecompBase.cpp:538
+
DomainDecompBase::getTime
virtual double getTime() const
returns the time in seconds since some time in the past
Definition: DomainDecompBase.cpp:418
+
DomainDecompBase::collCommAllreduceSum
virtual void collCommAllreduceSum()
has to call allreduceSum method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:593
+
DomainDecompBase::collCommGetLongDouble
virtual long double collCommGetLongDouble()
has to call getLongDouble method of a CollComm class
Definition: DomainDecompBase.cpp:589
+
DomainDecompBase::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension, Domain *domain)
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecompBase.cpp:410
+
DomainDecompBase::assertIntIdentity
virtual void assertIntIdentity(int IX)
checks identity of random number generators
Definition: DomainDecompBase.cpp:428
+
DomainDecompBase::barrier
virtual void barrier() const
synchronizes all processes
Definition: DomainDecompBase.cpp:446
+
DomainDecompBase::getNumProcs
virtual int getNumProcs() const
returns the number of processes
Definition: DomainDecompBase.cpp:442
+
DomainDecompBase::getRank
virtual int getRank() const
returns the own rank
Definition: DomainDecompBase.cpp:438
+
DomainDecompBase::handleDomainLeavingParticles
void handleDomainLeavingParticles(unsigned dim, ParticleContainer *moleculeContainer) const
Definition: DomainDecompBase.cpp:171
+
DomainDecompBase::handleForceExchange
void handleForceExchange(unsigned dim, ParticleContainer *moleculeContainer) const
Does the force exchange for each dimension. Will be called for dim=0, 1 and 2.
Definition: DomainDecompBase.cpp:94
+
DomainDecompBase::writeMoleculesToFile
void writeMoleculesToFile(const std::string &filename, ParticleContainer *moleculeContainer, bool binary=false) const
appends molecule data to the file. The format is the same as that of the input file If MPI is enabled...
Definition: DomainDecompBase.cpp:500
+
DomainDecompBase::printDecomp
virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer)
writes information about the current decomposition into the given file
Definition: DomainDecompBase.cpp:434
+
DomainDecompBase::collCommScanSum
virtual void collCommScanSum()
has to call scanSum method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:605
+
DomainDecompBase::exchangeMolecules
void exchangeMolecules(ParticleContainer *moleculeContainer, Domain *domain)
exchange molecules between processes
Definition: DomainDecompBase.cpp:52
+
DomainDecompBase::collCommGetFloat
virtual float collCommGetFloat()
has to call getFloat method of a CollComm class
Definition: DomainDecompBase.cpp:581
+
DomainDecompBase::Ndistribution
virtual unsigned Ndistribution(unsigned localN, float *minrnd, float *maxrnd)
returns total number of molecules
Definition: DomainDecompBase.cpp:422
+
DomainDecompBase::collCommFinalize
virtual void collCommFinalize()
has to call finalize method of a CollComm class
Definition: DomainDecompBase.cpp:549
+
DomainDecompBase::collCommAppendLongDouble
virtual void collCommAppendLongDouble(long double longDoubleValue)
has to call appendLongDouble method of a CollComm class
Definition: DomainDecompBase.cpp:569
+
DomainDecompBase::collCommAllreduceCustom
virtual void collCommAllreduceCustom(ReduceType type)
has to call allreduceCustom method of a CollComm class (none in sequential version)
Definition: DomainDecompBase.cpp:601
+
DomainDecompBase::collCommAppendUnsLong
virtual void collCommAppendUnsLong(unsigned long unsLongValue)
has to call appendUnsLong method of a CollComm class
Definition: DomainDecompBase.cpp:557
+
DomainDecompBase::exchangeForces
virtual void exchangeForces(ParticleContainer *moleculeContainer, Domain *domain)
Exchanges forces at the domain boundaries if it's required by the cell container.
Definition: DomainDecompBase.cpp:88
+
DomainDecompBase::DomainDecompBase
DomainDecompBase()
The Constructor determines the own rank and the number of the neighbours *‍/.
Definition: DomainDecompBase.cpp:19
+
DomainDecompBase::getNonBlockingStageCount
virtual int getNonBlockingStageCount()
Definition: DomainDecompBase.cpp:392
+
DomainDecompBase::procOwnsPos
virtual bool procOwnsPos(double x, double y, double z, Domain *domain) final
find out whether the given position belongs to the domain of this process
Definition: DomainDecompBase.cpp:404
+
DomainDecompBase::getBoundingBoxMax
virtual double getBoundingBoxMax(int dimension, Domain *domain)
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecompBase.cpp:414
+
DomainDecompBase::handleForceExchangeDirect
virtual void handleForceExchangeDirect(const HaloRegion &haloRegion, ParticleContainer *moleculeContainer) const
Definition: DomainDecompBase.cpp:141
+
DomainDecompBase::~DomainDecompBase
~DomainDecompBase() override
The Destructor finalizes MPI.
Definition: DomainDecompBase.cpp:22
+
DomainDecompBase::collCommAllreduceSumAllowPrevious
virtual void collCommAllreduceSumAllowPrevious()
has to call allreduceSum method of a CollComm class (none in sequential version), allows for values o...
Definition: DomainDecompBase.cpp:597
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:46
IndirectNeighbourCommunicationScheme
Definition: NeighbourCommunicationScheme.h:172
MemoryProfilable
Definition: MemoryProfiler.h:13
@@ -315,7 +315,7 @@
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                                                                                                                  Publications

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                                                                                                                  Background

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                                                                                                                  Old Config file format (used up to ls1-MarDyn 1.1)

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                                                                                                                  Parallelization

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                                                                                                                      Writing the test header

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                                                                                                                      -Generated on Sat Dec 7 2024 15:20:38 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Dec 9 2024 08:59:06 for ls1-MarDyn by doxygen 1.9.2