source: src/lib/chemistry/cca/MPQC_ChemistryOpt_CoordinateModel_Impl.cc@ 09bc09

Last change on this file since 09bc09 was 5d30c1, checked in by Frederik Heber <heber@…>, 13 years ago

Initial commit based on 3.0.0alpha (here claimed as 2.4).

  • simply added all files.
  • Property mode set to 100644
File size: 23.8 KB
Line 
1//
2// File: MPQC_ChemistryOpt_CoordinateModel_Impl.cc
3// Symbol: MPQC.ChemistryOpt_CoordinateModel-v0.2
4// Symbol Type: class
5// Babel Version: 0.10.2
6// Description: Server-side implementation for MPQC.ChemistryOpt_CoordinateModel
7//
8// WARNING: Automatically generated; only changes within splicers preserved
9//
10// babel-version = 0.10.2
11//
12#include "MPQC_ChemistryOpt_CoordinateModel_Impl.hh"
13
14// DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel._includes)
15#include <iostream>
16#include <sstream>
17#include "util/keyval/keyvalval.h"
18#include "math/scmat/matrix.h"
19#include "math/scmat/local.h"
20#include "math/scmat/repl.h"
21
22#define DEFAULT_COORTYPE symm
23
24sidl::array<double>
25vector_to_array(const sc::RefSCVector &v);
26
27sc::RefSCVector
28array_to_vector(sidl::array<double>, const sc::RefSCVector &v);
29
30sidl::array<double>
31matrix_to_array(const sc::RefSymmSCMatrix &v);
32
33sc::RefSymmSCMatrix
34array_to_matrix(sidl::array<double>, const sc::RefSymmSCMatrix &v);
35
36// DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel._includes)
37
38// user-defined constructor.
39void MPQC::ChemistryOpt_CoordinateModel_impl::_ctor() {
40 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel._ctor)
41 have_guess_h_ = 0;
42 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel._ctor)
43}
44
45// user-defined destructor.
46void MPQC::ChemistryOpt_CoordinateModel_impl::_dtor() {
47 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel._dtor)
48 // add destruction details here
49 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel._dtor)
50}
51
52// static class initializer.
53void MPQC::ChemistryOpt_CoordinateModel_impl::_load() {
54 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel._load)
55 // guaranteed to be called at most once before any other method in this class
56 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel._load)
57}
58
59// user-defined static methods: (none)
60
61// user-defined non-static methods:
62/**
63 * Registers and gets ports, and requests Model object(s) from the
64 * ModelFactory component(s). This must be the first method called
65 * following instantiation.
66 */
67int32_t
68MPQC::ChemistryOpt_CoordinateModel_impl::initialize ()
69throw ()
70
71{
72 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.initialize)
73
74 int i;
75
76 std::cout << "\nInitializing MPQC::ChemistryOpt_CoordinateModel\n";
77
78 CcaChemGeneric::CoordinateModel::set_tolerances(grad_rms_->value,
79 grad_max_->value,
80 disp_rms_->value,
81 disp_max_->value);
82 CcaChemGeneric::CoordinateModel::initialize(services_);
83
84 //get matrix kits
85 kit_ = new sc::LocalSCMatrixKit;
86 rkit_ = new sc::ReplSCMatrixKit;
87
88 //get coordinate type
89 std::string coorString;
90 coorString = std::string( coordinates_->getValueString() );
91 std::cout << " Using coordinate type: " << coorString << std::endl;
92 if(coorString == "cartesian") coorType_ = cart;
93 else if(coorString == "symmetrized") coorType_ = symm;
94 else if(coorString == "redundant") coorType_ = redund;
95 else {
96 std::cout << " Unrecognized coordinate type, using default\n";
97 coorType_ = DEFAULT_COORTYPE;
98 }
99 services_.releasePort("CoordinateType");
100
101 //get extra_bonds
102 std::string bondsString( extra_bonds_->getValueString() );
103
104 //get model and molecule
105 model_ = CcaChemGeneric::CoordinateModel::get_model();
106 molecule_ = model_.get_molecule();
107 double conv = molecule_.get_units().convert_to("bohr");
108 convFrom_ = molecule_.get_units().convert_from("bohr");
109 int natom = molecule_.get_n_atom();
110
111 std::cout << "\n CoordinateModel: setting up coordinates\n";
112
113 //create input strings for MPQC classes
114 std::ostringstream input;
115 input
116 << " molecule<Molecule>:(\n"
117 << " symmetry = auto\n"
118 << " unit = bohr\n"
119 << " { n atoms geometry }={\n";
120 for(i=0;i<natom;++i) {
121 input
122 << "\t" << i << "\t" << molecule_.get_atomic_number(i)
123 << "\t[ " << molecule_.get_cart_coor(i,0)*conv
124 << " " << molecule_.get_cart_coor(i,1)*conv
125 << " " << molecule_.get_cart_coor(i,2)*conv << " ]\n";
126 }
127 input
128 << " }\n )\n";
129
130 std::cout << input.str();
131
132 switch(coorType_) {
133 case cart:
134 input << " coor<CartMolecularCoor>: (\n"
135 << " molecule = $..:molecule\n"
136 << " )\n";
137 break;
138 case symm:
139 input << " coor<SymmMolecularCoor>: (\n"
140 << " molecule = $..:molecule\n"
141 << " update_bmat = 1\n"
142 << " cartesian_tolerance = 1e-9\n"
143 << " generator<IntCoorGen>: (\n"
144 << " molecule = $..:..:molecule\n";
145 if( bondsString.size() != 0 )
146 input << " extra_bonds = [" << bondsString << "]\n";
147 input << " )\n )\n";
148 break;
149 case redund:
150 input << " coor<RedundMolecularCoor>: (\n"
151 << " molecule = $..:molecule\n"
152 << " update_bmat = 1\n"
153 << " cartesian_tolerance = 1e-9\n"
154 << " generator<IntCoorGen>: (\n"
155 << " molecule = $..:..:molecule\n";
156 if( bondsString.size() != 0 )
157 input << " extra_bonds = [" << bondsString << "]\n";
158 input << " )\n )\n";
159 break;
160 }
161
162 std::cout << input.str();
163
164 //create the MPQC classes
165 sc::Ref<sc::ParsedKeyVal> kv = new sc::ParsedKeyVal();
166 kv->parse_string(input.str().c_str());
167 sc::Ref<sc::DescribedClass> dccoor = kv->describedclassvalue("coor");
168 sc::Ref<sc::DescribedClass> dcmol = kv->describedclassvalue("molecule");
169 scMol_ = dynamic_cast<sc::Molecule*>(dcmol.pointer());
170 switch(coorType_) {
171 case cart:
172 scCoor_ = dynamic_cast<sc::CartMolecularCoor*>(dccoor.pointer());
173 break;
174 case symm:
175 scCoor_ = dynamic_cast<sc::SymmMolecularCoor*>(dccoor.pointer());
176 break;
177 case redund:
178 scCoor_ = dynamic_cast<sc::RedundMolecularCoor*>(dccoor.pointer());
179 break;
180 }
181
182 scCoor_->print();
183 numCoor_ = scCoor_->dim().n();
184 natom3_ = scCoor_->dim_natom3().n();
185 std::cout << "\n";
186
187 // convergence checking needs this method invoked
188 CcaChemGeneric::CoordinateModel::get_n_coor();
189
190 return 0;
191 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.initialize)
192}
193
194/**
195 * Releases and unregisters ports. This should be called when the
196 * CoordinateModel object is no longer needed.
197 */
198int32_t
199MPQC::ChemistryOpt_CoordinateModel_impl::finalize ()
200throw ()
201
202{
203 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.finalize)
204 return CcaChemGeneric::CoordinateModel::finalize();
205 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.finalize)
206}
207
208/**
209 * Sets the contained chemistry Model object (currently unused as the
210 * chemistry Model object is normally obtained from a ModelFactory
211 * during initialization).
212 * @param model The chemistry model object.
213 */
214void
215MPQC::ChemistryOpt_CoordinateModel_impl::set_model (
216 /* in */ ::Chemistry::QC::Model model )
217throw ()
218{
219 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.set_model)
220 CcaChemGeneric::CoordinateModel::set_model( model );
221 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.set_model)
222}
223
224/**
225 * Returns the contained chemistry Model object.
226 * @return The chemistry Model object.
227 */
228::Chemistry::QC::Model
229MPQC::ChemistryOpt_CoordinateModel_impl::get_model ()
230throw ()
231
232{
233 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_model)
234 return CcaChemGeneric::CoordinateModel::get_model();
235 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_model)
236}
237
238/**
239 * Returns the number of coordinates.
240 * @return The number of coordinates.
241 */
242int32_t
243MPQC::ChemistryOpt_CoordinateModel_impl::get_n_coor ()
244throw ()
245
246{
247 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_n_coor)
248 return numCoor_;
249 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_n_coor)
250}
251
252/**
253 * Returns the array of (cartesian or internal) coordinates which are
254 * being optimized.
255 * @return The array of coordinates which are being optimized.
256 */
257::sidl::array<double>
258MPQC::ChemistryOpt_CoordinateModel_impl::get_coor ()
259throw ()
260
261{
262 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_coor)
263
264 ::sidl::array<double> sidlCoor;
265
266 switch(coorType_) {
267 case cart:
268 sidlCoor = molecule_.get_coor();
269 break;
270 default:
271 sc::Ref<sc::SCMatrixKit> kit = new sc::LocalSCMatrixKit;
272 sc::RefSCVector scCoor = kit->vector(scCoor_->dim());
273 scCoor_->to_internal(scCoor);
274 sidlCoor = vector_to_array(scCoor);
275 break;
276 }
277
278 return sidlCoor;
279 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_coor)
280}
281
282/**
283 * Returns the energy of the currently contained model with the values
284 * of the optimization coordinates given in x. This requires
285 * that the CoordinateModel updates the cartesian coordinates of a
286 * contained Molecule object (possibly requiring transformation) and set
287 * this Molecule object on a contained Model object, prior to calling
288 * get_energy() on the Model object.
289 * @param x The optimization coordinate values.
290 * @return The energy of the chemistry model at x.
291 */
292double
293MPQC::ChemistryOpt_CoordinateModel_impl::get_energy (
294 /* in */ ::sidl::array<double> x )
295throw ()
296{
297 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_energy)
298
299 std::cout << "***** MPQC ChemistryOpt Calculate Energy *****\n";
300 double f;
301
302 //get energy, transform coordinates if neeeded
303 switch(coorType_) {
304 case cart:
305 f = CcaChemGeneric::CoordinateModel::get_energy(x);
306 break;
307 default:
308 sc::RefSCVector scCoor = kit_->vector(scCoor_->dim());
309 sidl::array<double> cartx =
310 sidl::array<double>::create1d(natom3_);
311 array_to_vector(x,scCoor);
312 scCoor_->to_cartesian(scMol_,scCoor);
313 for(int i=0; i<(natom3_/3); ++i)
314 for( int j=0; j<3; ++j)
315 cartx.set(i*3+j, scMol_->r(i,j)*convFrom_);
316 f = CcaChemGeneric::CoordinateModel::get_energy(cartx);
317 scCoor_->print();
318 break;
319 }
320
321 return f;
322
323 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_energy)
324}
325
326/**
327 * Returns the energy gradient of the currently contained model with
328 * the values of the optimization coordinates given in x. This requires
329 * that the CoordinateModel updates the cartesian coordinates of a
330 * contained Molecule object (possibly requiring transformation) and set
331 * this Molecule object on a contained Model object, prior to calling
332 * get_gradient() on the Model object. If the optimization coordinate
333 * system is not cartesian, the gradient is transformed.
334 * @param x The optimization coordinate values.
335 * @return The energy gradient of the chemistry model at x.
336 */
337::sidl::array<double>
338MPQC::ChemistryOpt_CoordinateModel_impl::get_gradient (
339 /* in */ ::sidl::array<double> x )
340throw ()
341{
342 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_gradient)
343
344 std::cout << "***** MPQC ChemistryOpt Calculate Gradient *****\n";
345
346 ::sidl::array<double> cartg = ::sidl::array<double>::create1d(natom3_);
347
348 //get gradient, transform coordinates if needed
349 switch(coorType_) {
350 case cart:
351 cartg.copy(CcaChemGeneric::CoordinateModel::get_gradient(x));
352 break;
353 default:
354 sc::RefSCVector scCoor = kit_->vector(scCoor_->dim());
355 array_to_vector(x,scCoor);
356 scCoor_->to_cartesian(scMol_,scCoor);
357 sidl::array<double> cartx =
358 sidl::array<double>::create1d(natom3_);
359 for(int i=0; i<(natom3_/3); ++i)
360 for( int j=0; j<3; ++j)
361 cartx.set(i*3+j, scMol_->r(i,j)*convFrom_);
362 cartg.copy(CcaChemGeneric::CoordinateModel::get_gradient(cartx));
363 scCoor_->print();
364 break;
365 }
366
367 //transform gradient if using internals
368 ::sidl::array<double> g;
369 switch(coorType_) {
370 case cart:
371 g = cartg;
372 break;
373 default:
374 sc::RefSCVector scCartGrad = rkit_->vector(scCoor_->dim_natom3());
375 sc::RefSCVector scGrad = rkit_->vector(scCoor_->dim());
376 array_to_vector(cartg,scCartGrad);
377 scCoor_->to_internal(scGrad,scCartGrad);
378 g.copy(vector_to_array(scGrad));
379 break;
380 }
381
382 return g;
383
384 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_gradient)
385}
386
387/**
388 * Returns the energy Hessian of the currently contained model with
389 * the values of the optimization coordinates given in x. This requires
390 * that the CoordinateModel updates the cartesian coordinates of a
391 * contained Molecule object (possibly requiring transformation) and set
392 * this Molecule object on a contained Model object, prior to calling
393 * get_hessian() on the Model object. If the optimization coordinate
394 * system is not cartesian, the Hessian is transformed.
395 * @param x The optimization coordinate values.
396 * @return The energy Hessian of the chemistry model at x.
397 */
398::sidl::array<double>
399MPQC::ChemistryOpt_CoordinateModel_impl::get_hessian (
400 /* in */ ::sidl::array<double> x )
401throw ()
402{
403 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_hessian)
404
405 std::cout << "***** MPQC ChemistryOpt Calculate Hessian *****\n";
406 std::cout << " WARNING: this method has not been tested yet\n";
407
408 ::sidl::array<double> cartH =
409 ::sidl::array<double>::create2dRow(natom3_,natom3_);
410
411 //get hessian, transform coordinates if needed
412 switch(coorType_) {
413 case cart:
414 cartH.copy(CcaChemGeneric::CoordinateModel::get_hessian(x));
415 break;
416 default:
417 sc::RefSCVector scCoor = kit_->vector(scCoor_->dim());
418 array_to_vector(x,scCoor);
419 scCoor_->to_cartesian(scMol_,scCoor);
420 sidl::array<double> cartx =
421 sidl::array<double>::create1d(natom3_);
422 for(int i=0; i<(natom3_/3); ++i)
423 for( int j=0; j<3; ++j)
424 cartx.set(i*3+j, scMol_->r(i,j)*convFrom_);
425 cartH.copy(CcaChemGeneric::CoordinateModel::get_hessian(cartx));
426 scCoor_->print();
427 break;
428 }
429
430 //transform Hessian if using internals
431 ::sidl::array<double> H;
432 switch(coorType_) {
433 case cart:
434 H = cartH;
435 break;
436 default:
437 sc::RefSymmSCMatrix scCartH =
438 rkit_->symmmatrix(scCoor_->dim_natom3());
439 sc::RefSymmSCMatrix scH =
440 rkit_->symmmatrix(scCoor_->dim());
441 array_to_matrix(cartH,scCartH);
442 scCoor_->to_internal(scH,scCartH);
443 H = matrix_to_array(scH);
444 break;
445 }
446
447 return H;
448
449 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_hessian)
450}
451
452/**
453 * Sets f and g to the energy and energy gradient, respectively,
454 * of the chemistry model at x. This is similar to calling
455 * get_energy() and get_gradient() separately, but set_molecule()
456 * must be called on the Model object only once. This is necessary
457 * for some model implementations, as a second molecule update
458 * would invalidate results from an energy computation. An alternative
459 * would be to always return the energy as well when get_gradient() is
460 * called.
461 * @param x The optimization coordinate values.
462 * @param f Variable that energy will be assigned to.
463 * @param g Array that the gradient will be assigned to.
464 */
465void
466MPQC::ChemistryOpt_CoordinateModel_impl::get_energy_and_gradient (
467 /* in */ ::sidl::array<double> x,
468 /* out */ double& f,
469 /* in */ ::sidl::array<double> g )
470throw ()
471{
472 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.get_energy_and_gradient)
473 std::cout << "***** MPQC ChemistryOpt Calculate Energy and Gradient *****\n";
474
475 ::sidl::array<double> cartg = ::sidl::array<double>::create1d(natom3_);
476
477 //get gradient, transform coordinates if needed
478 switch(coorType_) {
479 case cart:
480 CcaChemGeneric::CoordinateModel::get_energy_and_gradient(x,&f,g);
481 break;
482 default:
483 sc::RefSCVector scCoor = kit_->vector(scCoor_->dim());
484 array_to_vector(x,scCoor);
485 scCoor_->to_cartesian(scMol_,scCoor);
486 sidl::array<double> cartx =
487 sidl::array<double>::create1d(natom3_);
488 for(int i=0; i<(natom3_/3); ++i)
489 for( int j=0; j<3; ++j)
490 cartx.set(i*3+j, scMol_->r(i,j)*convFrom_);
491 CcaChemGeneric::CoordinateModel::get_energy_and_gradient(cartx,&f,cartg);
492 scCoor_->print();
493 break;
494 }
495
496 //transform gradient if using internals
497 switch(coorType_) {
498 case cart:
499 break;
500 default:
501 sc::RefSCVector scCartGrad = rkit_->vector(scCoor_->dim_natom3());
502 sc::RefSCVector scGrad = rkit_->vector(scCoor_->dim());
503 array_to_vector(cartg,scCartGrad);
504 scCoor_->to_internal(scGrad,scCartGrad);
505 g.copy(vector_to_array(scGrad));
506 break;
507 }
508
509 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.get_energy_and_gradient)
510}
511
512/**
513 * Returns the product of the guess hessian inverse and an effective
514 * gradient. Probably unique to TAO's limited memory variable metric
515 * algorithm, which uses this method to accomodate dense guess hessians.
516 * "first_geom_ptr" provides the Cartesian coordinates for which the
517 * guess Hessian should be computed (first_geom_ptr=0 for current
518 * geometry).
519 * @param effective_grad An effective gradient.
520 * @param effective_step Array that effective step is assigned to.
521 * @param first_geom Pointer to array of Cartesians
522 */
523void
524MPQC::ChemistryOpt_CoordinateModel_impl::guess_hessian_solve (
525 /* in */ ::sidl::array<double> effective_grad,
526 /* in */ ::sidl::array<double> effective_step,
527 /* in */ void* first_geom )
528throw ()
529{
530 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.guess_hessian_solve)
531
532 sidl::array<double> *sidl_geom_ptr =
533 static_cast< sidl::array<double>* >( first_geom );
534
535 if(multiple_guess_h_->value && !use_current_geom_->value && sidl_geom_ptr){
536 std::cout << "Using geometry for first correction pair\n";
537 sc::RefSCVector scCoor = kit_->vector(scCoor_->dim());
538 array_to_vector( *sidl_geom_ptr, scCoor );
539 scCoor_->to_cartesian(scMol_,scCoor);
540 }
541
542 if( multiple_guess_h_->value || !have_guess_h_ ) {
543 std::cout << "Determining approximate Hessian\n";
544 sc::RefSymmSCMatrix hess = rkit_->symmmatrix(scCoor_->dim());
545 scCoor_->guess_hessian(hess);
546 ihess_ = scCoor_->inverse_hessian(hess);
547 have_guess_h_ = 1;
548 }
549
550 std::cout << "Solving approximate Hessian system\n";
551 sc::RefSCVector scV = rkit_->vector(scCoor_->dim());
552 array_to_vector(effective_grad, scV);
553 sc::RefSCVector result = ihess_*scV;
554 effective_step.copy(vector_to_array( result ));
555
556 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.guess_hessian_solve)
557}
558
559/**
560 * Determines if the optimization has converged, flag is set to 1
561 * if convergence has been achieved and 0 otherwise.
562 * @param flag Variable that convergence value is assigned to.
563 */
564void
565MPQC::ChemistryOpt_CoordinateModel_impl::checkConvergence (
566 /* inout */ int32_t& flag )
567throw ()
568{
569 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.checkConvergence)
570 CcaChemGeneric::CoordinateModel::checkConvergence( flag );
571 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.checkConvergence)
572}
573
574/**
575 * For visualization, possibly unused (?). CoordinateModel objects
576 * may callback to viewers that implement the Chemistry.MoleculeViewer
577 * interface, such as the cca-chem python GUI, making this method
578 * unnecessary.
579 */
580void
581MPQC::ChemistryOpt_CoordinateModel_impl::monitor ()
582throw ()
583
584{
585 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.monitor)
586 // insert implementation here
587 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.monitor)
588}
589
590/**
591 * Starts up a component presence in the calling framework.
592 * @param Svc the component instance's handle on the framework world.
593 * Contracts concerning Svc and setServices:
594 *
595 * The component interaction with the CCA framework
596 * and Ports begins on the call to setServices by the framework.
597 *
598 * This function is called exactly once for each instance created
599 * by the framework.
600 *
601 * The argument Svc will never be nil/null.
602 *
603 * Those uses ports which are automatically connected by the framework
604 * (so-called service-ports) may be obtained via getPort during
605 * setServices.
606 */
607void
608MPQC::ChemistryOpt_CoordinateModel_impl::setServices (
609 /* in */ ::gov::cca::Services services )
610throw (
611 ::gov::cca::CCAException
612){
613 // DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel.setServices)
614
615 services_ = services;
616 if (services_._is_nil()) return;
617
618 try {
619 services_.addProvidesPort(self,
620 "CoordinateModel",
621 "ChemistryOpt.CoordinateModel",
622 0);
623 services_.registerUsesPort("ModelFactory",
624 "Chemistry.QC.ModelFactory",
625 0);
626 services_.registerUsesPort("BackupModelFactory",
627 "Chemistry.QC.ModelFactory",
628 0);
629 services_.registerUsesPort("MoleculeViewer",
630 "Chemistry.MoleculeViewer",
631 0);
632 services_.registerUsesPort("CoordinateType",
633 "Util.StringProvider",
634 0);
635 }
636 catch (gov::cca::CCAException e) {
637 std::cout << "Error using services: "
638 << e.getNote() << std::endl;
639 }
640
641 // setup parameters
642 try {
643
644 if (services_._not_nil()) {
645 gov::cca::TypeMap tm = services_.createTypeMap();
646 ::gov::cca::Port self_port = self;
647 services_.addProvidesPort(self_port,
648 "string",
649 "Util.StringProvider",tm);
650
651 services_.registerUsesPort("classicParam",
652 "gov.cca.ParameterPortFactoryService",tm);
653 gov::cca::Port p = services_.getPort("classicParam");
654 ccaffeine::ports::PortTranslator portX = p;
655 if(portX._not_nil()) {
656 classic::gov::cca::Port *cp
657 =static_cast<classic::gov::cca::Port*>(portX.getClassicPort());
658 if(!cp) {
659 std::cout << "Couldn't get classic port" << std::endl;
660 return;
661 }
662 ConfigurableParameterFactory *cpf
663 = dynamic_cast<ConfigurableParameterFactory *>(cp);
664 ConfigurableParameterPort *pp = setup_parameters(cpf);
665 classic::gov::cca::Port *clscp
666 = dynamic_cast<classic::gov::cca::Port*>(pp);
667 if (!clscp) {
668 std::cout << "Couldn't cast to classic::gov::cca::Port"
669 << std::endl;
670 }
671 void *vp = static_cast<void*>(clscp);
672 ccaffeine::ports::PortTranslator provideX
673 = ccaffeine::ports::PortTranslator::createFromClassic(vp);
674
675 services_.addProvidesPort(provideX,
676 "configure", "ParameterPort", tm);
677
678 services_.releasePort("classicParam");
679 services_.unregisterUsesPort("classicParam");
680 }
681 }
682
683 }
684 catch(std::exception& e) {
685 std::cout << "Exception caught: " << e.what() << std::endl;
686 }
687
688 // DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel.setServices)
689}
690
691
692// DO-NOT-DELETE splicer.begin(MPQC.ChemistryOpt_CoordinateModel._misc)
693
694ConfigurableParameterPort*
695MPQC::ChemistryOpt_CoordinateModel_impl::setup_parameters(ConfigurableParameterFactory *cpf)
696{
697 ConfigurableParameterPort * pp = cpf->createConfigurableParameterPort();
698
699 pp->setBatchTitle("PortTranslatorStarter Configuration");
700 pp->setGroupName("Coordinate Model Input");
701 grad_rms_ = new DoubleParameter("grad_rms",
702 "RMS gradient convergence tolerance",
703 "grad_rms", 0.00030,0,1000000);
704 grad_max_ = new DoubleParameter("grad_max",
705 "Max gradient convergence tolerance",
706 "grad_max", 0.00045,0,1000000);
707 disp_rms_ = new DoubleParameter("disp_rms",
708 "RMS displacement convergence tolerance",
709 "disp_rms", 0.00120,0,1000000);
710 disp_max_ = new DoubleParameter("disp_max",
711 "Max displacement convergence tolerance",
712 "disp_max", 0.00180,0,1000000);
713 multiple_guess_h_ = new BoolParameter("multiple_guess_h",
714 "Guess H at every guess_hessian_solve",
715 "multiple_guess_h",1);
716 use_current_geom_ = new BoolParameter("use_current_geom",
717 "Guess Hessian at current geometry",
718 "use_current_geom",0);
719 coordinates_ = new StringParameter("coordinate_type",
720 "Coordinate type: cartesian, symmetrized, or redundant",
721 "coordinate_type", "symmetrized");
722 extra_bonds_ = new StringParameter("extra_bonds", "extra_bonds vector",
723 "extra_bonds", "");
724 pp->addRequest(grad_rms_);
725 pp->addRequest(grad_max_);
726 pp->addRequest(disp_rms_);
727 pp->addRequest(disp_max_);
728 pp->addRequest(multiple_guess_h_);
729 pp->addRequest(use_current_geom_);
730 pp->addRequest(coordinates_);
731 pp->addRequest(extra_bonds_);
732
733 return pp;
734}
735
736// DO-NOT-DELETE splicer.end(MPQC.ChemistryOpt_CoordinateModel._misc)
737
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