NAMD
Public Member Functions | Public Attributes | List of all members
PatchData Class Reference

#include <PatchData.h>

Inheritance diagram for PatchData:

Public Member Functions

 PatchData ()
 
 ~PatchData ()
 
void setDeviceKernelUpdateCounter ()
 

Public Attributes

cudaTensord_langevinPiston_strainRate
 
cudaTensord_langevinPiston_origStrainRate
 
cudaTensord_strainRate_old
 
cudaTensord_positionRescaleFactor
 
NodeReductionreductionBackend
 
NodeReductionreductionBackendSave
 
NodeReductionreduction
 
NodeBroadcastnodeBroadcast
 
Flags flags
 
Controllerc_out
 
Latticelat
 
Tensorfactor
 
Vectororigin
 
CollectionMasterptrCollectionMaster
 
OutputptrOutput
 
IMDOutputimd
 
PDBpdb
 
ScriptTclscript
 
CmiNodeLock printlock
 

Detailed Description

Definition at line 116 of file PatchData.h.

Constructor & Destructor Documentation

◆ PatchData()

PatchData::PatchData ( )

Definition at line 49 of file PatchData.C.

References imd, NodeBroadcast::lock, nodeBroadcast, pdb, printlock, ptrCollectionMaster, ptrOutput, reductionBackend, and reductionBackendSave.

49  {
50  ptrCollectionMaster = NULL;
51  ptrOutput = NULL;
52  imd = NULL;
53  pdb = NULL;
54 
57 #ifdef NODEGROUP_FORCE_REGISTER
58  cudaBondedList = new ComputeBondedCUDA*[CkNumPes()];
59  cudaNonbondedList = new CudaComputeNonbonded*[CkNumPes()];
60  printlock = CmiCreateLock();
61  nodeLock = CmiCreateLock();
62  suspendCounter.store(CmiMyNodeSize());
63  updateCounter.store(0);
64 #endif
65 
67  nodeBroadcast->lock = CmiCreateLock();
68 }
CmiNodeLock printlock
Definition: PatchData.h:163
IMDOutput * imd
Definition: PatchData.h:156
NodeReduction * reductionBackend
Definition: PatchData.h:134
NodeReduction * reductionBackendSave
Definition: PatchData.h:136
CollectionMaster * ptrCollectionMaster
Definition: PatchData.h:154
PDB * pdb
Definition: PatchData.h:157
Output * ptrOutput
Definition: PatchData.h:155
NodeBroadcast * nodeBroadcast
Definition: PatchData.h:141
CmiNodeLock lock

◆ ~PatchData()

PatchData::~PatchData ( )

Definition at line 76 of file PatchData.C.

References nodeBroadcast, reductionBackend, and reductionBackendSave.

76  {
77  delete reductionBackend;
78  delete reductionBackendSave;
79  delete nodeBroadcast;
80 #ifdef NODEGROUP_FORCE_REGISTER
81  free(h_soa_fb_x);
82  free(h_soa_fb_y);
83  free(h_soa_fb_z);
84  free(h_soa_fn_x);
85  free(h_soa_fn_y);
86  free(h_soa_fn_z);
87  free(h_soa_fs_x);
88  free(h_soa_fs_y);
89  free(h_soa_fs_z);
90  free(h_soa_pos_x);
91  free(h_soa_pos_y);
92  free(h_soa_pos_z);
93  free(h_soa_vel_x);
94  free(h_soa_vel_y);
95  free(h_soa_vel_z);
96 
97  free(h_soa_charge);
98 
99  // Device Migration
100  free(h_soa_id);
101  free(h_soa_vdwType);
102  free(h_soa_sortOrder);
103  free(h_soa_unsortOrder);
104  free(h_soa_patchCenter);
105  free(h_soa_migrationDestination);
106  free(h_soa_sortSoluteIndex);
107 
108  free(h_atomdata_AoS);
109  free(h_peer_record);
110 
111  free(h_soa_partition);
112 
113  free(h_tupleCount.bond);
114  free(h_tupleCount.angle);
115  free(h_tupleCount.dihedral);
116  free(h_tupleCount.improper);
117  free(h_tupleCount.modifiedExclusion);
118  free(h_tupleCount.exclusion);
119  free(h_tupleCount.crossterm);
120  free(h_tupleOffset.bond);
121  free(h_tupleOffset.angle);
122  free(h_tupleOffset.dihedral);
123  free(h_tupleOffset.improper);
124  free(h_tupleOffset.modifiedExclusion);
125  free(h_tupleOffset.exclusion);
126  free(h_tupleOffset.crossterm);
127  free(h_tupleDataStage.bond);
128  free(h_tupleDataStage.angle);
129  free(h_tupleDataStage.dihedral);
130  free(h_tupleDataStage.improper);
131  free(h_tupleDataStage.modifiedExclusion);
132  free(h_tupleDataStage.exclusion);
133  free(h_tupleDataStage.crossterm);
134  CmiDestroyLock(nodeLock);
135 
136 #endif
137 }
NodeReduction * reductionBackend
Definition: PatchData.h:134
NodeReduction * reductionBackendSave
Definition: PatchData.h:136
NodeBroadcast * nodeBroadcast
Definition: PatchData.h:141

Member Function Documentation

◆ setDeviceKernelUpdateCounter()

void PatchData::setDeviceKernelUpdateCounter ( )

Definition at line 70 of file PatchData.C.

70  {
71 #ifdef NODEGROUP_FORCE_REGISTER
72  updateCounter.store(devData.size());
73 #endif
74 }

Member Data Documentation

◆ c_out

Controller* PatchData::c_out

Definition at line 147 of file PatchData.h.

◆ d_langevinPiston_origStrainRate

cudaTensor* PatchData::d_langevinPiston_origStrainRate

Definition at line 127 of file PatchData.h.

◆ d_langevinPiston_strainRate

cudaTensor* PatchData::d_langevinPiston_strainRate

Definition at line 126 of file PatchData.h.

◆ d_positionRescaleFactor

cudaTensor* PatchData::d_positionRescaleFactor

Definition at line 129 of file PatchData.h.

◆ d_strainRate_old

cudaTensor* PatchData::d_strainRate_old

Definition at line 128 of file PatchData.h.

◆ factor

Tensor* PatchData::factor

Definition at line 150 of file PatchData.h.

◆ flags

Flags PatchData::flags

Definition at line 144 of file PatchData.h.

◆ imd

IMDOutput* PatchData::imd

Definition at line 156 of file PatchData.h.

Referenced by PatchData().

◆ lat

Lattice* PatchData::lat

Definition at line 149 of file PatchData.h.

◆ nodeBroadcast

NodeBroadcast* PatchData::nodeBroadcast

Definition at line 141 of file PatchData.h.

Referenced by Controller::Controller(), PatchData(), Sequencer::Sequencer(), and ~PatchData().

◆ origin

Vector* PatchData::origin

Definition at line 151 of file PatchData.h.

◆ pdb

PDB* PatchData::pdb

Definition at line 157 of file PatchData.h.

Referenced by PatchData().

◆ printlock

CmiNodeLock PatchData::printlock

Definition at line 163 of file PatchData.h.

Referenced by PatchData().

◆ ptrCollectionMaster

CollectionMaster* PatchData::ptrCollectionMaster

Definition at line 154 of file PatchData.h.

Referenced by PatchData().

◆ ptrOutput

Output* PatchData::ptrOutput

Definition at line 155 of file PatchData.h.

Referenced by PatchData().

◆ reduction

NodeReduction* PatchData::reduction

Definition at line 139 of file PatchData.h.

Referenced by colvarproxy_namd::colvarproxy_namd().

◆ reductionBackend

NodeReduction* PatchData::reductionBackend

◆ reductionBackendSave

NodeReduction* PatchData::reductionBackendSave

Definition at line 136 of file PatchData.h.

Referenced by PatchData(), and ~PatchData().

◆ script

ScriptTcl* PatchData::script

Definition at line 160 of file PatchData.h.

Referenced by after_backend_init(), and Node::getScript().


The documentation for this class was generated from the following files: