diff --git a/tools/lammps-gui/lammpsgui.cpp b/tools/lammps-gui/lammpsgui.cpp
index dabc5f60df..904cab796f 100644
--- a/tools/lammps-gui/lammpsgui.cpp
+++ b/tools/lammps-gui/lammpsgui.cpp
@@ -369,7 +369,7 @@ void LammpsGui::logupdate()
     double t_elapsed, t_remain, t_total;
     int completed = 1000;
 
-    if (is_running) {
+    if (lammps.is_running()) {
         t_elapsed = lammps.get_thermo("cpu");
         t_remain  = lammps.get_thermo("cpuremain");
         t_total   = t_elapsed + t_remain + 1.0e-10;
@@ -441,7 +441,8 @@ void LammpsGui::run_buffer()
     clear();
     capturer->BeginCapture();
 
-    char *input = mystrdup(ui->textEdit->toPlainText().toStdString());
+    // always add final newline since the text edit widget does not
+    char *input = mystrdup(ui->textEdit->toPlainText().toStdString() + "\n");
     is_running  = true;
 
     LammpsRunner *runner = new LammpsRunner(this);
@@ -524,7 +525,6 @@ void LammpsGui::view_image()
 
 void LammpsGui::clear()
 {
-    if (!lammps.is_open()) lammps.command("clear");
     ui->textEdit->moveCursor(QTextCursor::Start, QTextCursor::MoveAnchor);
 }
 
diff --git a/tools/lammps-gui/lammpsrunner.h b/tools/lammps-gui/lammpsrunner.h
index ea3eaab9a6..241e5dcc55 100644
--- a/tools/lammps-gui/lammpsrunner.h
+++ b/tools/lammps-gui/lammpsrunner.h
@@ -20,13 +20,14 @@ class LammpsRunner : public QThread {
     Q_OBJECT
 
 public:
-    LammpsRunner(QObject *parent = nullptr)  : QThread(parent), lammps(nullptr), input(nullptr) {}
+    LammpsRunner(QObject *parent = nullptr) : QThread(parent), lammps(nullptr), input(nullptr) {}
     ~LammpsRunner() = default;
 
 public:
     // execute LAMMPS in runner thread
     void run() override
     {
+        lammps->command("clear");
         lammps->commands_string(input);
         emit resultReady();
     }